[English] 日本語
Yorodumi
- PDB-3qps: Crystal structures of CmeR-bile acid complexes from Campylobacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qps
TitleCrystal structures of CmeR-bile acid complexes from Campylobacter jejuni
ComponentsCmeR
KeywordsTRANSCRIPTION / Alpha-helical / Helix-Turn-Helix / DNA-binding / Transcription regulation / Transcription repressor / drug binding
Function / homology
Function and homology information


Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.351 Å
AuthorsLei, H.T. / Routh, M.D. / Shen, Z. / Su, C.C. / Zhang, Q. / Yu, E.W.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structures of CmeR-bile acid complexes from Campylobacter jejuni.
Authors: Lei, H.T. / Shen, Z. / Surana, P. / Routh, M.D. / Su, C.C. / Zhang, Q. / Yu, E.W.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Oct 15, 2014Group: Structure summary
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: CmeR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5002
Polymers25,0921
Non-polymers4091
Water90150
1
A: CmeR
hetero molecules

A: CmeR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0014
Polymers50,1842
Non-polymers8172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5720 Å2
ΔGint-29 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.955, 37.370, 57.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein CmeR / Transcriptional repressor


Mass: 25091.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cmeR, CmeR / Production host: Escherichia coli (E. coli) / References: UniProt: Q7B8P6
#2: Chemical ChemComp-CHD / CHOLIC ACID / Cholic acid


Mass: 408.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 30 % PEG 3350, 0.1 M Tris, pH 8.0, 0.16M MgCl2, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 16126 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.063 / Χ2: 1.13 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.433.20.42116180.709199.2
2.43-2.533.20.29216280.69198.8
2.53-2.653.20.23416240.762199.2
2.65-2.793.20.17715950.766198.7
2.79-2.963.20.12616300.931199.1
2.96-3.193.10.08916221.179199.3
3.19-3.513.10.07116321.518199.2
3.51-4.023.10.05216161.839198.4
4.02-5.063.10.03615831.642196.6
5.06-403.30.02715781.321195.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QCO

2qco


Resolution: 2.351→31.381 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8014 / SU ML: 0.34 / σ(F): 0.17 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 397 4.79 %
Rwork0.2007 --
obs0.2038 8288 92.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.491 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 93.48 Å2 / Biso mean: 43.2424 Å2 / Biso min: 15.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.4438 Å20 Å20 Å2
2--1.7024 Å2-0 Å2
3---0.7414 Å2
Refinement stepCycle: LAST / Resolution: 2.351→31.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 29 50 1728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091748
X-RAY DIFFRACTIONf_angle_d1.3772366
X-RAY DIFFRACTIONf_chiral_restr0.086269
X-RAY DIFFRACTIONf_plane_restr0.004287
X-RAY DIFFRACTIONf_dihedral_angle_d22.357666

+
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