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- PDB-3hep: Ferric Horse Heart Myoglobin; H64V Mutant, Nitrite Modified -

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Basic information

Entry
Database: PDB / ID: 3hep
TitleFerric Horse Heart Myoglobin; H64V Mutant, Nitrite Modified
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / ferric myoglobin / horse heart / H64V mutant / nitrite adduct / Heme / Iron / Metal-binding / Muscle protein / Transport
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYi, J. / Thomas, L.M. / Richter-Addo, G.B.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: The distal pocket histidine residue in horse heart myoglobin directs the o-binding mode of nitrite to the heme iron.
Authors: Yi, J. / Heinecke, J. / Tan, H. / Ford, P.C. / Richter-Addo, G.B.
History
DepositionMay 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6534
Polymers16,9441
Non-polymers7083
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.389, 119.390, 57.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-172-

HOH

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Components

#1: Protein Myoglobin


Mass: 16944.498 Da / Num. of mol.: 1 / Mutation: H64V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Plasmid: pGYM / Production host: Escherichia coli (E. coli) / References: UniProt: P68082
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: ammonium phosphate, EDTA, crystal soaking with sodium nitrite, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 6, 2009 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→23.15 Å / Num. obs: 15767 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.99 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.07 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1544 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HC9

3hc9


Resolution: 1.95→23.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.576 / SU ML: 0.104 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.149 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25007 787 5 %RANDOM
Rwork0.19782 ---
all0.218 15767 --
obs0.20045 14980 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.571 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.46 Å20 Å2
3----1.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 1.95→23.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 49 122 1367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221276
X-RAY DIFFRACTIONr_angle_refined_deg2.0952.0621726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7535152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01925.19252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95115229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.889152
X-RAY DIFFRACTIONr_chiral_restr0.1430.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02943
X-RAY DIFFRACTIONr_nbd_refined0.2210.2612
X-RAY DIFFRACTIONr_nbtor_refined0.30.2863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.214
X-RAY DIFFRACTIONr_mcbond_it1.4811.5790
X-RAY DIFFRACTIONr_mcangle_it2.23921199
X-RAY DIFFRACTIONr_scbond_it3.7573567
X-RAY DIFFRACTIONr_scangle_it5.3874.5525
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 34 -
Rwork0.263 981 -
obs-981 100 %

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