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- PDB-4pta: Structure of MDR initiator -

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Basic information

Entry
Database: PDB / ID: 4pta
TitleStructure of MDR initiator
ComponentsReplication initiator protein
KeywordsREPLICATION / initiation / multidrug resistance / PROTEIN BINDING
Function / homologyReplication initiator A, N-terminal / Replication initiator protein A, C-terminal domain / Replication initiator protein A (RepA) N-terminus / Replication initiator protein A C-terminal domain / Replication initiator protein / Replication initiator protein
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.6003 Å
AuthorsSchumacher, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein.
Authors: Schumacher, M.A. / Tonthat, N.K. / Kwong, S.M. / Chinnam, N.B. / Liu, M.A. / Skurray, R.A. / Firth, N.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Replication initiator protein


Theoretical massNumber of molelcules
Total (without water)15,5191
Polymers15,5191
Non-polymers00
Water57632
1
D: Replication initiator protein

D: Replication initiator protein

D: Replication initiator protein

D: Replication initiator protein


Theoretical massNumber of molelcules
Total (without water)62,0754
Polymers62,0754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area12830 Å2
ΔGint-45 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.460, 101.460, 62.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Replication initiator protein


Mass: 15518.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: USA300 / Gene: repA, SAUSA300_pUSA030001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FDD7, UniProt: A0A0H2XIV8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 275 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1 M Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 275K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2012 / Details: mirrors
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→67 Å / Num. all: 5120 / Num. obs: 5166 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.057 / Rsym value: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 2.44 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.332 / % possible all: 91.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.6003→23.62 Å / SU ML: 0.39 / σ(F): 1.46 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.281 511 9.99 %
Rwork0.225 --
obs0.231 5116 97 %
all-5120 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.92 Å2 / ksol: 0.45 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5209 Å20 Å2-0 Å2
2--4.5209 Å20 Å2
3----9.0418 Å2
Refinement stepCycle: LAST / Resolution: 2.6003→23.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 0 32 1043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031038
X-RAY DIFFRACTIONf_angle_d0.6481402
X-RAY DIFFRACTIONf_dihedral_angle_d17.507396
X-RAY DIFFRACTIONf_chiral_restr0.042159
X-RAY DIFFRACTIONf_plane_restr0.002177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6003-2.86160.48081280.30621157X-RAY DIFFRACTION100
2.8616-3.27470.28631300.24561169X-RAY DIFFRACTION100
3.2747-4.12230.25491310.18911177X-RAY DIFFRACTION100
4.1223-23.62360.24841220.21911102X-RAY DIFFRACTION89

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