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- PDB-7lgk: Crystal structure of soluble guanylate cyclase activator runcacig... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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