3C3K | pdb_00003c3k

Crystal structure of an uncharacterized protein from Actinobacillus succinogenes

• PDB DOI: https://doi.org/10.2210/pdb3C3K/pdb

• Classification: ISOMERASE
• Organism(s): Actinobacillus succinogenes 130Z
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-28 Released: 2008-02-05 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Meyer, A.J., 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: 1.99 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Crystal structure of an uncharacterized protein from Actinobacillus succinogenes.

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.58 kDa 
• Atom Count: 4,386 
• Modeled Residue Count: 539 
• Deposited Residue Count: 570 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase	A, B	285	Actinobacillus succinogenes 130Z	Mutation(s): 0  Gene Names: Asuc_0357 EC: 5.1.1.1
UniProt
Find proteins for A6VL88 (Actinobacillus succinogenes (strain ATCC 55618 / DSM 22257 / CCUG 43843 / 130Z)) Explore A6VL88  Go to UniProtKB:  A6VL88

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.888	α = 90
b = 67.602	β = 90
c = 204.802	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Malashkevich, V.N., Toro, R., Meyer, A.J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references