2POZ | pdb_00002poz

Crystal structure of a putative dehydratase from Mesorhizobium loti

• PDB DOI: https://doi.org/10.2210/pdb2POZ/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Mesorhizobium japonicum MAFF 303099
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-04-27 Released: 2007-05-15 
• Deposition Author(s): Sugadev, R., Eswaramoorthy, S., 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: 2.04 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal structure of a putative dehydratase from Mesorhizobium loti.

Sugadev, R., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

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: 347.55 kDa 
• Atom Count: 24,043 
• Modeled Residue Count: 3,032 
• Deposited Residue Count: 3,136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dehydratase	A, B, C, D, E, F, G, H	392	Mesorhizobium japonicum MAFF 303099	Mutation(s): 9  Gene Names: mll9372
UniProt
Find proteins for Q981H6 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q981H6  Go to UniProtKB:  Q981H6

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.269	α = 90
b = 189.825	β = 90
c = 192.579	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	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: 2007-05-15 
Deposition Author(s): Sugadev, R., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-05-15
  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: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary