4HES | pdb_00004hes

Structure of a Beta-Lactamase Class A-like Protein from Veillonella parvula.

• PDB DOI: https://doi.org/10.2210/pdb4HES/pdb

• Classification: HYDROLASE
• Organism(s): Veillonella parvula DSM 2008
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-04 Released: 2012-10-17 
• Deposition Author(s): Cuff, M.E., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Literature

Structure of a Beta-Lactamase Class A-like Protein from Veillonella parvula.

Cuff, M.E., Li, H., Clancy, S., Joachimiak, A.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 161.31 kDa 
• Atom Count: 12,560 
• Modeled Residue Count: 1,354 
• Deposited Residue Count: 1,375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase class A-like protein	A, B, C, D, E	275	Veillonella parvula DSM 2008	Mutation(s): 0  Gene Names: Vpar_0488

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	AA [auth E], BA [auth E], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], Q [auth D], R [auth D], S [auth D], T [auth D], W [auth E], X [auth E], Y [auth E], Z [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	DA [auth E], I [auth A], M [auth B], P [auth C], U [auth D]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	CA [auth E], H [auth A], V [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.398	α = 90
b = 163.106	β = 90.38
c = 113.009	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Cuff, M.E., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary