3K2V | pdb_00003k2v

Structure of the CBS pair of a putative D-arabinose 5-phosphate isomerase from Klebsiella pneumoniae subsp. pneumoniae.

• PDB DOI: https://doi.org/10.2210/pdb3K2V/pdb

• Classification: ISOMERASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-09-30 Released: 2009-12-22 
• Deposition Author(s): Cuff, M.E., Volkart, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.182 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Structure of the CBS pair of a putative D-arabinose 5-phosphate isomerase from Klebsiella pneumoniae subsp. pneumoniae.

Cuff, M.E., Volkart, L., Bearden, J., Joachimiak, A.

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: 34.49 kDa 
• Atom Count: 2,476 
• Modeled Residue Count: 258 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative D-arabinose 5-phosphate isomerase	A, B	149	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: KPN78578_35760, KPN_03607, yrbH EC: 5.3.1.13
UniProt
Find proteins for A6TEL6 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TEL6  Go to UniProtKB:  A6TEL6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMK	C [auth A], G [auth B]	CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID C17 H26 N3 O15 P YWWJKULNWGRYAS-UOVSKDHASA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.95 Å
• R-Value Free:  0.182 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.151	α = 90
b = 102.151	β = 90
c = 214.85	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Cuff, M.E., Volkart, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary