[English] 日本語
Yorodumi
- PDB-7mq1: C9A Streptococcus pneumoniae CstR in the reduced state, space group C2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mq1
TitleC9A Streptococcus pneumoniae CstR in the reduced state, space group C2
ComponentsCopper-sensing transcriptional repressor csoR
KeywordsTRANSCRIPTION / transcriptional regulator / persulfide sensor / CsoR family / CstR family
Function / homologyMetal-sensitive transcriptional repressor / Metal-sensitive repressor, helix protomer superfamily / Metal-sensitive transcriptional repressor / negative regulation of DNA-templated transcription / DNA binding / metal ion binding / TRIETHYLENE GLYCOL / Copper-sensing transcriptional repressor csoR
Function and homology information
Biological speciesStreptococcus pneumoniae D39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsFakhoury, J.N. / Gonzalez-Gutierrez, G. / Giedroc, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118157-02 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Functional asymmetry and chemical reactivity of CsoR family persulfide sensors.
Authors: Fakhoury, J.N. / Zhang, Y. / Edmonds, K.A. / Bringas, M. / Luebke, J.L. / Gonzalez-Gutierrez, G. / Capdevila, D.A. / Giedroc, D.P.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Copper-sensing transcriptional repressor csoR
B: Copper-sensing transcriptional repressor csoR
C: Copper-sensing transcriptional repressor csoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,93412
Polymers29,2153
Non-polymers7209
Water2,090116
1
A: Copper-sensing transcriptional repressor csoR
B: Copper-sensing transcriptional repressor csoR
C: Copper-sensing transcriptional repressor csoR
hetero molecules

A: Copper-sensing transcriptional repressor csoR
B: Copper-sensing transcriptional repressor csoR
C: Copper-sensing transcriptional repressor csoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,86924
Polymers58,4296
Non-polymers1,44018
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area18380 Å2
ΔGint-163 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.302, 54.869, 57.514
Angle α, β, γ (deg.)90.000, 115.733, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-226-

HOH

DetailsSAXS DATA AND ANALYTICAL GEL FILTRATION SHOW THAT THE BIOLOGICAL ASSEMBLY OF THIS PROTEIN IS TETRAMERIC. THE PARTICULAR ASSEMBLY OBSERVED IN THIS PDB ENTRY (A DIMER OF TRIMERS) AUTHORS THINK IS A CRYSTALLOGRAPHIC ARTIFACT.

-
Components

#1: Protein Copper-sensing transcriptional repressor csoR / Metal-sensing transcriptional repressor


Mass: 9738.191 Da / Num. of mol.: 3 / Mutation: C9A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae D39 (bacteria)
Gene: csoR, ERS019420_01408, GM542_04805, SAMEA2335968_01957
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B7LQC0
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MES 0.1 M pH 5.5, (NH4)2SO4 0.25 M, PEG 4000 15-18%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.02→43.04 Å / Num. obs: 17243 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 36.7 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Rsym value: 0.047 / Net I/σ(I): 10.8
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1273 / CC1/2: 0.633 / Rpim(I) all: 0.497 / Rrim(I) all: 0.91 / Rsym value: 0.759 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.02→43.04 Å / SU ML: 0.259 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9857
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2576 897 5.2 %
Rwork0.2048 16339 -
obs0.2075 17236 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.05 Å2
Refinement stepCycle: LAST / Resolution: 2.02→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 41 116 2082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771970
X-RAY DIFFRACTIONf_angle_d0.97812635
X-RAY DIFFRACTIONf_chiral_restr0.0525316
X-RAY DIFFRACTIONf_plane_restr0.0054339
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.150.30991230.25412750X-RAY DIFFRACTION99.83
2.15-2.310.27341540.22842689X-RAY DIFFRACTION99.72
2.31-2.540.30121600.21922713X-RAY DIFFRACTION99.93
2.55-2.910.27511660.21492692X-RAY DIFFRACTION99.79
2.91-3.670.26541370.20622735X-RAY DIFFRACTION99.03
3.67-43.040.2281570.18682760X-RAY DIFFRACTION98.75
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)
14.95121181321-0.3659889204390.8129490618055.92949496802-2.553303388718.396950978090.0260418957360.229266931748-0.00586654627945-0.490423957451-0.165283262443-0.5974667742690.05568985389431.61093443790.08739778924890.360749215534-0.01477856064130.1099225026870.626307430929-0.1740059506820.54453430356334.29881961234.41848638589-34.7699833868
20.612401527192-0.8605612052170.1395617425870.836121046715-2.07999224113.910643682180.1580223598060.0081231248549-0.134142147771-0.06282433578640.0141916371721-0.05523004286810.8716610025680.565900883388-0.2790480713540.323490202438-0.03422044318220.03047712994890.343309757667-0.04559047536750.4528033200326.4842471686-0.146276003754-23.2003988425
36.224156392890.3402968984772.44338837076.21995973333.351804656846.36711923619-0.09884813377130.1520347583340.010896474676-0.3479266334180.3520313265930.0348908734511-0.7354746972950.385550169294-0.0933284716150.311055810681-0.05700778862350.05094772151130.3103110618530.008348753753180.32082633490218.43970004596.20722974996-4.49594350225
47.08398631710.9973628115243.252958016144.401562991320.2288199386714.04484438618-0.431813493918-0.5438402615120.7788719285560.006658211667680.122795994937-0.125509770287-2.354428798270.09943690397760.02783744888960.677319186674-0.1761507300450.118323122690.486802592513-0.03401013066820.62651474324730.243714762612.5714727974-30.46095286
55.347855032381.798103486875.815816677154.553835794132.607170257156.6273003397-0.395799105276-0.1296542907650.303411376496-0.1776934513970.09537780056660.253592854571-1.12989217135-0.3776674491830.157314048150.2592945769860.0243789798860.118500251730.2690808935950.01529388712340.33440996511119.07889354025.08390236051-35.6192120122
66.817765979890.710983674731.329075958589.169285963062.926514724533.822696521280.2550536996670.61072008381-1.16327723916-0.277594296304-0.0815104000162-0.3653675153041.905230420281.09392485996-0.3112164488360.4438468655450.080569740719-0.008353744462080.363967158736-0.06154633988820.53637686534413.9624323529-9.13601428435-49.9563741411
72.943927083351.6081843371-0.6896184340512.930068426211.160775161841.496451766280.975605863685-0.127667437934-1.229203412680.0152682052466-0.371930558797-0.3552415092282.517397178570.980997631698-0.6204614967131.213225338630.233661380534-0.2003136849470.528622431287-0.06317018731290.83621283681817.9966360373-28.1101802092-25.1724842439
85.22704328215-3.696545827553.067925868344.88714716189-4.028942750488.40593008788-0.1790431758870.4662231375520.341414772094-0.0494238963978-0.220570451688-0.1003674445950.04309242020631.409070425750.2829640918520.2040680617730.00590022843517-0.02264081307390.181747486889-0.005975612205880.35731234065713.6501181392-16.4627282954-33.3677640917
99.228922941550.4816678351011.070060043236.256752650633.083890247184.439386691570.132050094852-0.7061158348090.13744391990.021606244863-0.1943820096790.4349664697350.589542424871-0.6198663132150.0150784875370.415674033764-0.0124540267103-0.01402723950260.274999878380.01445312619150.464036705932-1.56737704809-8.33051364656-43.9601118289
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 29 )AA3 - 291 - 27
22chain 'A' and (resid 30 through 61 )AA30 - 6128 - 59
33chain 'A' and (resid 62 through 83 )AA62 - 8360 - 81
44chain 'B' and (resid 1 through 29 )BB1 - 291 - 29
55chain 'B' and (resid 30 through 61 )BB30 - 6130 - 62
66chain 'B' and (resid 62 through 83 )BB62 - 8363 - 84
77chain 'C' and (resid 3 through 29 )CC3 - 291 - 27
88chain 'C' and (resid 30 through 61 )CC30 - 6128 - 59
99chain 'C' and (resid 62 through 84 )CC62 - 8460 - 82

+
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