2OZ8 | pdb_00002oz8

Crystal structure of putative mandelate racemase from Mesorhizobium loti

• PDB DOI: https://doi.org/10.2210/pdb2OZ8/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Mesorhizobium japonicum MAFF 303099
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-02-25 Released: 2007-03-13 
• Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Wu, B., Sridhar, V., Smith, D., Wasserman, S., 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: 2.48 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of putative mandelate racemase from Mesorhizobium loti

Bonanno, J.B., Freeman, J., Bain, K.T., Wu, B., Sridhar, V., Smith, D., Wasserman, S., 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.

Macromolecule Content

• Total Structure Weight: 88.23 kDa 
• Atom Count: 6,286 
• Modelled Residue Count: 742 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mll7089 protein	A, B	389	Mesorhizobium japonicum MAFF 303099	Mutation(s): 0  Gene Names: mll7089
UniProt
Find proteins for Q987E0 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q987E0  Go to UniProtKB:  Q987E0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.176	α = 90
b = 160.176	β = 90
c = 82.56	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-13 
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Wu, B., Sridhar, V., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2012-10-24
  Changes: Structure summary
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.6: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.7: 2024-02-21
  Changes: Data collection, Database references