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- PDB-3ogb: Sperm whale myoglobin mutant H64W deoxy-form -

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Basic information

Entry
Database: PDB / ID: 3ogb
TitleSperm whale myoglobin mutant H64W deoxy-form
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Myoglobin / ligand migration pathways / oxygen storage
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsBirukou, I. / Soman, J. / Olson, J.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Blocking the gate to ligand entry in human hemoglobin.
Authors: Birukou, I. / Soman, J. / Olson, J.S.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 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_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: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,89411
Polymers17,4131
Non-polymers1,48110
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.830, 47.130, 88.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin


Mass: 17413.225 Da / Num. of mol.: 1 / Mutation: H65W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): PHAGE RESISTANT TB1 / References: UniProt: P02185
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 9
Details: Solution of MB (carbonmonoxy-form) (20mg/ml protein in 0.02M TRIS-HCl pH 9.0) mixed with mother liquor (3.2M ammonium sulphate, 0.05M TRIS-HCl, pH 9.0) for final concentrations of 2.5M ...Details: Solution of MB (carbonmonoxy-form) (20mg/ml protein in 0.02M TRIS-HCl pH 9.0) mixed with mother liquor (3.2M ammonium sulphate, 0.05M TRIS-HCl, pH 9.0) for final concentrations of 2.5M ammonium sulphate to obtain crystals of MBCO. MBCO crystals were oxidyzed by excess of potassium ferricyanide, washed in mother liquor and reduced under anaerobic conditions with sodium dithionite, SMALL TUBES, temperature 293K

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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: Jul 23, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→23.57 Å / Num. obs: 21466 / % possible obs: 96.6 % / Redundancy: 3.65 % / Rmerge(I) obs: 0.043 / Χ2: 0.95 / Net I/σ(I): 15.5 / Scaling rejects: 695
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured all% possible all
1.6-1.663.660.2634.1198891
1.66-1.723.630.2584.7189491.4
1.72-1.83.550.2165.5205293.4
1.8-1.93.530.1716.5207894.5
1.9-2.023.480.1278.7213597.5
2.02-2.173.480.09811.1219699
2.17-2.393.710.07914219599
2.39-2.733.790.05918.62234100
2.73-3.443.840.0427.2225699.2
3.44-23.573.750.02745.9234898.4

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.3Ldata processing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3NML

3nml


Resolution: 1.6→23.565 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 1055 4.92 %RANDOM
Rwork0.1798 ---
obs0.1809 21429 96.38 %-
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.122 Å2 / ksol: 0.435 e/Å3
Displacement parametersBiso max: 73.49 Å2 / Biso mean: 20.7404 Å2 / Biso min: 9.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.9137 Å2-0 Å2-0 Å2
2---0.4889 Å2-0 Å2
3----0.4248 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 88 249 1566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061475
X-RAY DIFFRACTIONf_angle_d1.0882021
X-RAY DIFFRACTIONf_chiral_restr0.07198
X-RAY DIFFRACTIONf_plane_restr0.003252
X-RAY DIFFRACTIONf_dihedral_angle_d14.507542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.67280.54691080.46012375248391
1.6728-1.7610.37391210.32942377249892
1.761-1.87130.30561290.23812422255194
1.8713-2.01570.21681100.17312567267797
2.0157-2.21840.18251220.16992610273299
2.2184-2.5390.19711610.162926112772100
2.539-3.19770.19311610.161826482809100
3.1977-23.56750.15571430.15352764290799

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