[English] 日本語
Yorodumi
- PDB-5v85: The crystal structure of the protein of DegV family COG1307 from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v85
TitleThe crystal structure of the protein of DegV family COG1307 from Ruminococcus gnavus ATCC 29149 (alternative refinement of PDB 3JR7 with Vaccenic acid)
ComponentsEDD domain protein, DegV family
KeywordsTRANSPORT PROTEIN / DEGV / GUT MICROBIOME / STRUCTURAL GENOMICS / PSI-2 / C18:1 / Vaccenic acid
Function / homology
Function and homology information


DegV, N-terminal domain, peripheral subdomain / Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Dihydroxyacetone kinase; domain 1 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / : / Rubrerythrin, domain 2 ...DegV, N-terminal domain, peripheral subdomain / Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Dihydroxyacetone kinase; domain 1 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / : / Rubrerythrin, domain 2 / Single Sheet / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / VACCENIC ACID / EDD domain protein, DegV family
Similarity search - Component
Biological speciesRuminococcus gnavus ATCC 29149 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.003 Å
AuthorsCuypers, M.G. / Ericson, M. / subramanian, C. / White, S.W. / Rock, C.O.
CitationJournal: to be published
Title: The crystal structure of the protein of DegV family COG1307 with unknown function from Ruminococcus gnavus ATCC 29149
Authors: Zhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength
Remark 0This entry reflects an alternative modeling of the original data in 3JR7, determined by R.ZHANG,C. ...This entry reflects an alternative modeling of the original data in 3JR7, determined by R.ZHANG,C.HATZOS,S.CLANCY,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG)
Remark 200SEE THE ORIGINAL DATA, ENTRY 3JR7
Remark 280SEE THE ORIGINAL DATA, ENTRY 3JR7

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EDD domain protein, DegV family
B: EDD domain protein, DegV family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,25910
Polymers67,2682
Non-polymers9918
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-34 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.899, 96.899, 159.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein EDD domain protein, DegV family


Mass: 33634.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus ATCC 29149 (bacteria)
Gene: RUMGNA_03254 / Plasmid: PMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A7B6P0
#2: Chemical ChemComp-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 289 K / Details: THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR7 / Method: vapor diffusion, sitting drop
Details: 0.2M SODIUM CHLORIDE, 0.1M PHOSPHATE-CITRATE, 10%PEG3000, PH 4.2

-
Data collection

DiffractionMean temperature: 100 K / Details: THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR7
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Details: THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR7 / Wavelength: 0.97915 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 4, 2008 / Details: THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR7
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→83.92 Å / Num. obs: 58785 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Details: THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR7 / Net I/σ(I): 17.85

-
Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.003→29.887 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.2
RfactorNum. reflection% reflection
Rfree0.1977 2970 5.05 %
Rwork0.1685 --
obs0.1699 58785 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.003→29.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 62 609 4958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034503
X-RAY DIFFRACTIONf_angle_d0.5336068
X-RAY DIFFRACTIONf_dihedral_angle_d6.4233771
X-RAY DIFFRACTIONf_chiral_restr0.044686
X-RAY DIFFRACTIONf_plane_restr0.003784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0028-2.03560.27821350.2282637X-RAY DIFFRACTION99
2.0356-2.07070.23721390.19612640X-RAY DIFFRACTION100
2.0707-2.10840.21071370.18542644X-RAY DIFFRACTION100
2.1084-2.14890.21071290.17562657X-RAY DIFFRACTION100
2.1489-2.19280.2241530.18312624X-RAY DIFFRACTION100
2.1928-2.24040.20841280.17852623X-RAY DIFFRACTION100
2.2404-2.29250.24011520.17852634X-RAY DIFFRACTION100
2.2925-2.34980.24071400.17892642X-RAY DIFFRACTION100
2.3498-2.41330.18891400.17582655X-RAY DIFFRACTION100
2.4133-2.48430.19261350.17252661X-RAY DIFFRACTION100
2.4843-2.56450.20971380.17582640X-RAY DIFFRACTION100
2.5645-2.65610.21181480.17752642X-RAY DIFFRACTION100
2.6561-2.76230.2261600.18122649X-RAY DIFFRACTION100
2.7623-2.8880.2261230.19052677X-RAY DIFFRACTION100
2.888-3.04010.21751420.17472661X-RAY DIFFRACTION100
3.0401-3.23030.19171670.18142642X-RAY DIFFRACTION99
3.2303-3.47940.20251580.15952633X-RAY DIFFRACTION99
3.4794-3.82890.19251360.14742681X-RAY DIFFRACTION99
3.8289-4.38150.15391410.13532671X-RAY DIFFRACTION99
4.3815-5.51450.15571420.14052704X-RAY DIFFRACTION98
5.5145-29.89030.18631270.18842798X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 22.3722 Å / Origin y: 41.8283 Å / Origin z: 40.4923 Å
111213212223313233
T0.1071 Å20.0001 Å2-0.0089 Å2-0.1365 Å2-0.0038 Å2--0.1569 Å2
L0.3545 °2-0.1156 °2-0.0071 °2-0.2636 °2-0.0763 °2--0.543 °2
S0.0304 Å °0.0349 Å °0.0067 Å °-0.0393 Å °-0.0046 Å °0.0215 Å °0.0074 Å °-0.0202 Å °0.0003 Å °
Refinement TLS groupSelection details: all

+
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