6KVW | pdb_00006kvw

The complex structure of EanB/C339A/C370A and hercynine

PDB DOI: https://doi.org/10.2210/pdb6KVW/pdb

Classification: TRANSFERASE
Organism(s): Chlorobium limicola
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2019-09-05 Released: 2020-09-09
Deposition Author(s): Wu, L., Liu, P.H., Zhou, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.217 (Depositor), 0.218 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The complex structure of EanB/C339A/C370A and hercynine

Wu, L., Liu, P.H., Zhou, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 105.24 kDa
Atom Count: 7,537
Modeled Residue Count: 862
Deposited Residue Count: 920
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfurtransferase	A, B	460	Chlorobium limicola	Mutation(s): 2 Gene Names: Clim_1149
UniProt
Find proteins for B3ECE3 (Chlorobium limicola (strain DSM 245 / NBRC 103803 / 6330)) Explore B3ECE3 Go to UniProtKB: B3ECE3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3ECE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AVJ (Subject of Investigation/LOI) Query on AVJ Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A]	H [auth A], O [auth B]	N,N,N-trimethyl-histidine C₉ H₁₆ N₃ O₂ GPPYTCRVKHULJH-QMMMGPOBSA-O		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain F [auth A]	F [auth A], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain N [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B] Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.217 (Depositor), 0.218 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.823	α = 90
b = 110.851	β = 90
c = 120.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Wu, L.

Liu, P.H.

Zhou, J.H.

Revision History (Full details and data files)

Version 1.0: 2020-09-09
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary