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- PDB-4iah: Crystal Structure of BAY 60-2770 bound C139A H-NOX domain with S-... -

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Basic information

Entry
Database: PDB / ID: 4iah
TitleCrystal Structure of BAY 60-2770 bound C139A H-NOX domain with S-nitrosylated conserved C122
ComponentsAlr2278 protein
KeywordsLYASE / H-NOX domain / soluble guanylyl cyclase / BAY 60-2770 / S-nitrosylation / conserved C122 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKumar, V. / van den Akker, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,2276
Polymers40,7762
Non-polymers1,4514
Water63135
1
A: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1133
Polymers20,3881
Non-polymers7262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1133
Polymers20,3881
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)63,3409
Polymers61,1633
Non-polymers2,1776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area3640 Å2
ΔGint-18 kcal/mol
Surface area25190 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)63,3409
Polymers61,1633
Non-polymers2,1776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area3740 Å2
ΔGint-20 kcal/mol
Surface area24820 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)126,68118
Polymers122,3276
Non-polymers4,35412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10130 Å2
ΔGint-53 kcal/mol
Surface area47270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.573, 122.573, 122.573
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: 20387.799 Da / Num. of mol.: 2 / Fragment: HNOX domain, UNP residues 1-182 / 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: PC 7120 / Gene: alr2278 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta 2(DE3) pLysS / 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.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.76 Å3/Da / Density % sol: 67.32 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 2, 2011 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.543
11-K, -H, -L20.457
ReflectionResolution: 2.8→86.7 Å / Num. all: 14582 / Num. obs: 14472 / % possible obs: 99.25 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.069 / Net I/σ(I): 20.7
Reflection shellResolution: 2.8→2.93 Å / % possible all: 99.1

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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 2O0C

2o0c


Resolution: 2.8→86.69 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.799 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 2.3 / ESU R: 0.109 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21763 807 5.3 %RANDOM
Rwork0.1628 ---
all0.1657 14582 --
obs0.165 14472 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.702 Å2
Refinement stepCycle: LAST / Resolution: 2.8→86.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 104 35 3005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0213042
X-RAY DIFFRACTIONr_bond_other_d00.022012
X-RAY DIFFRACTIONr_angle_refined_deg0.8891.9914112
X-RAY DIFFRACTIONr_angle_other_deg0.60134902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.1225362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.6824.789142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.39915491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8441510
X-RAY DIFFRACTIONr_chiral_restr0.0620.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023392
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
X-RAY DIFFRACTIONr_mcbond_it0.1731.51798
X-RAY DIFFRACTIONr_mcbond_other0.0141.5746
X-RAY DIFFRACTIONr_mcangle_it0.32422870
X-RAY DIFFRACTIONr_scbond_it0.28631244
X-RAY DIFFRACTIONr_scangle_it0.5124.51242
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 57 -
Rwork0.193 1028 -
obs--97.22 %

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