3FVD | pdb_00003fvd

Crystal structure of a member of enolase superfamily from ROSEOVARIUS NUBINHIBENS ISM complexed with magnesium

• PDB DOI: https://doi.org/10.2210/pdb3FVD/pdb

• Classification: HYDROLASE
• Organism(s): Roseovarius nubinhibens ISM
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-15 Released: 2009-01-27 
• Deposition Author(s): Malashkevich, V.N., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., 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: 2.30 Å
• R-Value Free: 
  0.225 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of a member of enolase superfamily from ROSEOVARIUS NUBINHIBENS ISM complexed with magnesium

Malashkevich, V.N., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 81.4 kDa 
• Atom Count: 5,859 
• Modeled Residue Count: 728 
• 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 [auth B], B [auth A]	378	Roseovarius nubinhibens ISM	Mutation(s): 0  Gene Names: 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
MG	C [auth B], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.225 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.518	α = 90
b = 126.518	β = 90
c = 97.294	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-27 
Deposition Author(s): Malashkevich, V.N., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., 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: 2009-01-27
  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: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references