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- PDB-5kbj: Structure of Rep-DNA complex -

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Basic information

Entry
Database: PDB / ID: 5kbj
TitleStructure of Rep-DNA complex
Components
  • (DNA (32-MER)) x 2
  • Replication initiator A, N-terminal
KeywordsTRANSCRIPTION/DNA / Replication initiation / Rep protein / S. aureus / TRANSCRIPTION-DNA complex
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 / DNA / DNA (> 10) / Replication initiator A, N-terminal
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsSchumacher, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / 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
DepositionJun 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Replication initiator A, N-terminal
B: Replication initiator A, N-terminal
C: Replication initiator A, N-terminal
H: Replication initiator A, N-terminal
D: Replication initiator A, N-terminal
E: Replication initiator A, N-terminal
F: Replication initiator A, N-terminal
G: Replication initiator A, N-terminal
R: DNA (32-MER)
W: DNA (32-MER)


Theoretical massNumber of molelcules
Total (without water)147,41210
Polymers147,41210
Non-polymers00
Water00
1
A: Replication initiator A, N-terminal
B: Replication initiator A, N-terminal
C: Replication initiator A, N-terminal
H: Replication initiator A, N-terminal
R: DNA (32-MER)
W: DNA (32-MER)


Theoretical massNumber of molelcules
Total (without water)83,5476
Polymers83,5476
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19350 Å2
ΔGint-88 kcal/mol
Surface area34630 Å2
MethodPISA
2
D: Replication initiator A, N-terminal
E: Replication initiator A, N-terminal
F: Replication initiator A, N-terminal
G: Replication initiator A, N-terminal


Theoretical massNumber of molelcules
Total (without water)63,8654
Polymers63,8654
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13010 Å2
ΔGint-55 kcal/mol
Surface area27170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.200, 77.500, 100.700
Angle α, β, γ (deg.)80.800, 75.500, 71.900
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Replication initiator A, N-terminal


Mass: 15966.347 Da / Num. of mol.: 8 / Fragment: UNP residues 2-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SAP042A_013, SAP058A_012, SAP071A_014 / Production host: Escherichia coli (E. coli) / References: UniProt: D2JDC3
#2: DNA chain DNA (32-MER)


Mass: 9843.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (32-MER)


Mass: 9838.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 28% PEG 400, 0.1 M sodium/potassium phosphate (pH 6.9), 4% PEG 3350, and 10% polyethylene glycol

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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: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→97.1 Å / Num. obs: 28484 / % possible obs: 94.5 % / Redundancy: 1.8 % / Net I/σ(I): 7

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PQL

4pql


Resolution: 3.09→97.1 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.49
RfactorNum. reflection% reflection
Rfree0.277 3682 12.93 %
Rwork0.2245 --
obs0.2313 28484 94.55 %
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Bsol: 50.273 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 174.19 Å2 / Biso mean: 88.46 Å2 / Biso min: 30.68 Å2
Baniso -1Baniso -2Baniso -3
1-28.5235 Å220.9395 Å2-19.3635 Å2
2---4.3348 Å2-4.5826 Å2
3----24.1887 Å2
Refinement stepCycle: final / Resolution: 3.09→97.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8747 1312 0 0 10059
Num. residues----1095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310368
X-RAY DIFFRACTIONf_angle_d0.64114206
X-RAY DIFFRACTIONf_chiral_restr0.0391542
X-RAY DIFFRACTIONf_plane_restr0.0021580
X-RAY DIFFRACTIONf_dihedral_angle_d19.5474162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0876-3.1980.40183500.36852411276193
3.198-3.3260.36693960.30082449284594
3.326-3.47740.34883900.26842485287594
3.4774-3.66070.28683510.22642473282494
3.6607-3.89010.28453560.20882514287095
3.8901-4.19050.25993780.19232448282695
4.1905-4.61220.23673530.17122490284394
4.6122-5.27950.24683440.19382439278393
5.2795-6.65140.29413920.2552515290796
6.6514-97.15180.23193720.21352578295098

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