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- PDB-8rv3: Structure of the domain IV of the replication factor RctB from Vi... -

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Basic information

Entry
Database: PDB / ID: 8rv3
TitleStructure of the domain IV of the replication factor RctB from Vibrio cholerae
ComponentsRctB
KeywordsREPLICATION / replication initiation factor / RctB / Vibrio cholerae / DNA-protein interactions
Function / homologyReplication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / IODIDE ION / Uncharacterized protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.35 Å
AuthorsGarcia-Pino, A. / Talavera Perez, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)864311European Union
CitationJournal: Nat Commun / Year: 2025
Title: Dynamic transitions of initiator binding coordinate the replication of the two chromosomes in Vibrio cholerae.
Authors: Niault, T. / Talavera, A. / Le Cam, E. / Baconnais, S. / Skovgaard, O. / Fournes, F. / Wagner, L. / Tamman, H. / Thompson, A. / Echemendia-Blanco, D. / Guzzi, N. / Garcia-Pino, A. / Mazel, D. / Val, M.E.
History
DepositionJan 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RctB
B: RctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,58111
Polymers41,6822
Non-polymers8989
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-10 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.910, 94.760, 47.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-857-

HOH

21B-832-

HOH

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Components

#1: Protein RctB


Mass: 20841.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_A0002
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9KNG2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 200 mM NaI, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.35→53.55 Å / Num. obs: 11991 / % possible obs: 80.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 39.84 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.06 / Net I/σ(I): 13.1
Reflection shellResolution: 2.35→2.398 Å / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 521 / CC1/2: 0.934 / Rpim(I) all: 0.209

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (24-FEB-2021)refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.35→53.55 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.372 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.498 / SU Rfree Blow DPI: 0.286 / SU Rfree Cruickshank DPI: 0.273
RfactorNum. reflection% reflectionSelection details
Rfree0.267 580 4.84 %RANDOM
Rwork0.19 ---
obs0.1937 11991 93.8 %-
Displacement parametersBiso mean: 46.23 Å2
Baniso -1Baniso -2Baniso -3
1-5.1159 Å20 Å20 Å2
2---9.7611 Å20 Å2
3---4.6452 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.35→53.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 49 214 2180
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.021977HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.552667HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d702SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes324HARMONIC5
X-RAY DIFFRACTIONt_it1977HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.36
X-RAY DIFFRACTIONt_other_torsion17.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion278SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1770SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.38 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.3353 -7.73 %
Rwork0.2393 382 -
all0.2468 414 -
obs--94.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4359-5.0381-2.29735.91253.45170.91490.4403-0.1816-0.1733-0.25890.0964-0.066-0.94770.4297-0.5366-0.34-0.01270.00710.5445-0.0313-0.2571-12.99127.976716.8894
20.41450.37810.99080.23811.7894.5869-0.166-0.1016-0.048-0.0433-0.02630.1237-0.03480.05210.1923-0.21990.0094-0.00820.36950.0135-0.1892-24.018726.130319.8271
36.0568-0.1526-3.91830.00022.929710.88140.03020.30170.3135-0.30150.0786-0.1881-0.8519-0.1135-0.1088-0.16310.0076-0.00860.41540.0391-0.3025-24.212533.263913.4152
44.6973-5.8208-1.857113.79023.687200.3090.118-0.2692-0.8998-0.1171-0.5732-0.4931-0.564-0.1919-0.28090.02620.02880.5316-0.0199-0.2689-12.800716.18393.7761
56.54115.8208-5.82080.2337-3.15339.94990.1052-0.0808-0.2694-0.3777-0.71050.05690.9762-0.59210.6053-0.2693-0.0630.05490.4055-0.0842-0.2226-16.61676.443117.004
60-4.91961.58051.3407-4.00090-0.16450.09010.17170.4730.0929-0.01910.8764-0.04970.0717-0.1196-0.0864-0.00130.5452-0.0195-0.3114-13.924810.02824.6503
70-3.0662.83840-0.740810.86130.0396-0.8146-0.0307-0.39310.02-0.13540.5151-0.1372-0.0597-0.2424-0.0332-0.0550.4062-0.0222-0.1974-10.227615.685616.2366
812.35821.87525.82082.25951.586700.31930.5062-0.6903-0.31220.1162-0.64690.08570.1701-0.4356-0.24260.02420.04040.4309-0.037-0.1877-5.24878.53657.8556
94.24060.74252.22282.54424.848513.6404-0.0182-0.0495-0.51790.4606-0.30790.3640.41210.22740.3261-0.24020.0293-0.0010.3667-0.031-0.2427-5.70375.707316.8043
103.98883.57993.27911.8579-3.08110.29470.3903-0.034-0.3631-0.2952-0.0375-0.28970.3355-0.002-0.3528-0.24180.11780.0110.4316-0.021-0.1877-14.612720.340436.1861
111.67181.0722.09110.10970.16674.40730.0131-0.04670.0008-0.0356-0.00850.05940.09150.0742-0.0047-0.2770.01870.02570.428-0.0009-0.223-21.193226.283239.5566
123.9991-0.16480.13592.53842.1533.13280.12120.20760.2626-0.17350.0412-0.0177-0.00390.0768-0.1624-0.25230.01810.01770.39320.0322-0.2037-3.144737.779939.15
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|531 - A|543 }
2X-RAY DIFFRACTION2{ A|544 - A|570 }
3X-RAY DIFFRACTION3{ A|571 - A|587 }
4X-RAY DIFFRACTION4{ A|588 - A|599 }
5X-RAY DIFFRACTION5{ A|600 - A|613 }
6X-RAY DIFFRACTION6{ A|614 - A|620 }
7X-RAY DIFFRACTION7{ A|621 - A|630 }
8X-RAY DIFFRACTION8{ A|631 - A|639 }
9X-RAY DIFFRACTION9{ A|640 - A|658 }
10X-RAY DIFFRACTION10{ B|531 - B|543 }
11X-RAY DIFFRACTION11{ B|544 - B|599 }
12X-RAY DIFFRACTION12{ B|600 - B|657 }

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