3NKH | pdb_00003nkh

Crystal Structure of Integrase from MRSA strain Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3NKH/pdb

Classification: RECOMBINATION
Organism(s): Staphylococcus aureus subsp. aureus USA300_TCH1516
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-06-19 Released: 2010-08-18
Deposition Author(s): Kim, Y., Tesar, C., Gornicki, P., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.189 (Depositor), 0.187 (DCC)
R-Value Work:
0.156 (Depositor), 0.154 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Integrase from MRSA strain Staphylococcus aureus

Kim, Y., Tesar, C., Gornicki, P., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 58.14 kDa
Atom Count: 4,015
Modeled Residue Count: 446
Deposited Residue Count: 488
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B	244	Staphylococcus aureus subsp. aureus USA300_TCH1516	Mutation(s): 0 Gene Names: USA300HOU_0850

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A], J [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth B]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A]	F [auth A], H [auth A], M [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	D [auth A], G [auth A], L [auth B], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A], K [auth B], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.189 (Depositor), 0.187 (DCC)
R-Value Work: 0.156 (Depositor), 0.154 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.278	α = 90
b = 102.34	β = 90
c = 157.256	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing
BUCCANEER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-08-18

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary