3N4F | pdb_00003n4f

CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing protein from Geobacillus sp. Y412MC10

• PDB DOI: https://doi.org/10.2210/pdb3N4F/pdb

• Classification: ISOMERASE
• Organism(s): Paenibacillus sp. Y412MC10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-21 Released: 2010-06-09 
• Deposition Author(s): Malashkevich, V.N., Toro, R., 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: 1.88 Å
• R-Value Free: 
  0.242 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing protein from Geobacillus sp. Y412MC10

Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 177.39 kDa 
• Atom Count: 13,659 
• Modeled Residue Count: 1,538 
• Deposited Residue Count: 1,568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A, B, C, D	392	Paenibacillus sp. Y412MC10	Mutation(s): 0  Gene Names: 192811615, GYMC10_3367
UniProt
Find proteins for A0ACD6B8H0 (Geobacillus sp. (strain Y412MC10)) Explore A0ACD6B8H0  Go to UniProtKB:  A0ACD6B8H0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.242 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.387	α = 90
b = 66.1	β = 94.33
c = 151.536	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-09 
Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-06
  Changes: Data collection, Database references, Structure summary