[English] 日本語
Yorodumi
- PDB-8rv3: Structure of the domain IV of the replication factor RctB from Vi... -

+
Open data


ID or keywords:

Loading...

-
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: To Be Published
Title: Structure of the domain IV of the replication factor RctB from Vibrio cholerae
Authors: Garcia-Pino, A. / Talavera Perez, A.
History
DepositionJan 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more