[English] 日本語
Yorodumi
- PDB-5go3: Crystal structure of a di-nucleotide cyclase Vibrio mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5go3
TitleCrystal structure of a di-nucleotide cyclase Vibrio mutant
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / di-nucleotide cyclase Vibrio / mutant
Function / homology
Function and homology information


3',3'-cyclic GMP-AMP synthase activity / diguanylate cyclase activity / negative regulation of chemotaxis / cyclic nucleotide biosynthetic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding
Similarity search - Function
: / : / : / Cyclic GMP-AMP synthase DncV-like, nucleotidyltransferase domain / Cyclic GMP-AMP synthase, C-terminal domain
Similarity search - Domain/homology
Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMing, Z.H. / Wang, W. / Xie, Y.C. / Chen, Y.C. / Yan, L.M. / Lou, Z.Y.
Funding support China, 7items
OrganizationGrant numberCountry
National Basic Research Program of China2013CB911103 China
National Basic Research Program of China2012CB518904 China
National Natural Science Foundation of China81322023 China
National Natural Science Foundation of China31170678 China
National Natural Science Foundation of China31170158 China
National Natural Science Foundation of China31370733 China
National Natural Science Foundation of China31000332 China
Citation
Journal: To Be Published
Title: Crystal structure of a di-nucleotide cyclase Vibrio mutant
Authors: Ming, Z.H. / Wang, W. / Xie, Y.C. / Chen, Y.C. / Yan, L.M. / Lou, Z.Y.
#1: Journal: Cell Res. / Year: 2014
Title: Crystal structure of the novel di-nucleotide cyclase from Vibrio cholerae (DncV) responsible for synthesizing a hybrid cyclic GMP-AMP
Authors: Ming, Z. / Wang, W. / Xie, Y. / Ding, P. / Chen, Y. / Jin, D. / Sun, Y. / Xia, B. / Yan, L. / Lou, Z.
History
DepositionJul 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
B: Cyclic GMP-AMP synthase


Theoretical massNumber of molelcules
Total (without water)101,3392
Polymers101,3392
Non-polymers00
Water5,008278
1
A: Cyclic GMP-AMP synthase


Theoretical massNumber of molelcules
Total (without water)50,6691
Polymers50,6691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclic GMP-AMP synthase


Theoretical massNumber of molelcules
Total (without water)50,6691
Polymers50,6691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.745, 46.272, 121.791
Angle α, β, γ (deg.)90.00, 99.82, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cyclic GMP-AMP synthase / / c-GMP-AMP synthase / 3'3'-cGAMP synthase / Cyclic AMP-GMP synthase / c-AMP-GMP synthase / ...c-GMP-AMP synthase / 3'3'-cGAMP synthase / Cyclic AMP-GMP synthase / c-AMP-GMP synthase / Dinucleotide cyclase DncV


Mass: 50669.496 Da / Num. of mol.: 2 / Mutation: D133N, D131N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: dncV, VC_0179 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KVG7, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 25% PEG 3350, 100 mM HEPES (pH 7.5), 200 mM magnesium chloride hexahydrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 50934 / % possible obs: 98 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.6
Reflection shellResolution: 2.05→2.09 Å

-
Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→43.174 Å / SU ML: 0.84 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2921 2116 5.05 %
Rwork0.2282 --
obs0.2314 41882 99.19 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.005 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0319 Å20 Å2-2.9782 Å2
2---3.5032 Å2-0 Å2
3---3.4713 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5826 0 0 278 6104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085974
X-RAY DIFFRACTIONf_angle_d1.2028050
X-RAY DIFFRACTIONf_dihedral_angle_d15.9072286
X-RAY DIFFRACTIONf_chiral_restr0.082886
X-RAY DIFFRACTIONf_plane_restr0.0051034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25120.36011250.27592570X-RAY DIFFRACTION98
2.2512-2.30750.36291340.25922590X-RAY DIFFRACTION98
2.3075-2.36990.31691540.24852575X-RAY DIFFRACTION98
2.3699-2.43960.36521360.25032640X-RAY DIFFRACTION98
2.4396-2.51830.32611300.24452616X-RAY DIFFRACTION99
2.5183-2.60830.30561440.23322605X-RAY DIFFRACTION99
2.6083-2.71270.3091300.24572692X-RAY DIFFRACTION100
2.7127-2.83620.36621600.26882634X-RAY DIFFRACTION100
2.8362-2.98570.30311370.26962644X-RAY DIFFRACTION100
2.9857-3.17270.34961520.24842641X-RAY DIFFRACTION100
3.1727-3.41750.29731400.23562688X-RAY DIFFRACTION100
3.4175-3.76130.27561550.21382682X-RAY DIFFRACTION100
3.7613-4.30510.24331350.19232685X-RAY DIFFRACTION100
4.3051-5.42230.21111390.17772715X-RAY DIFFRACTION99
5.4223-43.18210.27651450.23122789X-RAY DIFFRACTION99

+
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