2QDD

Crystal structure of a member of enolase superfamily from Roseovarius nubinhibens ISM

• PDB DOI: https://doi.org/10.2210/pdb2QDD/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Roseovarius nubinhibens ISM
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-06-20 Released: 2007-06-26 
• Deposition Author(s): Patskovsky, Y., Bonanno, J., Sauder, J.M., Gilmore, J.M., Iizuka, M., Groshong, C., Gheyi, T., Sojitra, S., Wasserman, S.R., Koss, J., Gerlt, J., 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: 2.30 Å
• R-Value Free: 0.228 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Crystal structure of a member of enolase superfamily from Roseovarius nubinhibens ISM.

Patskovsky, Y., Bonanno, J., Sauder, J.M., Gilmore, J.M., Iizuka, M., Groshong, C., Gheyi, T., Sojitra, S., Wasserman, S.R., Koss, J., 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: 81.54 kDa 
• Atom Count: 5,975 
• Modelled Residue Count: 736 
• Deposited Residue Count: 756 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme	A, B	378	Roseovarius nubinhibens ISM	Mutation(s): 0  Gene Names: COG4948, ISM_14065
UniProt
Find proteins for A3SNF7 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM)) Explore A3SNF7  Go to UniProtKB:  A3SNF7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.228 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.842	α = 90
b = 126.842	β = 90
c = 96.608	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Patskovsky, Y., Bonanno, J., Sauder, J.M., Gilmore, J.M., Iizuka, M., Groshong, C., Gheyi, T., Sojitra, S., Wasserman, S.R., Koss, J., Gerlt, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, 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: 2024-02-21
  Changes: Data collection, Database references, Refinement description