[English] 日本語
Yorodumi
- PDB-2cpg: TRANSCRIPTIONAL REPRESSOR COPG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cpg
TitleTRANSCRIPTIONAL REPRESSOR COPG
ComponentsTRANSCRIPTIONAL REPRESSOR COPG
KeywordsGENE REGULATION / TRANSCRIPTIONAL REPRESSOR / DNA-BINDING PROTEIN / PLASMID
Function / homology
Function and homology information


plasmid maintenance / protein-DNA complex / sequence-specific DNA binding / regulation of DNA-templated transcription
Similarity search - Function
Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.6 Å
AuthorsGomis-Rueth, F.X. / Sola, M. / Acebo, P. / Parraga, A. / Guasch, A. / Eritja, R. / Gonzalez, A. / Espinosa, M. / del Solar, G. / Coll, M.
Citation
Journal: EMBO J. / Year: 1998
Title: The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator.
Authors: Gomis-Ruth, F.X. / Sola, M. / Acebo, P. / Parraga, A. / Guasch, A. / Eritja, R. / Gonzalez, A. / Espinosa, M. / del Solar, G. / Coll, M.
#1: Journal: FEBS Lett. / Year: 1998
Title: Overexpression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of the Pmv158-Encoded Plasmid Transcriptional Repressor Protein Copg
Authors: Gomis-Rueth, F.X. / Sola, M. / Perez-Luque, R. / Acebo, P. / Alda, M.T. / Gonzalez, A. / Espinosa, M. / del Solar, G. / Coll, M.
History
DepositionNov 15, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG
C: TRANSCRIPTIONAL REPRESSOR COPG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5636
Polymers15,4563
Non-polymers1063
Water3,495194
1
A: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3754
Polymers10,3042
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-47 kcal/mol
Surface area5600 Å2
MethodPISA
2
C: TRANSCRIPTIONAL REPRESSOR COPG
hetero molecules

C: TRANSCRIPTIONAL REPRESSOR COPG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3754
Polymers10,3042
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Unit cell
Length a, b, c (Å)67.190, 102.490, 40.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-47-

HOH

21A-48-

HOH

31C-47-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.787024, 0.562355, -0.253674), (0.567706, -0.821116, -0.058975), (-0.241461, -0.097597, -0.96549)-14.06171, 66.94317, 52.00411
2given(0.27167, 0.939943, 0.206648), (-0.936007, 0.307992, -0.170386), (-0.223799, -0.147135, 0.963465)72.26735, 4.70603, 11.38816
DetailsTHE SMALLEST FUNCTIONAL UNIT IS A HOMODIMER. IN THE PRESENT STRUCTURE, ONE A PROTOMER AND ONE B PROTOMER ESTABLISH SUCH AN INTERACTION. THE THIRD MOLECULE PRESENT IN THE ASYMMETRIC UNIT, MOLECULE C, ESTABLISHES ANOTHER HOMODIMER STRUCTURE WITH A SYMMETRY EQUIVALENT C MOLECULE.

-
Components

#1: Protein/peptide TRANSCRIPTIONAL REPRESSOR COPG / REPA PROTEIN


Mass: 5152.106 Da / Num. of mol.: 3 / Fragment: DNA-BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: PLS1 / Cellular location: plasmid pMV158 / Plasmid: PMV158 / Production host: Escherichia coli (E. coli) / References: UniProt: P13920
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.7 / Details: 72% MPD, 0.1 M HEPES PH 6.7, 3% BENZAMIDINE
Components of the solutions
IDNameCrystal-IDSol-ID
1BENZAMIDINE11
2MPD11
3MPD12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop / Details: Gomis-Rueth, F.X., (1998) FEBS Lett., 425, 161.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113-16 mg/mlprotein1drop
210 mMTris-HCl1drop
3275 mM1reservoirNaCl
40.5 mM1reservoirNaN3

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X311
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
2IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→19.61 Å / Num. obs: 91693 / % possible obs: 98.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 3 / % possible all: 96.4
Reflection
*PLUS
Num. obs: 18358 / Num. measured all: 91693 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 96.4 %

-
Processing

Software
NameVersionClassification
CCP4model building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.6→8 Å / Num. parameters: 4861 / Num. restraintsaints: 4018 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 -14 %EVERY 7TH REFLECTION
obs0.2017 16782 --
all-16782 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1016 0 3 194 1213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / σ(F): 0 / % reflection Rfree: 14 % / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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