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Basic information

Entry
Database: PDB / ID: 4cwe
TitleStructural studies of rolling circle replication initiation protein from Staphylococcus aureus
ComponentsREPLICATION INITIATION PROTEIN, REPLICATION INITIATION PROTEIN
KeywordsISOMERASE / ANTIBIOTIC RESISTANCE / PCRA HELICASE / DNA RELAXASE / CHIMERA
Function / homologyReplication initiation factor / Replication initiation factor / DNA topoisomerase activity / DNA replication initiation / DNA replication / DNA binding / Replication initiation protein / Replication initiation protein
Function and homology information
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCarr, S.B. / Phillips, S.E.V. / Thomas, C.D.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structures of Replication Initiation Proteins from Staphylococcal Antibiotic Resistance Plasmids Reveal Protein Asymmetry and Flexibility are Necessary for Replication.
Authors: Carr, S.B. / Phillips, S.E. / Thomas, C.D.
History
DepositionApr 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Data collection
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Mar 30, 2016Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REPLICATION INITIATION PROTEIN, REPLICATION INITIATION PROTEIN
C: REPLICATION INITIATION PROTEIN, REPLICATION INITIATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)68,4722
Polymers68,4722
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-14.7 kcal/mol
Surface area30580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.242, 168.242, 168.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein REPLICATION INITIATION PROTEIN, REPLICATION INITIATION PROTEIN / REPD / REPN


Mass: 34236.105 Da / Num. of mol.: 2
Fragment: REPLICATION INITIATION PROTEIN RESIDUES 32-216, REPLICATION INITIATION PROTEIN RESIDUES 220-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Plasmid: PET-15M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): PLYSS
References: UniProt: P03065, UniProt: P19529, DNA topoisomerase
Sequence detailsPROTEIN WAS CONSTRUCTED BY FUSING THE N-TERMINAL DOMAIN OF REPD - BASES 1295-1849 FROM PLASMID ...PROTEIN WAS CONSTRUCTED BY FUSING THE N-TERMINAL DOMAIN OF REPD - BASES 1295-1849 FROM PLASMID PC221 (GENBANK ACCESSION X02166) WITH THE C-TERMINAL DOMAIN OF REPN - BASES 856-1143 FROM PLASMID PCW7 (GENBANK ACCESSION J03323)

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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: 2.92 Å3/Da / Density % sol: 57.8 % / Description: NONE
Crystal growpH: 5.5 / Details: 0.1 M SODIUM CITRATE PH 5.5, 2.5 M 1,6-HEXANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC Q4 / Detector: CCD / Date: Jun 7, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.499
11-H, -L, -K20.501
ReflectionResolution: 3→39.7 Å / Num. obs: 15902 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.7
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CIJ

4cij


Resolution: 3→39.66 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.844 / SU B: 19.145 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29711 770 4.8 %RANDOM
Rwork0.24106 ---
obs0.24364 15210 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.066 Å2
Baniso -1Baniso -2Baniso -3
1--25.5 Å2-6.14 Å25.8 Å2
2--5.57 Å2-65.84 Å2
3---19.93 Å2
Refinement stepCycle: LAST / Resolution: 3→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 0 0 4596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024690
X-RAY DIFFRACTIONr_bond_other_d0.0050.024490
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.956300
X-RAY DIFFRACTIONr_angle_other_deg1.002310352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76824.688256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01915940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0631534
X-RAY DIFFRACTIONr_chiral_restr0.0950.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025204
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021098
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.4678.1042158
X-RAY DIFFRACTIONr_mcbond_other7.4688.1042157
X-RAY DIFFRACTIONr_mcangle_it11.6312.1412694
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.2538.3312532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it11.85712.3443607
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 48 -
Rwork0.312 1102 -
obs--99.39 %

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