3CIH | pdb_00003cih

Crystal structure of a putative alpha-rhamnosidase from Bacteroides thetaiotaomicron

• PDB DOI: https://doi.org/10.2210/pdb3CIH/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-03-11 Released: 2008-04-01 
• Deposition Author(s): Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal structure of a putative alpha-rhamnosidase from Bacteroides thetaiotaomicron.

Kumaran, D., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 86.71 kDa 
• Atom Count: 6,218 
• Modeled Residue Count: 714 
• Deposited Residue Count: 739 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative alpha-rhamnosidase	A	739	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_1001
UniProt
Find proteins for Q8A916 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A916  Go to UniProtKB:  Q8A916

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 2.33 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.895	α = 90
b = 146.895	β = 90
c = 198.847	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary