[English] 日本語
Yorodumi
- PDB-2hh7: Crystal Structure of Cu(I) bound CsoR from Mycobacterium tuberculosis. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hh7
TitleCrystal Structure of Cu(I) bound CsoR from Mycobacterium tuberculosis.
ComponentsHypothetical protein CsoR
KeywordsUNKNOWN FUNCTION / 4-helix bundle
Function / homology
Function and homology information


copper ion sensor activity / response to silver ion / DNA-binding transcription repressor activity / response to copper ion / protein-DNA complex / transcription cis-regulatory region binding / copper ion binding / negative regulation of DNA-templated transcription / DNA binding / plasma membrane / cytoplasm
Similarity search - Function
Metal-sensitive repressor, helix protomer / Metal-sensitive transcriptional repressor / Metal-sensitive repressor, helix protomer superfamily / Metal-sensitive transcriptional repressor / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (I) ION / Copper-sensing transcriptional repressor CsoR / Copper-sensing transcriptional repressor CsoR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsSacchettini, J.C. / Ramesh, A.
CitationJournal: Nat.Chem.Biol. / Year: 2007
Title: CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator.
Authors: Liu, T. / Ramesh, A. / Ma, Z. / Ward, S.K. / Zhang, L. / George, G.N. / Talaat, A.M. / Sacchettini, J.C. / Giedroc, D.P.
History
DepositionJun 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein CsoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8812
Polymers12,8181
Non-polymers641
Water36020
1
A: Hypothetical protein CsoR
hetero molecules

A: Hypothetical protein CsoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7624
Polymers25,6352
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area4130 Å2
ΔGint-60 kcal/mol
Surface area9100 Å2
MethodPISA
2
A: Hypothetical protein CsoR
hetero molecules

A: Hypothetical protein CsoR
hetero molecules

A: Hypothetical protein CsoR
hetero molecules

A: Hypothetical protein CsoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5258
Polymers51,2714
Non-polymers2544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area10750 Å2
ΔGint-146 kcal/mol
Surface area15710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.059, 91.059, 46.779
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsThe second part of the biological assembly is generated by the symmetry operation : x, x-y-1, -z-1/3

-
Components

#1: Protein Hypothetical protein CsoR


Mass: 12817.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P71543, UniProt: P9WP49*PLUS
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% Peg4000,0.1Msodium citrate tribasic dihydrate, 0.2M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97927
SYNCHROTRONALS 8.3.120.97962, 0.97974, 0.95373
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 27, 2005
ADSC QUANTUM 3152CCDOct 28, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.979621
30.979741
40.953731
ReflectionResolution: 2.55→50 Å / Num. all: 4011 / Num. obs: 3987 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4.24
Reflection shellHighest resolution: 2.55 Å / % possible all: 99.2

-
Processing

Software
NameClassification
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.55→20 Å / σ(F): 4.24 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 184 random
Rwork0.231 --
all-3989 -
obs-3952 -
Refinement stepCycle: LAST / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 0 1 20 679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.267
X-RAY DIFFRACTIONf_bond_d0.011
LS refinement shellHighest resolution: 2.55 Å
RfactorNum. reflection% reflection
Rfree0.279 184 -
Rwork0.231 --
obs-3989 99.4 %

+
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