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- PDB-4iae: Crystal structure of BAY 60-2770 bound to nostoc H-NOX domain -

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Basic information

Entry
Database: PDB / ID: 4iae
TitleCrystal structure of BAY 60-2770 bound to nostoc H-NOX domain
ComponentsAlr2278 protein
KeywordsLYASE / activation / HNOX domain / Heme binding / NO binding
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-1DX / MALONATE ION / Alr2278 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKumar, V. / van den Akker, F. / Martin, F.
CitationJournal: Biochemistry / Year: 2013
Title: Insights into BAY 60-2770 Activation and S-Nitrosylation-Dependent Desensitization of Soluble Guanylyl Cyclase via Crystal Structures of Homologous Nostoc H-NOX Domain Complexes.
Authors: Kumar, V. / Martin, F. / Hahn, M.G. / Schaefer, M. / Stamler, J.S. / Stasch, J.P. / van den Akker, F.
History
DepositionDec 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,9177
Polymers42,3632
Non-polymers1,5535
Water2,792155
1
A: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0094
Polymers21,1821
Non-polymers8283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9073
Polymers21,1821
Non-polymers7262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Alr2278 protein
hetero molecules

A: Alr2278 protein
hetero molecules

A: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,02812
Polymers63,5453
Non-polymers2,4839
Water543
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 area3830 Å2
ΔGint-24 kcal/mol
Surface area23530 Å2
MethodPISA
4
B: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7229
Polymers63,5453
Non-polymers2,1776
Water543
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 area5030 Å2
ΔGint-10 kcal/mol
Surface area24460 Å2
MethodPISA
5
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)131,75021
Polymers127,0896
Non-polymers4,66015
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 area13360 Å2
ΔGint-54 kcal/mol
Surface area43480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.913, 121.913, 121.913
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: 21181.578 Da / Num. of mol.: 2 / Fragment: HNOX domain / Mutation: C139A
Source method: isolated from a genetically manipulated source
Details: similar to soluble guanylyl cyclase beta subunit / 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, guanylate cyclase
#2: Chemical ChemComp-1DX / 4-({(4-carboxybutyl)[2-(5-fluoro-2-{[4'-(trifluoromethyl)biphenyl-4-yl]methoxy}phenyl)ethyl]amino}methyl)benzoic acid


Mass: 623.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H33F4NO5
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 3.56 Å3/Da / Density % sol: 65.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 18, 2010 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.05→86.2 Å / Num. all: 36315 / Num. obs: 36251 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 34.4 Å2 / Rsym value: 0.048 / Net I/σ(I): 19.2
Reflection shellResolution: 2.05→2.12 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O09

2o09


Resolution: 2.05→86.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.359 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 1.72 / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19526 1850 4.9 %RANDOM
Rwork0.16341 ---
all0.165 36315 --
obs0.16494 36251 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.373 Å2
Refinement stepCycle: LAST / Resolution: 2.05→86.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 111 155 3130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213058
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9924136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2525366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.41324.789142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89615497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9751510
X-RAY DIFFRACTIONr_chiral_restr0.1210.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212358
X-RAY DIFFRACTIONr_mcbond_it2.2251.51804
X-RAY DIFFRACTIONr_mcangle_it3.1322883
X-RAY DIFFRACTIONr_scbond_it5.0431254
X-RAY DIFFRACTIONr_scangle_it6.7614.51251
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 120 -
Rwork0.162 2668 -
obs--98.66 %

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