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- PDB-4iam: Crystal Structure of the C139A mutant of nostoc H-NOX domain -

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Basic information

Entry
Database: PDB / ID: 4iam
TitleCrystal Structure of the C139A mutant of nostoc H-NOX domain
ComponentsAlr2278 protein
KeywordsLYASE / HNOX domain / soluble guanylyl cyclase / C139A mutant / nostoc / 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
PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / Alr2278 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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_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)42,1556
Polymers40,7182
Non-polymers1,4374
Water5,513306
1
A: Alr2278 protein
hetero molecules

A: Alr2278 protein
hetero molecules

A: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,46418
Polymers122,1536
Non-polymers4,31112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
crystal symmetry operation6_545z+1/2,-x-1/2,-y1
crystal symmetry operation9_555y,z,x1
Buried area11210 Å2
ΔGint-47 kcal/mol
Surface area46830 Å2
MethodPISA
2
A: Alr2278 protein
hetero molecules

A: Alr2278 protein
hetero molecules

A: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2329
Polymers61,0763
Non-polymers2,1566
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area3850 Å2
ΔGint-16 kcal/mol
Surface area25010 Å2
MethodPISA
3
B: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2329
Polymers61,0763
Non-polymers2,1566
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 area4020 Å2
ΔGint-21 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.626, 122.626, 122.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

21B-326-

HOH

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Components

#1: Protein Alr2278 protein


Mass: 20358.799 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 beta1 / 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 306 / 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: 3.77 Å3/Da / Density % sol: 67.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.9M 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: Feb 6, 2012 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: 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, L10.597
11K, H, -L20.403
ReflectionResolution: 1.99→86.7 Å / Num. all: 40235 / Num. obs: 39902 / % possible obs: 99.25 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 33.24 Å2 / Rsym value: 0.059 / Net I/σ(I): 22.6
Reflection shellResolution: 1.99→2.08 Å / % possible all: 97.9

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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: 1.99→86.7 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.198 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 2.9 / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15945 2085 5 %RANDOM
Rwork0.12565 ---
all0.1595 40235 --
obs0.12733 39902 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.238 Å2
Refinement stepCycle: LAST / Resolution: 1.99→86.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 100 306 3270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223062
X-RAY DIFFRACTIONr_angle_refined_deg1.7862.0444168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6855366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34724.789142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22515494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0111510
X-RAY DIFFRACTIONr_chiral_restr0.2240.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212368
X-RAY DIFFRACTIONr_mcbond_it1.5771.51810
X-RAY DIFFRACTIONr_mcangle_it2.63822894
X-RAY DIFFRACTIONr_scbond_it4.27331252
X-RAY DIFFRACTIONr_scangle_it6.3264.51274
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 135 -
Rwork0.184 2901 -
obs--97.9 %

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