3QZ4 | pdb_00003qz4

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth A], L [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO	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
UNX	C [auth A], D [auth A], J [auth B], K [auth B]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33QZ4

Space Group: P 1 2₁ 1

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

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary