1TVF | pdb_00001tvf

Crystal Structure of penicillin-binding protein 4 (PBP4) from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb1TVF/pdb

• Classification: PENICILLIN BINDING
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-06-29 Released: 2004-07-06 
• Deposition Author(s): Rajashankar, K.R., Ray, S.S., Bonanno, J.B., Pinho, M., Tomasz, A., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of penicillin-binding protein 4 (PBP4) from Staphylococcus aureus

Rajashankar, K.R., Ray, S.S., Bonanno, J.B., Pinho, M., Tomasz, A., Burley, S.K.

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.

Macromolecule Content 

• Total Structure Weight: 82.96 kDa 
• Atom Count: 6,620 
• Modeled Residue Count: 738 
• Deposited Residue Count: 738 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
penicillin binding protein 4	A, B	369	Staphylococcus aureus	Mutation(s): 0  Gene Names: PBP4
UniProt
Find proteins for Q57540 (Staphylococcus aureus) Explore Q57540  Go to UniProtKB:  Q57540

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNL	F [auth A], I [auth B]	Unknown ligand QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.713	α = 90
b = 140.189	β = 90
c = 145.775	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-06 
Deposition Author(s): Rajashankar, K.R., Ray, S.S., Bonanno, J.B., Pinho, M., Tomasz, A., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-07-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description