[English] 日本語
Yorodumi
- PDB-4za6: Structure of the R. erythropolis transcriptional repressor QsdR f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4za6
TitleStructure of the R. erythropolis transcriptional repressor QsdR from TetR family
ComponentsTetR family transcriptional regulator
KeywordsSIGNALING PROTEIN / Quorum-sensing / NAHL degradation / qsdA transcriptional regulator / Rhodococcus erythropolis R138
Function / homologyQsdR, TetR regulatory C-terminal domain / Tetracyclin repressor-like, C-terminal domain / Homeobox-like domain superfamily / metal ion binding / ACETATE ION / TetR family transcriptional regulator
Function and homology information
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsEl Sahili, A. / Morera, S.
CitationJournal: Plos One / Year: 2015
Title: Natural Guided Genome Engineering Reveals Transcriptional Regulators Controlling Quorum-Sensing Signal Degradation.
Authors: El Sahili, A. / Kwasiborski, A. / Mothe, N. / Velours, C. / Legrand, P. / Morera, S. / Faure, D.
History
DepositionApr 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2May 1, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,50812
Polymers42,6012
Non-polymers90710
Water5,711317
1
A: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8727
Polymers21,3011
Non-polymers5726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6365
Polymers21,3011
Non-polymers3354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.630, 91.630, 145.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

21B-344-

HOH

-
Components

#1: Protein TetR family transcriptional regulator / QsdR


Mass: 21300.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: QV65_28910 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C2W9F0
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% 2-Methyl-2,4-pentanediol, 0.2 M CaCl2, 0.1 M Na Acetate pH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 42157 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 34.16 Å2 / Rsym value: 0.086 / Net I/σ(I): 12.44
Reflection shellResolution: 1.97→2.09 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.86 / Rsym value: 0.902 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phasing from S-SAD model

Resolution: 1.97→45.81 Å / Cor.coef. Fo:Fc: 0.9376 / Cor.coef. Fo:Fc free: 0.9319 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 2107 5 %RANDOM
Rwork0.206 ---
obs0.2071 42146 99.9 %-
Displacement parametersBiso mean: 40.21 Å2
Baniso -1Baniso -2Baniso -3
1--4.5943 Å20 Å20 Å2
2---4.5943 Å20 Å2
3---9.1885 Å2
Refine analyzeLuzzati coordinate error obs: 0.266 Å
Refinement stepCycle: 1 / Resolution: 1.97→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 58 317 3277
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092988HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034044HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1076SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes430HARMONIC5
X-RAY DIFFRACTIONt_it2988HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion16.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
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_contact3676SEMIHARMONIC4
LS refinement shellResolution: 1.97→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2652 155 5.01 %
Rwork0.2182 2937 -
all0.2205 3092 -
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)
11.10980.01750.65530.48640.04551.2550.09690.0895-0.1561-0.0111-0.03740.04930.19250.0441-0.0595-0.19960.0038-0.0259-0.1545-0.0002-0.1834-9.7469-8.63570.6073
20.67490.00890.05021.2820.4561.2807-0.00980.0354-0.11810.17760.0714-0.17540.08060.184-0.0616-0.1597-0.0021-0.0404-0.1421-0.0373-0.1584-37.0975-9.633120.0355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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