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- PDB-5ube: Crystal structure of the N-terminal domain (domain 1) of RctB -

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Basic information

Entry
Database: PDB / ID: 5ube
TitleCrystal structure of the N-terminal domain (domain 1) of RctB
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOrlova, N. / Ivashkiv, O. / 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 1.4Oct 4, 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: RctB replication initiator protein
B: RctB replication initiator protein


Theoretical massNumber of molelcules
Total (without water)29,6802
Polymers29,6802
Non-polymers00
Water1,15364
1
A: RctB replication initiator protein


Theoretical massNumber of molelcules
Total (without water)14,8401
Polymers14,8401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RctB replication initiator protein


Theoretical massNumber of molelcules
Total (without water)14,8401
Polymers14,8401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.803, 52.127, 63.414
Angle α, β, γ (deg.)90.00, 101.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RctB replication initiator protein


Mass: 14840.109 Da / Num. of mol.: 2 / Fragment: domain 1 (UNP residues 1-124)
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.: 64 / 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: 2.5 Å3/Da / Density % sol: 50.77 % / Description: plate
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystals of RctB domain 1 (1-124) were prepared using the sitting drop vapor diffusion method by mixing 0.1, or 0.2, or 0.4 uL of the protein solution (22.4 mg/ml RctB-2-124 in 20 mM Tris pH ...Details: Crystals of RctB domain 1 (1-124) were prepared using the sitting drop vapor diffusion method by mixing 0.1, or 0.2, or 0.4 uL of the protein solution (22.4 mg/ml RctB-2-124 in 20 mM Tris pH 7.4, 50 mM sodium chloride, 5% glycerol, 5 mM 2-mercaptoethanol) and 0.2 uL of reservoir solution (0.24 M Sodium malonate pH 7.0, 20% w/v PEG 3350).
Temp details: cold room

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen cryo stream
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16800 / % possible obs: 84.3 % / Redundancy: 1.6 % / Rsym value: 0.057 / Net I/σ(I): 17
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 16.6 / CC1/2: 0.878 / % possible all: 64.6

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
HKL-2000v714data reduction
HKL-2000v714data scaling
PHASER1.11_2567-000phasing
PHENIX1.11_2567-000model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UBD

5ubd


Resolution: 2→33.326 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.19
RfactorNum. reflection% reflection
Rfree0.2656 1561 10.01 %
Rwork0.2274 --
obs0.2313 15588 78.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→33.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 0 64 1910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061874
X-RAY DIFFRACTIONf_angle_d0.7572526
X-RAY DIFFRACTIONf_dihedral_angle_d11.8491140
X-RAY DIFFRACTIONf_chiral_restr0.045296
X-RAY DIFFRACTIONf_plane_restr0.004322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9998-2.06430.3643940.3042880X-RAY DIFFRACTION54
2.0643-2.13810.34941130.27431013X-RAY DIFFRACTION63
2.1381-2.22370.29461270.26641124X-RAY DIFFRACTION70
2.2237-2.32480.31491430.26091270X-RAY DIFFRACTION78
2.3248-2.44740.32121470.24751317X-RAY DIFFRACTION81
2.4474-2.60060.29231540.25241392X-RAY DIFFRACTION87
2.6006-2.80130.31331610.23751428X-RAY DIFFRACTION88
2.8013-3.08310.30761610.23481467X-RAY DIFFRACTION89
3.0831-3.52880.27261580.24131423X-RAY DIFFRACTION86
3.5288-4.44420.23911470.20461316X-RAY DIFFRACTION81
4.4442-33.33060.21211560.2031397X-RAY DIFFRACTION82

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