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- PDB-5ubf: Crystal structure of the RctB domains 2-3, RctB-155-483 -

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Basic information

Entry
Database: PDB / ID: 5ubf
TitleCrystal structure of the RctB domains 2-3, RctB-155-483
ComponentsRctB replication initiator protein
KeywordsDNA BINDING PROTEIN / DNA replication initiation / DNA binding / secondary chromosome / Vibrio cholerae
Function / homologyReplication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / DUF3346 domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsOrlova, N. / Waldor, M.K. / Jeruzalmi, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM084162 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators.
Authors: Orlova, N. / Gerding, M. / Ivashkiv, O. / Olinares, P.D.B. / Chait, B.T. / Waldor, M.K. / Jeruzalmi, D.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: RctB replication initiator protein
B: RctB replication initiator protein


Theoretical massNumber of molelcules
Total (without water)79,7212
Polymers79,7212
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-11 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.535, 128.535, 127.775
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein RctB replication initiator protein


Mass: 39860.711 Da / Num. of mol.: 2 / Fragment: domains 2-3 (UNP residues 155-483)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: DN30_18, EN12_14105 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085QGR2, UniProt: Q9KNG2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.75 % / Description: rod
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals of selenomethionine-substituted RctB domains 2-3 (155-483) were prepared by mixing 0.1, or 0.2, or 0.4 uL of the protein solution (22.7 mg/ml RctB-155-483 in 20 mM Tris pH 7.4, 500 ...Details: Crystals of selenomethionine-substituted RctB domains 2-3 (155-483) were prepared by mixing 0.1, or 0.2, or 0.4 uL of the protein solution (22.7 mg/ml RctB-155-483 in 20 mM Tris pH 7.4, 500 mM sodium chloride, 5% glycerol, 5 mM 2-mercaptoethanol) and 0.2 uL of reservoir solution (0.1 M Bis-Tris propane pH 6.5, 0.2 M Magnesium chloride, 2% w/v PEG 8000).

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen cryo stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 24150 / % possible obs: 99.4 % / Redundancy: 5.7 % / Rsym value: 0.053 / Net I/σ(I): 21.73
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.4 % / CC1/2: 0.506 / Rsym value: 0.828 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000v714data reduction
HKL-2000v714data scaling
AutoSol1.11.1-2575-000phasing
PHENIX1.11.1-2575-000model building
RefinementMethod to determine structure: SAD / Resolution: 2.6→41.966 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 30.77
RfactorNum. reflection% reflection
Rfree0.2765 1744 7.35 %
Rwork0.235 --
obs0.2379 23743 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→41.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4578 0 0 31 4609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024672
X-RAY DIFFRACTIONf_angle_d0.5466298
X-RAY DIFFRACTIONf_dihedral_angle_d12.6231782
X-RAY DIFFRACTIONf_chiral_restr0.043694
X-RAY DIFFRACTIONf_plane_restr0.003802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.67660.36431450.3211761X-RAY DIFFRACTION93
2.6766-2.76290.32261440.30911767X-RAY DIFFRACTION95
2.7629-2.86170.36051420.28671800X-RAY DIFFRACTION95
2.8617-2.97620.33511430.28281814X-RAY DIFFRACTION98
2.9762-3.11160.36071430.28651812X-RAY DIFFRACTION98
3.1116-3.27560.31851510.27271848X-RAY DIFFRACTION99
3.2756-3.48070.31571510.25511866X-RAY DIFFRACTION100
3.4807-3.74930.29091440.25731850X-RAY DIFFRACTION99
3.7493-4.12630.27561480.24361881X-RAY DIFFRACTION100
4.1263-4.72270.23541460.19721859X-RAY DIFFRACTION100
4.7227-5.94750.24851450.21131868X-RAY DIFFRACTION100
5.9475-41.97120.25891420.22161873X-RAY DIFFRACTION100

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