[English] 日本語
Yorodumi
- PDB-6aoa: Monomeric crystal structure of the E497/C566D double mutant of th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aoa
TitleMonomeric crystal structure of the E497/C566D double mutant of the guanylyl cyclase domain of the RhoGC fusion protein from the aquatic fungus Blastocladiella emersonii
ComponentsBacterio-rhodopsin/guanylyl cyclase 1 fusion protein
KeywordsLYASE / GC / RhoGC / enzyme / nucleotide cyclase / class III nucleotidyl cyclase
Function / homology
Function and homology information


receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase activity / adenylate cyclase activity / intracellular signal transduction / metal ion binding / plasma membrane
Similarity search - Function
Nucleotide cyclase, GGDEF domain / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Alpha-Beta Plaits ...Nucleotide cyclase, GGDEF domain / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacterio-rhodopsin/guanylyl cyclase 1 fusion protein
Similarity search - Component
Biological speciesBlastocladiella emersonii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsPrem Kumar, R. / Oprian, D.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007596 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY007965 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure and monomer/dimer equilibrium for the guanylyl cyclase domain of the optogenetics protein RhoGC.
Authors: Kumar, R.P. / Morehouse, B.R. / Fofana, J. / Trieu, M.M. / Zhou, D.H. / Lorenz, M.O. / Oprian, D.D.
History
DepositionAug 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Feb 14, 2018Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_target_identifier
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacterio-rhodopsin/guanylyl cyclase 1 fusion protein


Theoretical massNumber of molelcules
Total (without water)21,5151
Polymers21,5151
Non-polymers00
Water5,765320
1
A: Bacterio-rhodopsin/guanylyl cyclase 1 fusion protein

A: Bacterio-rhodopsin/guanylyl cyclase 1 fusion protein


Theoretical massNumber of molelcules
Total (without water)43,0292
Polymers43,0292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area1090 Å2
ΔGint-11 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.350, 65.400, 88.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Bacterio-rhodopsin/guanylyl cyclase 1 fusion protein


Mass: 21514.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastocladiella emersonii (fungus) / Gene: gc1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A060H1D7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% PEG20000, 10 mM potassium hydrogen tartrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2016 / Details: Mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 40049 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 13.47 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.7
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.9 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AO9

6ao9


Resolution: 1.4→17.883 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 1965 4.92 %
Rwork0.1899 --
obs0.1908 39937 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→17.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 0 320 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051421
X-RAY DIFFRACTIONf_angle_d0.811935
X-RAY DIFFRACTIONf_dihedral_angle_d14.389508
X-RAY DIFFRACTIONf_chiral_restr0.072226
X-RAY DIFFRACTIONf_plane_restr0.004241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4350.28641400.25882689X-RAY DIFFRACTION100
1.435-1.47380.25931350.25182677X-RAY DIFFRACTION100
1.4738-1.51710.25411200.24112668X-RAY DIFFRACTION100
1.5171-1.56610.27221220.23262708X-RAY DIFFRACTION100
1.5661-1.6220.27421330.2282691X-RAY DIFFRACTION100
1.622-1.68690.23441410.22192680X-RAY DIFFRACTION100
1.6869-1.76360.26451690.21852659X-RAY DIFFRACTION100
1.7636-1.85650.23481400.21652695X-RAY DIFFRACTION100
1.8565-1.97270.23261460.20662695X-RAY DIFFRACTION100
1.9727-2.12480.19431490.18582726X-RAY DIFFRACTION100
2.1248-2.33820.21711390.18042723X-RAY DIFFRACTION100
2.3382-2.67560.20151440.18352748X-RAY DIFFRACTION100
2.6756-3.36720.18951440.16342783X-RAY DIFFRACTION100
3.3672-17.88450.16451430.16622830X-RAY DIFFRACTION97

+
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