[English] 日本語
Yorodumi
- PDB-6sir: Crystal structure of the guanylate cyclase domain of RhGC from Ca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sir
TitleCrystal structure of the guanylate cyclase domain of RhGC from Catenaria anguillulae in complex with GTP
ComponentsNucleotide cyclase
KeywordsLYASE / guanylate cyclase
Function / homology
Function and homology information


receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase activity / adenylate cyclase activity / intracellular signal transduction / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
: / Nucleotide cyclase, GGDEF domain / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Nucleotide cyclase
Similarity search - Component
Biological speciesCatenaria anguillulae PL171 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsButryn, A. / Orville, A.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust102593 United Kingdom
Wellcome Trust210734/Z/18/Z United Kingdom
Royal SocietyRSWF/R2/182017 United Kingdom
CitationJournal: Febs J. / Year: 2020
Title: Molecular basis for GTP recognition by light-activated guanylate cyclase RhGC.
Authors: Butryn, A. / Raza, H. / Rada, H. / Moraes, I. / Owens, R.J. / Orville, A.M.
History
DepositionAug 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleotide cyclase
B: Nucleotide cyclase
D: Nucleotide cyclase
C: Nucleotide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,69514
Polymers82,2584
Non-polymers2,43710
Water10,395577
1
A: Nucleotide cyclase
B: Nucleotide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3487
Polymers41,1292
Non-polymers1,2195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-42 kcal/mol
Surface area14990 Å2
MethodPISA
2
D: Nucleotide cyclase
C: Nucleotide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3487
Polymers41,1292
Non-polymers1,2195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-39 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.650, 95.170, 138.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
Nucleotide cyclase


Mass: 20564.471 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catenaria anguillulae PL171 (fungus) / Gene: BCR44DRAFT_1480233 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y2HEJ3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MIB pH 4.4, 22% PEG 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.7→40.52 Å / Num. obs: 85155 / % possible obs: 99 % / Redundancy: 13.2 % / Biso Wilson estimate: 24.74 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Net I/σ(I): 20.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4426 / CC1/2: 0.788 / Rpim(I) all: 0.36 / Rrim(I) all: 1.32 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
DIALS1.1data reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W01

2w01


Resolution: 1.7→36.95 Å / SU ML: 0.2165 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2692
RfactorNum. reflection% reflection
Rfree0.2094 4316 5.07 %
Rwork0.1816 --
obs0.1831 85085 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.92 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5633 0 144 577 6354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626094
X-RAY DIFFRACTIONf_angle_d0.81588322
X-RAY DIFFRACTIONf_chiral_restr0.0535955
X-RAY DIFFRACTIONf_plane_restr0.00441087
X-RAY DIFFRACTIONf_dihedral_angle_d9.48263636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.31431390.29162647X-RAY DIFFRACTION98
1.72-1.740.31171470.27442604X-RAY DIFFRACTION97.9
1.74-1.760.27761290.25352645X-RAY DIFFRACTION97.54
1.76-1.780.29911350.25782655X-RAY DIFFRACTION98.14
1.78-1.810.30061670.2482589X-RAY DIFFRACTION98.22
1.81-1.830.29521360.23192676X-RAY DIFFRACTION97.81
1.83-1.860.31611120.21892655X-RAY DIFFRACTION98.47
1.86-1.890.26441220.21452663X-RAY DIFFRACTION98.34
1.89-1.910.25011530.20672653X-RAY DIFFRACTION98.21
1.91-1.950.23871330.20652649X-RAY DIFFRACTION98.17
1.95-1.980.25731420.20012682X-RAY DIFFRACTION98.57
1.98-2.020.20861440.20222638X-RAY DIFFRACTION98.55
2.02-2.050.23691380.20122662X-RAY DIFFRACTION98.77
2.05-2.10.22371430.20022698X-RAY DIFFRACTION98.75
2.1-2.140.24441260.19482655X-RAY DIFFRACTION98.72
2.14-2.190.2261530.1932677X-RAY DIFFRACTION98.71
2.19-2.250.22181540.19132668X-RAY DIFFRACTION98.98
2.25-2.310.21881580.18762667X-RAY DIFFRACTION98.95
2.31-2.380.22771630.18592664X-RAY DIFFRACTION98.78
2.38-2.450.23281500.18892695X-RAY DIFFRACTION99.09
2.45-2.540.20551340.19022720X-RAY DIFFRACTION99.41
2.54-2.640.2121280.18612709X-RAY DIFFRACTION99.2
2.64-2.760.23481380.18342717X-RAY DIFFRACTION99.55
2.76-2.910.22161430.18542726X-RAY DIFFRACTION99.31
2.91-3.090.19011540.18262733X-RAY DIFFRACTION99.52
3.09-3.330.20221550.17782726X-RAY DIFFRACTION99.72
3.33-3.660.19931410.15862780X-RAY DIFFRACTION99.62
3.66-4.190.16731500.1522787X-RAY DIFFRACTION99.86
4.19-5.280.17041670.14492783X-RAY DIFFRACTION99.93
5.28-36.950.18351620.18052946X-RAY DIFFRACTION99.94

+
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