[English] 日本語
Yorodumi
- PDB-4rpo: PcpR inducer binding domain (Complex with 2,4,6-trichlorophenol) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rpo
TitlePcpR inducer binding domain (Complex with 2,4,6-trichlorophenol)
ComponentsPCP degradation transcriptional activation protein
KeywordsTRANSCRIPTION / LysR family transcriptional regulator / inducer binding domain
Function / homology
Function and homology information


catabolic process / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
: / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...: / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,4,6-trichlorophenol / PCP degradation transcriptional activation protein
Similarity search - Component
Biological speciesSphingobium chlorophenolicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHayes, R.P. / Moural, T.W. / Lewis, K.M. / Onofrei, D. / Xun, L. / Kang, C.
CitationJournal: Int J Mol Sci / Year: 2014
Title: Structures of the Inducer-Binding Domain of Pentachlorophenol-Degrading Gene Regulator PcpR from Sphingobium chlorophenolicum.
Authors: Hayes, R.P. / Moural, T.W. / Lewis, K.M. / Onofrei, D. / Xun, L. / Kang, C.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PCP degradation transcriptional activation protein
B: PCP degradation transcriptional activation protein
C: PCP degradation transcriptional activation protein
D: PCP degradation transcriptional activation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,47211
Polymers101,4204
Non-polymers1,0527
Water10,178565
1
A: PCP degradation transcriptional activation protein
B: PCP degradation transcriptional activation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2896
Polymers50,7102
Non-polymers5794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-10 kcal/mol
Surface area17380 Å2
MethodPISA
2
C: PCP degradation transcriptional activation protein
D: PCP degradation transcriptional activation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1835
Polymers50,7102
Non-polymers4733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-9 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.751, 169.751, 110.115
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
PCP degradation transcriptional activation protein


Mass: 25354.889 Da / Num. of mol.: 4 / Fragment: residues 85-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium chlorophenolicum (bacteria)
Gene: pcpR / Production host: Escherichia coli (E. coli) / References: UniProt: P52679
#2: Chemical
ChemComp-T6C / 2,4,6-trichlorophenol


Mass: 197.446 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H3Cl3O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium tartrate dibasic dihydrate, 20% w/v PEG 4,000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2014
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 86296 / % possible obs: 100 % / Observed criterion σ(F): -3 / Rmerge(I) obs: 0.08
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.95-1.981100
1.98-2.021100
2.02-2.061100
2.06-2.11100
2.1-2.151100
2.15-2.21100

-
Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RNS

4rns


Resolution: 1.95→49.606 Å / SU ML: 0.19 / σ(F): 1.98 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 1952 2.26 %
Rwork0.1775 --
obs0.1782 86287 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→49.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6995 0 56 565 7616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097240
X-RAY DIFFRACTIONf_angle_d1.1439852
X-RAY DIFFRACTIONf_dihedral_angle_d13.9172661
X-RAY DIFFRACTIONf_chiral_restr0.0541090
X-RAY DIFFRACTIONf_plane_restr0.0061289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99840.25861330.23516059X-RAY DIFFRACTION100
1.9984-2.05240.2551440.22726015X-RAY DIFFRACTION100
2.0524-2.11280.24371420.22116000X-RAY DIFFRACTION100
2.1128-2.1810.25791510.21156040X-RAY DIFFRACTION100
2.181-2.2590.23271200.20956027X-RAY DIFFRACTION100
2.259-2.34940.25531440.20125990X-RAY DIFFRACTION100
2.3494-2.45640.22791460.19986046X-RAY DIFFRACTION100
2.4564-2.58590.27851410.19985972X-RAY DIFFRACTION100
2.5859-2.74790.27471520.20646038X-RAY DIFFRACTION100
2.7479-2.960.20151370.19466018X-RAY DIFFRACTION100
2.96-3.25780.23121440.18526044X-RAY DIFFRACTION100
3.2578-3.72910.20971180.16776030X-RAY DIFFRACTION100
3.7291-4.69770.1541440.14416029X-RAY DIFFRACTION100
4.6977-49.62240.17071360.14716027X-RAY DIFFRACTION100

+
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