[English] 日本語
Yorodumi
- PDB-7e1h: crystal structure of RD-BEF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e1h
Titlecrystal structure of RD-BEF
ComponentsDNA-binding response regulator
KeywordsSIGNALING PROTEIN / Response regulator / receiver domain / phosphorylation
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / DNA-binding response regulator
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 Å
AuthorsHong, S. / Zhang, X. / Zhang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32025020, 31971120 China
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2023
Title: Structural basis of phosphorylation-induced activation of the response regulator VbrR.
Authors: Hong, S. / Guo, J. / Zhang, X. / Zhou, X. / Zhang, P. / Yu, F.
History
DepositionFeb 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding response regulator
B: DNA-binding response regulator
C: DNA-binding response regulator
D: DNA-binding response regulator
E: DNA-binding response regulator
F: DNA-binding response regulator
G: DNA-binding response regulator
H: DNA-binding response regulator
I: DNA-binding response regulator
J: DNA-binding response regulator
K: DNA-binding response regulator
L: DNA-binding response regulator
M: DNA-binding response regulator
N: DNA-binding response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,75720
Polymers183,48614
Non-polymers2716
Water53,5052970
1
A: DNA-binding response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1963
Polymers13,1061
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-5 kcal/mol
Surface area6150 Å2
MethodPISA
2
B: DNA-binding response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1963
Polymers13,1061
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-6 kcal/mol
Surface area5950 Å2
MethodPISA
3
C: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-6 kcal/mol
Surface area6110 Å2
MethodPISA
4
D: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6150 Å2
MethodPISA
5
E: DNA-binding response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1963
Polymers13,1061
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6130 Å2
MethodPISA
6
F: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6090 Å2
MethodPISA
7
G: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6170 Å2
MethodPISA
8
H: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5930 Å2
MethodPISA
9
I: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6260 Å2
MethodPISA
10
J: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6150 Å2
MethodPISA
11
K: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6180 Å2
MethodPISA
12
L: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6220 Å2
MethodPISA
13
M: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6280 Å2
MethodPISA
14
N: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.858, 130.858, 271.355
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
DNA-binding response regulator


Mass: 13106.112 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: C1S91_03975 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R9VV79
#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2970 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 66.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M CH3COONa 3H2O pH 4.5, and 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 2.8→30 Å / Num. obs: 99444 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.083 / Rrim(I) all: 0.193 / Χ2: 0.81 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.95.10.90463770.6250.4420.8180.826100
2.9-3.025.40.73863840.7440.3490.8180.824100
3.02-3.155.30.54963670.8440.260.6090.8100
3.15-3.325.20.38763890.9070.1860.430.805100
3.32-3.534.90.27264220.930.1350.3050.84399.9
3.53-3.85.40.20763700.9570.0970.2290.847100
3.8-4.185.30.14764110.9720.0690.1630.867100
4.18-4.7850.09863810.9850.0480.110.82999.9
4.78-6.025.40.09664130.9890.0450.1060.75100
6.02-305.10.06564680.9970.0310.0720.70999.7

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KFC

4kfc


Resolution: 2.805→29.467 Å / Cross valid method: THROUGHOUT / σ(F): 768.18 / Phase error: 27.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.253 1933 4.01 %
Rwork0.226 95981 -
obs0.2273 99444 78.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.38 Å2 / Biso mean: 38.0373 Å2 / Biso min: 0.56 Å2
Refinement stepCycle: final / Resolution: 2.805→29.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12665 0 15 2970 15650
Biso mean--23.9 40 -
Num. residues----1611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8082-2.85660.3109670.3109181128
2.8566-2.90850.3439900.3167216734
2.9085-2.96440.305910.2979277844
2.9644-3.02480.28891170.286328652
3.0248-3.09050.29961170.2653370059
3.0905-3.16230.25431410.2526394762
3.1623-3.24120.28321450.2437419166
3.2412-3.32870.27421670.2362443970
3.3287-3.42650.26431700.2302474574
3.4265-3.53690.22791780.2162508580
3.5369-3.6630.24622080.2154570190
3.663-3.80930.27771980.2052598894
3.8093-3.98220.25332130.2056604196
3.9822-4.19140.23222120.1981611396
4.1914-4.4530.20992250.1948602396
4.453-4.79510.23672150.191605195
4.7951-5.27450.21382110.2047610696
5.2745-6.03070.26832070.2371608796
6.0307-7.57130.28682180.2679599494
7.5713-27.38430.26711990.2722572890

+
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://pdbjlvh1.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