6KF7 | pdb_00006kf7

Microbial Hormone-sensitive lipase E53 mutant S285G

PDB DOI: https://doi.org/10.2210/pdb6KF7/pdb

Classification: HYDROLASE
Organism(s): Erythrobacter longus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2019-07-06 Released: 2020-07-08
Deposition Author(s): Xiaochen, Y., Zhengyang, L., Xuewei, X., Jixi, L.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.191 (Depositor), 0.191 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Microbial Hormone-sensitive lipase E53 mutant S285G

Xiaochen, Y.

To be published.

Macromolecule Content

Total Structure Weight: 136.46 kDa
Atom Count: 10,785
Modeled Residue Count: 1,236
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B, C, D	314	Erythrobacter longus	Mutation(s): 1 Gene Names: EH31_02760
UniProt
Find proteins for A0A074MDU6 (Erythrobacter longus) Explore A0A074MDU6 Go to UniProtKB: A0A074MDU6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A074MDU6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D8F (Subject of Investigation/LOI) Query on D8F Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain R [auth B] SDF format, chain HA [auth D] SDF format, chain E [auth A] MOL2 format, chain X [auth C] MOL2 format, chain R [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain E [auth A] mmCIF format, chain X [auth C] mmCIF format, chain R [auth B] mmCIF format, chain HA [auth D] mmCIF format, chain E [auth A]	E [auth A], HA [auth D], R [auth B], X [auth C]	(4-nitrophenyl) hexanoate C₁₂ H₁₅ N O₄ OLRXUEYZKCCEKK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain HA [auth D] Focus chain R [auth B] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain HA [auth D] Focus chain R [auth B] Focus chain X [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain GA [auth C] MOL2 format, chain GA [auth C] mmCIF format, chain GA [auth C]	GA [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Interactions & Density Focus chain GA [auth C]
NPO Query on NPO Download Ideal Coordinates CCD File SDF format, chain QA [auth D] MOL2 format, chain QA [auth D] mmCIF format, chain QA [auth D]	QA [auth D]	P-NITROPHENOL C₆ H₅ N O₃ BTJIUGUIPKRLHP-UHFFFAOYSA-N		Interactions Focus chain QA [auth D] Interactions & Density Focus chain QA [auth D]
6NA Query on 6NA Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain FA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain FA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain FA [auth C]	FA [auth C], Q [auth A]	HEXANOIC ACID C₆ H₁₂ O₂ FUZZWVXGSFPDMH-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain Q [auth A] Interactions & Density Focus chain FA [auth C] Focus chain Q [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain F [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain F [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain F [auth A]	F [auth A], IA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain IA [auth D] Interactions & Density Focus chain F [auth A] Focus chain IA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain PA [auth D] SDF format, chain P [auth A] SDF format, chain OA [auth D] SDF format, chain O [auth A] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] L [auth A] BA [auth C], CA [auth C], DA [auth C], EA [auth C], L [auth A], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], U [auth B], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain LA [auth D] SDF format, chain KA [auth D] SDF format, chain K [auth A] SDF format, chain JA [auth D] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain LA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth C]	AA [auth C] G [auth A] H [auth A] I [auth A] J [auth A] AA [auth C], G [auth A], H [auth A], I [auth A], J [auth A], JA [auth D], K [auth A], KA [auth D], LA [auth D], S [auth B], T [auth B], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.191 (Depositor), 0.191 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.657	α = 90
b = 129.715	β = 90
c = 219.464	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31770004

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-09-17
Changes: Advisory, Derived calculations, Structure summary