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- PDB-2oh9: Myoglobin cavity mutant V68W -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2oh9
TitleMyoglobin cavity mutant V68W
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. / Li, T. / Brucker, E.A. / 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)18,2614
Polymers17,4521
Non-polymers8093
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.490, 91.490, 45.890
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: 17452.240 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.: 111 / 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: 3.18 Å3/Da / Density % sol: 61.27 %
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, pH9.0), vapor diffusion, hanging drop, ...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, pH9.0), vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→45.89 Å / Num. all: 24077 / Num. obs: 24077 / Observed criterion σ(F): 0 / Biso Wilson estimate: 21.7 Å2 / Limit h max: 46 / Limit h min: 0 / Limit k max: 46 / Limit k min: 0 / Limit l max: 26 / Limit l min: 0 / Observed criterion F max: 535784.92 / Observed criterion F min: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.89 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2017 9.9 %random
Rwork0.174 ---
all-20501 --
obs-20329 99.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 63.8528 Å2 / ksol: 0.37372 e/Å3
Displacement parametersBiso max: 62.69 Å2 / Biso mean: 23.66 Å2 / Biso min: 11.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å23.23 Å20 Å2
2--2.03 Å20 Å2
3----4.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 53 111 1396
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_torsion_deg17.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.81
X-RAY DIFFRACTIONx_mcbond_it1.261.5
X-RAY DIFFRACTIONx_mcangle_it1.862
X-RAY DIFFRACTIONx_scbond_it2.512
X-RAY DIFFRACTIONx_scangle_it3.872.5
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 (%)
1.8-1.880.26626010.40.24622390.0172521249999.1
1.88-1.980.23525510.10.2122630.0152541251899.1
1.98-2.110.242469.70.19122940.0152551254099.6
2.11-2.270.18525810.10.16722930.0122567255199.4
2.27-2.50.22329.10.16323230.0132559255599.8
2.5-2.860.2122459.60.17523050.0142555255099.8
2.86-3.60.202256100.17723110.0132571256799.8
3.6-45.890.18626510.40.15722840.0112651254996.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2heme-ferric.paramheme-ferric.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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