3G6I | pdb_00003g6i

Crystal structure of an outer membrane protein, part of a putative carbohydrate binding complex (bt_1022) from bacteroides thetaiotaomicron vpi-5482 at 1.93 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3G6I/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-06 Released: 2009-02-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Crystal structure of outer membrane protein, part of carbohydrate binding complex (NP_809935.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.93 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.55 kDa 
• Atom Count: 1,917 
• Modeled Residue Count: 200 
• Deposited Residue Count: 204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative outer membrane protein, part of carbohydrate binding complex	A	204	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_1022, NP_809935.1
UniProt
Find proteins for Q8A8Z5 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A8Z5  Go to UniProtKB:  Q8A8Z5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A], C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33G6I

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.025	α = 90
b = 75.025	β = 90
c = 127.29	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary