2OX4 | pdb_00002ox4

Crystal structure of putative dehydratase from Zymomonas mobilis ZM4

• PDB DOI: https://doi.org/10.2210/pdb2OX4/pdb

• Classification: ISOMERASE
• Organism(s): Zymomonas mobilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-02-19 Released: 2007-03-06 
• Deposition Author(s): Patskovsky, Y., Toro, R., Sauder, J.M., Freeman, J.C., Bain, K., Gheyi, T., Wasserman, S.R., Smith, D., Gerlt, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Putative Dehydratase from Zymomonas Mobilis Zm4

Patskovsky, Y., Toro, R., Sauder, J.M., Freeman, J.C., Bain, K., Gheyi, T., Wasserman, S.R., Smith, D., Gerlt, J., 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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 359.9 kDa 
• Atom Count: 28,439 
• Modeled Residue Count: 3,152 
• Deposited Residue Count: 3,224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative mandelate racemase	A, B, C, D, E, F, G, H	403	Zymomonas mobilis	Mutation(s): 0  Gene Names: rspA, ZMO1264 EC: 5.1.2.2
UniProt
Find proteins for Q5NN22 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)) Explore Q5NN22  Go to UniProtKB:  Q5NN22

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	AA [auth F], DA [auth G], EA [auth G], FA [auth G], HA [auth H], J [auth A], K [auth A], N [auth B], P [auth C], Q [auth C], T [auth D], U [auth D], W [auth E], Z [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	BA [auth G], L [auth B], S [auth D], Y [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	CA [auth G], GA [auth H], I [auth A], M [auth B], O [auth C], R [auth D], V [auth E], X [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.178	α = 90
b = 190.409	β = 90
c = 85.922	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): Patskovsky, Y., Toro, R., Sauder, J.M., Freeman, J.C., Bain, K., Gheyi, T., Wasserman, S.R., Smith, D., Gerlt, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2023-08-30
  Changes: Data collection, Database references, Refinement description