[English] 日本語
Yorodumi
- PDB-7lgk: Crystal structure of soluble guanylate cyclase activator runcacig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lgk
TitleCrystal structure of soluble guanylate cyclase activator runcaciguat (BAY 1101042) bound to nostoc H-NOX domain
ComponentsH-NOX domain protein
KeywordsSIGNALING PROTEIN/ACTIVATOR / Soluble guanylyl cyclase / H-NOX / signal transduction / activator / SIGNALING PROTEIN / SIGNALING PROTEIN-SIGNALING PROTEIN ACTIVATOR complex / SIGNALING PROTEIN-ACTIVATOR complex
Function / homologyHeme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / heme binding / metal ion binding / Runcaciguat / Alr2278 protein
Function and homology information
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
Authorsvan den Akker, F. / Kumar, V. / Schaefer, M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of the Soluble Guanylate Cyclase Activator Runcaciguat (BAY 1101042).
Authors: Hahn, M.G. / Lampe, T. / El Sheikh, S. / Griebenow, N. / Woltering, E. / Schlemmer, K.H. / Dietz, L. / Gerisch, M. / Wunder, F. / Becker-Pelster, E.M. / Mondritzki, T. / Tinel, H. / Knorr, A. ...Authors: Hahn, M.G. / Lampe, T. / El Sheikh, S. / Griebenow, N. / Woltering, E. / Schlemmer, K.H. / Dietz, L. / Gerisch, M. / Wunder, F. / Becker-Pelster, E.M. / Mondritzki, T. / Tinel, H. / Knorr, A. / Kern, A. / Lang, D. / Hueser, J. / Schomber, T. / Benardeau, A. / Eitner, F. / Truebel, H. / Mittendorf, J. / Kumar, V. / van den Akker, F. / Schaefer, M. / Geiss, V. / Sandner, P. / Stasch, J.P.
History
DepositionJan 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: H-NOX domain protein
B: H-NOX domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,31812
Polymers40,7182
Non-polymers1,60010
Water1,62190
1
A: H-NOX domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1596
Polymers20,3591
Non-polymers8005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: H-NOX domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1596
Polymers20,3591
Non-polymers8005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.990, 123.990, 123.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

-
Components

#1: Protein H-NOX domain protein


Mass: 20358.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr2278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YUQ7
#2: Chemical ChemComp-XZ7 / Runcaciguat / (3S)-3-(4-chloro-3-{[(2S,3R)-2-(4-chlorophenyl)-4,4,4-trifluoro-3-methylbutanoyl]amino}phenyl)-3-cyclopropylpropanoic acid


Mass: 488.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22Cl2F3NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 12% glycerol, and 1.5 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→43.84 Å / Num. obs: 32542 / % possible obs: 100 % / Redundancy: 20 % / Rrim(I) all: 0.14 / Net I/σ(I): 18.98
Reflection shellResolution: 2.2→2.33 Å / Num. unique obs: 3000 / Rrim(I) all: 1.97

-
Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IAM

4iam


Resolution: 2.2→43.84 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.812 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 1628 5 %RANDOM
Rwork0.1617 ---
obs0.1639 30913 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 137.05 Å2 / Biso mean: 58.827 Å2 / Biso min: 36.63 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.2→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 102 90 3056
Biso mean--62.46 57.38 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193063
X-RAY DIFFRACTIONr_bond_other_d0.0020.022813
X-RAY DIFFRACTIONr_angle_refined_deg2.4371.9824146
X-RAY DIFFRACTIONr_angle_other_deg1.2123.0026453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8985370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66524.69145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00115500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8381511
X-RAY DIFFRACTIONr_chiral_restr0.1510.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023433
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02686
LS refinement shellResolution: 2.2→2.256 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.198 120 -
Rwork0.182 2271 -
obs--99.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43130.0592-0.34140.9311-0.38410.6571-0.0149-0.00230.06180.03970.0284-0.0096-0.07160.0055-0.01350.02680.00530.00350.01420.02240.0501-7.42228.7789-20.5585
20.5382-0.16170.03771.0391-0.45020.7821-0.01480.06830.0575-0.15990.0162-0.02370.0821-0.0046-0.00130.0364-0.00140.00510.03120.020.0148-20.8364-9.5649-38.7157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1001
2X-RAY DIFFRACTION2B1 - 1001

+
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