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- PDB-5ubd: Crystal structure of the N-terminal domain (domain 1) of RctB, Rc... -

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Basic information

Entry
Database: PDB / ID: 5ubd
TitleCrystal structure of the N-terminal domain (domain 1) of RctB, RctB-1-124-L48M
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: 2.002 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 1.4Nov 6, 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)29,9982
Polymers29,9982
Non-polymers00
Water2,738152
1
A: RctB replication initiator protein


Theoretical massNumber of molelcules
Total (without water)14,9991
Polymers14,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RctB replication initiator protein


Theoretical massNumber of molelcules
Total (without water)14,9991
Polymers14,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.451, 38.167, 63.042
Angle α, β, γ (deg.)97.46, 91.49, 98.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein RctB replication initiator protein


Mass: 14998.834 Da / Num. of mol.: 2 / Fragment: domain 1 (UNP residues 1-124) / Mutation: L48M
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.: 152 / 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: 2.58 Å3/Da / Density % sol: 52.41 % / Description: plate
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystals of selenomethionine-substituted RctB domain 1 (1 - 124, L48M) were grown by mixing 0.1, or 0.2, or 0.4 uL of the protein solution (20.1 mg/ml RctB-2-124-L48M in 20 mM Tris pH 7.4, ...Details: Crystals of selenomethionine-substituted RctB domain 1 (1 - 124, L48M) were grown by mixing 0.1, or 0.2, or 0.4 uL of the protein solution (20.1 mg/ml RctB-2-124-L48M 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 Sodium HEPES pH 7.5, 20% w/v PEG10000).
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: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 5, 2015
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: 19914 / % possible obs: 94.3 % / Redundancy: 2 % / Rsym value: 0.049 / Net I/σ(I): 26.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.44 / CC1/2: 0.712 / Rsym value: 0.496 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
HKL-2000v714data reduction
HKL-2000v714data scaling
AutoSol1.11-2567-000phasing
PHENIX1.11-2567-000model building
RefinementMethod to determine structure: SAD / Resolution: 2.002→34.191 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 31.58
RfactorNum. reflection% reflection
Rfree0.247 1818 10.01 %
Rwork0.2138 --
obs0.2171 18162 91.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→34.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 0 152 1998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031874
X-RAY DIFFRACTIONf_angle_d0.5812524
X-RAY DIFFRACTIONf_dihedral_angle_d10.7031142
X-RAY DIFFRACTIONf_chiral_restr0.04294
X-RAY DIFFRACTIONf_plane_restr0.003322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0025-2.05660.41311160.37041098X-RAY DIFFRACTION80
2.0566-2.11710.43151160.38071019X-RAY DIFFRACTION73
2.1171-2.18550.32691440.28061288X-RAY DIFFRACTION94
2.1855-2.26360.35541130.3191025X-RAY DIFFRACTION74
2.2636-2.35420.34461390.26691214X-RAY DIFFRACTION88
2.3542-2.46130.30041470.24221324X-RAY DIFFRACTION96
2.4613-2.5910.26711470.24111317X-RAY DIFFRACTION96
2.591-2.75330.28931510.24941334X-RAY DIFFRACTION95
2.7533-2.96570.30471500.23331360X-RAY DIFFRACTION98
2.9657-3.2640.25491500.23261347X-RAY DIFFRACTION98
3.264-3.73580.24581500.20661340X-RAY DIFFRACTION97
3.7358-4.70470.17151500.16131363X-RAY DIFFRACTION98
4.7047-34.19620.18811450.1671315X-RAY DIFFRACTION96

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