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- PDB-2ohb: Myoglobin cavity mutant I107W -

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Basic information

Entry
Database: PDB / ID: 2ohb
TitleMyoglobin cavity mutant I107W
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / MYOGLOBIN / LIGAND ENTRY AND EXIT PATHWAYS / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPhillips Jr., G.N. / Schweers, R.L. / 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 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 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 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)18,2474
Polymers17,4381
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)91.560, 91.560, 46.000
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: 17438.215 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 / Sulfate


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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / 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: 3.19 Å3/Da / Density % sol: 61.45 %
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), 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, pH 9.0), 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 / Date: Jun 10, 1998
RadiationMonochromator: FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→79.29 Å / Num. all: 18358 / Num. obs: 18360 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 18 Å2 / Limit h max: 43 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 25 / Limit l min: 0 / Observed criterion F max: 154847.73 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.075 / Χ2: 1.231 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.850.3554071.25823.8
1.85-1.910.2819171.15953
1.91-1.980.30214681.11586.9
1.98-2.060.2616901.11597.5
2.06-2.150.19317111.10399.8
2.15-2.270.15917141.193100
2.27-2.410.12817471.206100
2.41-2.60.10717101.295100
2.6-2.860.09417441.309100
2.86-3.270.07617181.32100
3.27-4.120.05717581.32799.9
4.12-1000.03717761.18398.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→79.29 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1738 9.9 %random
Rwork0.177 ---
all-20583 --
obs-17614 85.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 63.2324 Å2 / ksol: 0.370949 e/Å3
Displacement parametersBiso max: 73.64 Å2 / Biso mean: 22.34 Å2 / Biso min: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å21.54 Å20 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.17 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→79.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1231 0 53 111 1395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg17.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.77
X-RAY DIFFRACTIONx_mcbond_it1.411.5
X-RAY DIFFRACTIONx_mcangle_it2.142
X-RAY DIFFRACTIONx_scbond_it2.772
X-RAY DIFFRACTIONx_scangle_it4.322.5
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 (%)
1.8-1.880.296638.90.2846450.037254070827.9
1.88-1.980.22314680.24216760.0182535182271.9
1.98-2.110.22823910.10.19621350.0152566237492.5
2.11-2.270.18225810.40.17222260.0112574248496.5
2.27-2.50.2052489.90.16822690.0132567251798.1
2.5-2.860.1927310.70.1722690.0122577254298.6
2.86-3.60.2072469.70.17422980.0132581254498.6
3.6-79.290.18726510.10.16623580.0112658262398.7
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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