3KNY | pdb_00003kny

Crystal structure of a two domain protein with unknown function (bt_3535) from bacteroides thetaiotaomicron vpi-5482 at 2.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3KNY/pdb

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


• Deposited: 2009-11-12 Released: 2009-12-01 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of hypothetical protein BT_3535 (NP_812447.1) from BACTERIODES THETAIOTAOMICRON VPI-5482 at 2.60 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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.65 kDa 
• Atom Count: 1,537 
• Modeled Residue Count: 194 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein BT_3535	A	218	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_3535
UniProt
Find proteins for Q8A1X3 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A1X3  Go to UniProtKB:  Q8A1X3

Small Molecules

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: 2.60 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33KNY

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.029	α = 90
b = 120.029	β = 90
c = 94.767	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references
• Version 1.5: 2024-10-16
  Changes: Data collection, Structure summary