[English] 日本語
Yorodumi
- PDB-6prk: X-ray Crystal Structure of Bacillus subtilis RicA in complex with RicF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6prk
TitleX-ray Crystal Structure of Bacillus subtilis RicA in complex with RicF
Components
  • RicA
  • RicF
KeywordsMETAL BINDING PROTEIN / RNA processing / biofilms / competence / sporulation
Function / homology
Function and homology information


establishment of competence for transformation / sporulation resulting in formation of a cellular spore / cytoplasm
Similarity search - Function
Biofilm formation YmcA / YheA/YmcA-like / Control of competence regulator ComK, YlbF/YmcA / YheA/YmcA-like domain superfamily / Control of competence regulator ComK, YlbF/YmcA / YheA-like fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein YmcA / Regulatory protein YlbF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKhaja, F.T. / Jeffrey, P.D. / Neiditch, M.B. / Dubnau, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM057720 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125452 United States
CitationJournal: Mbio / Year: 2019
Title: Structure-Function Studies of the Bacillus subtilis Ric Proteins Identify the Fe-S Cluster-Ligating Residues and Their Roles in Development and RNA Processing.
Authors: Adusei-Danso, F. / Khaja, F.T. / DeSantis, M. / Jeffrey, P.D. / Dubnau, E. / Demeler, B. / Neiditch, M.B. / Dubnau, D.
History
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RicF
B: RicA


Theoretical massNumber of molelcules
Total (without water)28,5802
Polymers28,5802
Non-polymers00
Water0
1
A: RicF
B: RicA

A: RicF
B: RicA


Theoretical massNumber of molelcules
Total (without water)57,1604
Polymers57,1604
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area8610 Å2
ΔGint-67 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.090, 86.090, 87.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

-
Components

#1: Protein RicF


Mass: 14399.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ylbF, BSU14990 / Production host: Escherichia coli (E. coli) / References: UniProt: O34412
#2: Protein RicA


Mass: 14180.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ymcA, BSU17020 / Production host: Escherichia coli (E. coli) / References: UniProt: O31779

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% (vol/vol) PEG500 MME, 8% (vol/vol) MPD, 100 mM sodium nitrate, 100 mM MOPS, Sodium HEPES pH 7.3

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 6195 / % possible obs: 99.9 % / Redundancy: 9.95 % / Biso Wilson estimate: 105.49 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.085 / Rsym value: 0.08 / Net I/σ(I): 17.24
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 312 / CC1/2: 0.81

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PRH

6prh


Resolution: 3.2→43.04 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.475
RfactorNum. reflection% reflectionSelection details
Rfree0.278 297 4.83 %RANDOM
Rwork0.205 ---
obs0.209 6149 100 %-
Displacement parametersBiso max: 232.24 Å2 / Biso mean: 144.79 Å2 / Biso min: 89.92 Å2
Baniso -1Baniso -2Baniso -3
1--5.2915 Å20 Å20 Å2
2---5.2915 Å20 Å2
3---10.583 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 3.2→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 0 0 1905
Num. residues----232
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d746SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes262HARMONIC5
X-RAY DIFFRACTIONt_it1923HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion256SEMIHARMONIC5
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_contact2350SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1923HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2581HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion23.2
LS refinement shellResolution: 3.2→3.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.399 85 4.92 %
Rwork0.325 1641 -
all0.328 1726 -
obs--99.83 %
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)
14.98780.7208-1.2632.41620.34495.44150.3901-0.13530.85150.1263-0.0905-0.1965-1.30130.4953-0.29960.31640.0335-0.0213-0.00190.1824-0.310529.887951.814719.4028
22.70760.5523-0.81635.43711.12191.39180.07750.0268-0.7326-0.2518-0.1644-0.51580.48141.34320.0869-0.06710.299-0.27770.28960.0826-0.263745.179124.762126.2893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A6 - 120
2X-RAY DIFFRACTION2{ B|* }B3 - 119

+
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