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- PDB-4cwc: Structure of Rolling Circle Replication Initiator Protein (RepDE)... -

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Basic information

Entry
Database: PDB / ID: 4cwc
TitleStructure of Rolling Circle Replication Initiator Protein (RepDE) from Staphylococcus aureus
ComponentsREPLICATION INITIATION PROTEIN, REPLICATION INITIATION PROTEIN
KeywordsISOMERASE / ANTIBIOTIC RESISTANCE / RELAXASE / PCRA HELICASE / 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: 2.9 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 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Dec 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)68,5602
Polymers68,5602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-17.1 kcal/mol
Surface area30270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.300, 56.536, 62.357
Angle α, β, γ (deg.)90.00, 102.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34280.117 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: P12053, DNA topoisomerase
Sequence detailsPROTEIN WAS CONSTRUCTED BY FUSING THE N-TERMINAL DOMAIN OF REPD - BASES 1295-1489 FROM PLASMID ...PROTEIN WAS CONSTRUCTED BY FUSING THE N-TERMINAL DOMAIN OF REPD - BASES 1295-1489 FROM PLASMID PC221 (GENBANK ACCESSION X02166) WITH THE C-TERMINAL DOMAIN OF REPE - BASES 4028-4315 FROM PLASMID PS194 (GENBANK ACCESSION X06627)

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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: 3.04 Å3/Da / Density % sol: 59.6 % / Description: NONE
Crystal growpH: 8.5
Details: 0.5 M AMMONIUM CITRATE/AMMONIUM HYDROXIDE PH 8.5, 15% (W/V) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC Q4 / Detector: CCD / Date: Aug 8, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.9→49.94 Å / Num. obs: 17447 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.3
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.5 / % 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: 2.9→49.99 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.892 / SU B: 16.971 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25894 939 5.1 %RANDOM
Rwork0.2163 ---
obs0.21858 17447 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.095 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-0.83 Å2
2---1.03 Å20 Å2
3---1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4600 0 0 0 4600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024696
X-RAY DIFFRACTIONr_bond_other_d0.0040.024486
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9516306
X-RAY DIFFRACTIONr_angle_other_deg1.044310354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8935538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.524.724254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73215946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4951532
X-RAY DIFFRACTIONr_chiral_restr0.0860.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025196
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021092
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_it5.6667.862158
X-RAY DIFFRACTIONr_mcbond_other5.6637.8582157
X-RAY DIFFRACTIONr_mcangle_it8.92511.782694
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.5828.5442536
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.47512.5333611
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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 77 -
Rwork0.415 1296 -
obs--99.85 %

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