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- PDB-3nkh: Crystal Structure of Integrase from MRSA strain Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 3nkh
TitleCrystal Structure of Integrase from MRSA strain Staphylococcus aureus
ComponentsIntegrase
KeywordsRECOMBINATION / alpha-fold / MRSA protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyIntergrase catalytic core / hpI Integrase; Chain A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus USA300_TCH1516 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.502 Å
AuthorsKim, Y. / Tesar, C. / Gornicki, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2010
Title: Crystal Structure of Integrase from MRSA strain Staphylococcus aureus
Authors: Kim, Y. / Tesar, C. / Gornicki, P. / Joachimiak, A.
History
DepositionJun 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,14015
Polymers57,0232
Non-polymers1,11713
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-138 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.278, 102.340, 157.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Integrase


Mass: 28511.697 Da / Num. of mol.: 2 / Fragment: residues 187-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300_TCH1516 (bacteria)
Strain: strain USA300 / TCH1516 / Gene: USA300HOU_0850 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: A8Z1E8

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Non-polymers , 5 types, 201 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M TRIS pH 8, 20 %v/v MPD, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 33430 / Num. obs: 33430 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 47.12 Å2 / Rsym value: 0.107 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 1632 / Rsym value: 0.776 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.502→46.655 Å / SU ML: 0.32 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1676 5.05 %random
Rwork0.156 ---
all0.158 33166 --
obs0.158 33166 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.775 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 58.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.0566 Å20 Å2-0 Å2
2--16.2762 Å20 Å2
3----11.2195 Å2
Refinement stepCycle: LAST / Resolution: 2.502→46.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 64 188 3838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123890
X-RAY DIFFRACTIONf_angle_d1.4035240
X-RAY DIFFRACTIONf_dihedral_angle_d19.7151470
X-RAY DIFFRACTIONf_chiral_restr0.095560
X-RAY DIFFRACTIONf_plane_restr0.005677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5016-2.5910.31581480.23843004315297
2.591-2.69470.24661480.201631343282100
2.6947-2.81730.21031660.175131013267100
2.8173-2.96580.21381830.165831043287100
2.9658-3.15160.20031600.16431353295100
3.1516-3.39490.21800.153831413321100
3.3949-3.73640.15961680.131131373305100
3.7364-4.27670.14031600.112231893349100
4.2767-5.3870.15461690.124332153384100
5.387-46.66290.19681940.174933303524100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.02320.7101-1.19521.1023-1.57391.76620.0763-0.1266-0.00960.1664-0.0451-0.023-0.068-0.0588-0.03520.3396-0.0340.00850.38960.08590.264-0.41655.141430.6444
20.4630.2524-0.08730.6193-0.16840.8311-0.02170.14310.0306-0.0407-0.01250.009-0.0247-0.06380.03430.1061-0.0133-00.19850.01790.1255-21.5502-18.79764.3342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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