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- PDB-2oha: Myoglobin cavity mutant F138W -

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Basic information

Entry
Database: PDB / ID: 2oha
TitleMyoglobin cavity mutant F138W
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / MYOGLOBIN / LIGAND ENTRY AND EXIT PATHWAYS / OXYGEN STORAGE-TRANSPORT COMPLEX
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-like / Globin / Globin / Globin domain profile. / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPhillips Jr., G.N. / Soman, J. / Olson, J.S.
CitationJournal: Iubmb Life / Year: 2007
Title: Ligand pathways in myoglobin: A review of trp cavity mutations.
Authors: Olson, J.S. / Soman, J. / Phillips, G.N.
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)18,2134
Polymers17,4041
Non-polymers8093
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.180, 90.180, 45.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Myoglobin


Mass: 17404.199 Da / Num. of mol.: 1
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-resistent TB1 / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 59.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PROTEIN SOLUTION (20 MG/ML PROTEIN, 0.020 M TRIS-HCL, pH 9.0), MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (2.8 M AMMONIUM SULPHATE, 0.050 M TRIS-HCL, pH 9.0), cryo-protected with 20% ...Details: PROTEIN SOLUTION (20 MG/ML PROTEIN, 0.020 M TRIS-HCL, pH 9.0), MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (2.8 M AMMONIUM SULPHATE, 0.050 M TRIS-HCL, pH 9.0), cryo-protected with 20% SUCROSE, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2005
RadiationMonochromator: MULTI-LAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→29.59 Å / Num. all: 26942 / Num. obs: 26942 / % possible obs: 85.4 % / Observed criterion σ(F): 0 / Redundancy: 2.89 % / Biso Wilson estimate: 15 Å2 / Limit h max: 50 / Limit h min: 0 / Limit k max: 49 / Limit k min: 0 / Limit l max: 28 / Limit l min: 0 / Observed criterion F max: 514736.13 / Observed criterion F min: 0.54 / Rmerge(I) obs: 0.048 / Χ2: 0.99 / Net I/σ(I): 16 / Scaling rejects: 589
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.54-1.591.080.1442.66496030.6419.4
1.59-1.651.30.1653.3221117000.9254.1
1.65-1.731.670.1524.2431525750.8582
1.73-1.822.630.1396806830440.9297.5
1.82-1.943.210.1078.61015031480.9799.8
1.94-2.083.250.07811.61026931410.96100
2.08-2.293.30.05816.41047531550.98100
2.29-2.633.340.04919.61059231560.96100
2.63-3.313.380.04223.51075531700.96100
3.31-29.593.320.03731.41099632501.1799.7

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Processing

Software
NameVersionClassificationNB
d*TREK9.1SSIdata processing
CNS1.1refinement
PDB_EXTRACT2data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.59 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2 942 4.8 %random
Rwork0.166 ---
all-19691 --
obs-19642 99.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 58.4444 Å2 / ksol: 0.438614 e/Å3
Displacement parametersBiso max: 58.09 Å2 / Biso mean: 16.19 Å2 / Biso min: 5.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å21.76 Å20 Å2
2--0.83 Å20 Å2
3----1.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.06 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 53 239 1519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_torsion_deg17.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.97
X-RAY DIFFRACTIONx_mcbond_it1.281.5
X-RAY DIFFRACTIONx_mcangle_it1.772
X-RAY DIFFRACTIONx_scbond_it2.432
X-RAY DIFFRACTIONx_scangle_it3.52.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.2391496.10.20722850.022452243499.3
1.88-1.980.1711014.20.16623180.0172428241999.6
1.98-2.110.2151265.20.16723050.0192438243199.7
2.11-2.270.2041134.60.15823340.0192455244799.7
2.27-2.50.1951014.10.15223430.0192447244499.9
2.5-2.860.1991054.20.16623660.0192474247199.8
2.86-3.60.2221184.80.17223450.022466246399.9
3.6-29.590.1761295.10.16324040.0162548253399.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2heme-ferric.paramheme-feprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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