3RQT | pdb_00003rqt

1.5 Angstrom Crystal Structure of the Complex of Ligand Binding Component of ABC-type Import System from Staphylococcus aureus with Nickel and two Histidines

• PDB DOI: https://doi.org/10.2210/pdb3RQT/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-28 Released: 2011-05-11 
• Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kiryukhina, O., Falugi, F., Bottomley, M., Bagnoli, F., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.170 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Literature

1.5 Angstrom Crystal Structure of the Complex of Ligand Binding Component of ABC-type Import System from Staphylococcus aureus with Nickel and two Histidines.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kiryukhina, O., Falugi, F., Bottomley, M., Bagnoli, F., Grandi, G., Anderson, W.F.

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: 56.77 kDa 
• Atom Count: 4,947 
• Modeled Residue Count: 465 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	486	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: SAOUHSC_00001, SAOUHSC_00201
UniProt
Find proteins for Q2G2P5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G2P5  Go to UniProtKB:  Q2G2P5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth A], F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
HIS	B [auth A], C [auth A]	HISTIDINE C6 H10 N3 O2 HNDVDQJCIGZPNO-YFKPBYRVSA-O
SO4	G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 1.50 Å
• R-Value Free:  0.170 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33rqt

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.941	α = 90
b = 66.759	β = 90
c = 115.492	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kiryukhina, O., Falugi, F., Bottomley, M., Bagnoli, F., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-05-11
  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: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary