3QZ4

Crystal structure of an Endo-1,4-beta-xylanase D (BT_3675) from Bacteroides thetaiotaomicron VPI-5482 at 1.74 A resolution

PDB DOI: https://doi.org/10.2210/pdb3QZ4/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-03-04 Released: 2011-04-06
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.202
R-Value Work: 0.159
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of an Endo-1,4-beta-xylanase D (BT_3675) from Bacteroides thetaiotaomicron VPI-5482 at 1.74 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 71.35 kDa
Atom Count: 5,633
Modelled Residue Count: 612
Deposited Residue Count: 622
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase D	A, B	311	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: BT_3675
UniProt
Find proteins for Q8A1I6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A1I6 Go to UniProtKB: Q8A1I6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A1I6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B]	E [auth A], L [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] M [auth B] F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	C [auth A], D [auth A], J [auth B], K [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.202
R-Value Work: 0.159
R-Value Observed: 0.162
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M33QZ4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.163	α = 90
b = 99.252	β = 97.92
c = 65.003	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER-TNT	refinement
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-04-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations

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Help and Resources

3QZ4

Crystal structure of an Endo-1,4-beta-xylanase D (BT_3675) from Bacteroides thetaiotaomicron VPI-5482 at 1.74 A resolution

Crystal structure of an Endo-1,4-beta-xylanase D (BT_3675) from Bacteroides thetaiotaomicron VPI-5482 at 1.74 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)