6G3N | pdb_00006g3n

Mycobacterial hydrolase complex 14.

PDB DOI: https://doi.org/10.2210/pdb6G3N/pdb

Classification: HYDROLASE
Organism(s): Mycolicibacterium hassiacum DSM 44199
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-03-26 Released: 2019-04-10
Deposition Author(s): Cereija, T.B., Macedo-Ribeiro, S., Pereira, P.J.B.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia (FCT), Norte Portugal Regional Operational Programme NORTE 2020

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.203 (Depositor), 0.210 (DCC)
R-Value Work:
0.153 (Depositor), 0.160 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural characterization of mycobacterial hydrolase

Cereija, T.B., Alarico, S., Lourenco, E.C., Ventura, R., Empadinhas, N., Macedo-Ribeiro, S., Pereira, P.J.B.

To be published.

Macromolecule Content

Total Structure Weight: 102.81 kDa
Atom Count: 7,503
Modeled Residue Count: 890
Deposited Residue Count: 896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycobacterial hydrolase	A, B	448	Mycolicibacterium hassiacum DSM 44199	Mutation(s): 1 Gene Names: C731_0006 EC: 3.2.1.208
UniProt
Find proteins for K5BDL0 (Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)) Explore K5BDL0 Go to UniProtKB: K5BDL0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K5BDL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SER Query on SER Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	G [auth A], K [auth B]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.203 (Depositor), 0.210 (DCC)
R-Value Work: 0.153 (Depositor), 0.160 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.585	α = 90
b = 158.835	β = 90
c = 88.274	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Cereija, T.B.

Macedo-Ribeiro, S.

Pereira, P.J.B.

Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia (FCT)	Portugal	POCI-01-0145-FEDER-007274
Norte Portugal Regional Operational Programme NORTE 2020	Portugal	Norte-01-0145-FEDER-000012