3P75 | pdb_00003p75

Crystal structure of Staphylococcal nuclease variant Delta+PHS V104D at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb3P75/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-10-12 Released: 2010-11-17 
• Deposition Author(s): Khangulov, V.S., Schlessman, J.L., Heroux, A., Garcia-Moreno, E.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.239 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Staphylococcal nuclease variant Delta+PHS V104D at cryogenic temperature

Khangulov, V.S., Schlessman, J.L., Garcia-Moreno, E.B.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 15.21 kDa 
• Atom Count: 1,141 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	A	129	Staphylococcus aureus	Mutation(s): 6  EC: 3.1.31.1
UniProt
Find proteins for P00644 (Staphylococcus aureus) Explore P00644  Go to UniProtKB:  P00644

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THP	C [auth A]	THYMIDINE-3',5'-DIPHOSPHATE C10 H16 N2 O11 P2 CSNCBOPUCJOHLS-XLPZGREQSA-N
CA	B [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.239 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31	α = 90
b = 60.791	β = 93.45
c = 36.838	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Khangulov, V.S., Schlessman, J.L., Heroux, A., Garcia-Moreno, E.B.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description