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- PDB-3l6j: Structure of cinaciguat (bay 58-2667) bound to nostoc H-NOX domain -

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Basic information

Entry
Database: PDB / ID: 3l6j
TitleStructure of cinaciguat (bay 58-2667) bound to nostoc H-NOX domain
ComponentsAlr2278 protein
KeywordsSIGNALING PROTEIN / GUANYLYL CYCLASE / BAY58-2667
Function / homology
Function and homology information


heme binding / metal ion binding
Similarity search - Function
H-NOX domain / H-NOX domain / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-Z90 / Alr2278 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMartin, F. / van den Akker, F.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of cinaciguat (BAY 58-2667) bound to Nostoc H-NOX domain reveals insights into heme-mimetic activation of the soluble guanylyl cyclase.
Authors: Martin, F. / Baskaran, P. / Ma, X. / Dunten, P.W. / Schaefer, M. / Stasch, J.P. / Beuve, A. / van den Akker, F.
History
DepositionDec 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alr2278 protein
B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5594
Polymers42,4272
Non-polymers1,1312
Water1,47782
1
A: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7792
Polymers21,2141
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7792
Polymers21,2141
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Alr2278 protein
B: Alr2278 protein
hetero molecules

A: Alr2278 protein
B: Alr2278 protein
hetero molecules

A: Alr2278 protein
B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,67612
Polymers127,2826
Non-polymers3,3946
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area11570 Å2
ΔGint-58 kcal/mol
Surface area47080 Å2
MethodPISA
4
A: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5594
Polymers42,4272
Non-polymers1,1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area1930 Å2
ΔGint-10 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.268, 123.268, 123.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Alr2278 protein


Mass: 21213.643 Da / Num. of mol.: 2 / Fragment: residues 1-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr2278 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YUQ7
#2: Chemical ChemComp-Z90 / 4-({(4-carboxybutyl)[2-(2-{[4-(2-phenylethyl)benzyl]oxy}phenyl)ethyl]amino}methyl)benzoic acid / 4-((4-carboxybutyl)(2-((4-phenethylbenzol)oxy) phenethyl) amino)methyl(benzoic) acid) / Cinaciguat


Mass: 565.699 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H39NO5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 3.68 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 1.8M sodium malonate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.493
11-H, -L, -K20.507
ReflectionResolution: 2.3→50 Å / Num. all: 27974 / Num. obs: 27835 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Redundancy: 6.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 25
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2742 / % possible all: 97

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Processing

Software
NameClassification
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O09

2o09


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.869 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19325 1410 5.1 %RANDOM
Rwork0.15041 ---
obs0.15256 26386 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 84 82 3032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9814082
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2585362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0624.789142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03415494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8231510
X-RAY DIFFRACTIONr_chiral_restr0.0660.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212326
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3891.51798
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9322872
X-RAY DIFFRACTIONr_scbond_it6.30731226
X-RAY DIFFRACTIONr_scangle_it9.0434.51210
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 96 -
Rwork0.446 1854 -
obs--95.03 %

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