4DWD | pdb_00004dwd

Crystal structure of mandelate racemase/muconate lactonizing protein from Paracoccus denitrificans PD1222 complexed with magnesium

• PDB DOI: https://doi.org/10.2210/pdb4DWD/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Paracoccus denitrificans PD1222
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-24 Released: 2012-03-14 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mandelate racemase/muconate lactonizing protein from Paracoccus denitrificans PD1222 complexed with magnesium

Malashkevich, V.N., Toro, R., 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: 86 kDa 
• Atom Count: 6,526 
• Modeled Residue Count: 741 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein	A, B	393	Paracoccus denitrificans PD1222	Mutation(s): 0  Gene Names: Pden_0244
UniProt
Find proteins for A1AYL4 (Paracoccus denitrificans (strain Pd 1222)) Explore A1AYL4  Go to UniProtKB:  A1AYL4

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.598	α = 90
b = 136.598	β = 90
c = 80.603	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Structure summary
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-12-06
  Changes: Data collection
• Version 1.6: 2024-11-27
  Changes: Structure summary