5HE9 | pdb_00005he9

Bacterial initiation protein in complex with Phage inhibitor protein

• PDB DOI: https://doi.org/10.2210/pdb5HE9/pdb

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


• Deposited: 2016-01-05 Released: 2016-06-08 
• Deposition Author(s): Hood, I.V., Berger, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.218 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Structure of inhibited replicative helicase loader from Staphylococcus aureus at 1.9 Angstrom resolution

Hood, I.V., Berger, J.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 27.01 kDa 
• Atom Count: 2,031 
• Modeled Residue Count: 224 
• Deposited Residue Count: 230 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase loader	A	174	Staphylococcus aureus	Mutation(s): 0  Gene Names: dnaI
UniProt
Find proteins for Q2FXP5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXP5  Go to UniProtKB:  Q2FXP5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage inhibitor protein	B [auth E]	56	Staphylococcus aureus	Mutation(s): 0  Gene Names: OO23_07105
UniProt
Find proteins for Q6R837 (Biseptimavirus bv77) Explore Q6R837  Go to UniProtKB:  Q6R837

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF	D [auth A]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	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:  0.218 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.173	α = 90
b = 73.173	β = 90
c = 189.727	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): Hood, I.V., Berger, J.M.

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary