[English] 日本語
Yorodumi
- PDB-6hc1: Bdellovibrio bacteriovorus DgcB FHA in complex with phosphorylate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hc1
TitleBdellovibrio bacteriovorus DgcB FHA in complex with phosphorylated N-terminal peptide
Components
  • DgcB N-terminus, phosphorylated
  • GGDEF domain protein
KeywordsSIGNALING PROTEIN / GGDEF / FHA / c-di-GMP / diguanylate cyclase
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / nucleotide binding / plasma membrane
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Nucleotide cyclase / SMAD/FHA domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
GGDEF domain protein
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å
AuthorsLovering, A.L. / Meek, R.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for activation of a diguanylate cyclase required for bacterial predation in Bdellovibrio.
Authors: Meek, R.W. / Cadby, I.T. / Moynihan, P.J. / Lovering, A.L.
History
DepositionAug 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GGDEF domain protein
B: GGDEF domain protein
C: DgcB N-terminus, phosphorylated


Theoretical massNumber of molelcules
Total (without water)23,1763
Polymers23,1763
Non-polymers00
Water3,459192
1
A: GGDEF domain protein


Theoretical massNumber of molelcules
Total (without water)10,9671
Polymers10,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GGDEF domain protein


Theoretical massNumber of molelcules
Total (without water)10,9671
Polymers10,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DgcB N-terminus, phosphorylated


Theoretical massNumber of molelcules
Total (without water)1,2421
Polymers1,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.750, 68.750, 191.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A32 - 132
2010B32 - 132

-
Components

#1: Protein GGDEF domain protein


Mass: 10966.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd0742 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6MPU8
#2: Protein/peptide DgcB N-terminus, phosphorylated


Mass: 1242.272 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd0742 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6MPU8*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M sodium hepes pH 7, 20% PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.49→59.54 Å / Num. obs: 44707 / % possible obs: 100 % / Redundancy: 33.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.022 / Rrim(I) all: 0.132 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.49-1.5324.22.7967831732380.5450.5782.8561.2100
6.66-56.8428.50.065183406440.9990.0120.06645.199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.31data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→59.54 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.279 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0576 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.056
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 2175 4.9 %RANDOM
Rwork0.142 ---
obs0.1437 42427 99.97 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.77 Å2 / Biso mean: 26.901 Å2 / Biso min: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.49→59.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 0 192 1811
Biso mean---40.29 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191686
X-RAY DIFFRACTIONr_bond_other_d0.0010.021668
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9942297
X-RAY DIFFRACTIONr_angle_other_deg0.98833894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6385225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22526.1457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88615300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.303154
X-RAY DIFFRACTIONr_chiral_restr0.1220.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
X-RAY DIFFRACTIONr_rigid_bond_restr2.66633352
X-RAY DIFFRACTIONr_sphericity_free29.1835145
X-RAY DIFFRACTIONr_sphericity_bonded13.56153369
Refine LS restraints NCS

Ens-ID: 1 / Number: 5574 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.49→1.529 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 176 -
Rwork0.276 3058 -
all-3234 -
obs--100 %

+
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