3FZ6 | pdb_00003fz6

Crystal structure of glutamate decarboxylase beta from Escherichia coli: complex with xenon

PDB DOI: https://doi.org/10.2210/pdb3FZ6/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-23 Released: 2009-02-03
Deposition Author(s): Malashkevich, V.N., De Biase, D., Bossa, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.203 (Depositor), 0.200 (DCC)
R-Value Work:
0.135 (Depositor), 0.140 (DCC)
R-Value Observed:
0.138 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of glutamate decarboxylase beta from Escherichia coli: complex with xenon

Malashkevich, V.N., De Biase, D., Bossa, F.

To be published.

Macromolecule Content

Total Structure Weight: 318.64 kDa
Atom Count: 22,347
Modeled Residue Count: 2,747
Deposited Residue Count: 2,796
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate decarboxylase beta	A, B, C, D, E A, B, C, D, E, F	466	Escherichia coli K-12	Mutation(s): 0 Gene Names: b1493, gadB, JW1488 EC: 4.1.1.15
UniProt
Find proteins for P69910 (Escherichia coli (strain K12)) Explore P69910 Go to UniProtKB: P69910
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69910
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMP Query on PMP Download Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
XE Query on XE Download Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.203 (Depositor), 0.200 (DCC)
R-Value Work: 0.135 (Depositor), 0.140 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.729	α = 90
b = 116.729	β = 90
c = 208.423	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ELLIOTT	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-02-03

Deposition Author(s):

Malashkevich, V.N.

De Biase, D.

Bossa, F.

Revision History (Full details and data files)

Version 1.0: 2009-02-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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Crystal structure of glutamate decarboxylase beta from Escherichia coli: complex with xenon

Crystal structure of glutamate decarboxylase beta from Escherichia coli: complex with xenon

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

3FZ6 | pdb_00003fz6