3H12 | pdb_00003h12

Crystal structure of putative mandelate racemase from Bordetella Bronchiseptica RB50

• PDB DOI: https://doi.org/10.2210/pdb3H12/pdb

• Classification: ISOMERASE
• Organism(s): Bordetella bronchiseptica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-10 Released: 2009-04-21 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.146 (Depositor) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

Crystal structure of putative mandelate racemase from Bordetella Bronchiseptica RB50

Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 86.97 kDa 
• Atom Count: 6,853 
• Modeled Residue Count: 784 
• Deposited Residue Count: 794 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mandelate racemase	A, B	397	Bordetella bronchiseptica	Mutation(s): 0  Gene Names: BB4687
UniProt
Find proteins for A0A0H3LT39 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LT39  Go to UniProtKB:  A0A0H3LT39

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.146 (Depositor) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.148	α = 90
b = 116.148	β = 90
c = 128.136	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2012-10-24
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2024-02-21
  Changes: Data collection, Database references