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- PDB-4h07: Complex of G65T Myoglobin with Phenol in its Proximal Cavity -

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Basic information

Entry
Database: PDB / ID: 4h07
TitleComplex of G65T Myoglobin with Phenol in its Proximal Cavity
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / 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 / PHENOL / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.14 Å
AuthorsLebioda, L. / Lovelace, L.L. / Celeste, L.R. / Huang, X. / Wang, C. / Shengfang, S. / Dawson, J.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Complex of myoglobin with phenol bound in a proximal cavity.
Authors: Huang, X. / Wang, C. / Celeste, L.R. / Lovelace, L.L. / Sun, S. / Dawson, J.H. / Lebioda, L.
History
DepositionSep 7, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionNov 21, 2012ID: 3OBD
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Nov 15, 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)18,6299
Polymers17,4101
Non-polymers1,2198
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.531, 90.531, 45.158
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin


Mass: 17410.199 Da / Num. of mol.: 1 / Mutation: G65T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185

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Non-polymers , 5 types, 241 molecules

#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-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 59.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.6M AS, 50mM Tris 8.5, 1mM EDTA, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.14→50 Å / Num. obs: 76906 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 4.2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.052 / Χ2: 1.246 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.14-1.163.70.36637770.675198.1
1.16-1.184.90.34537950.734199.8
1.18-1.25.50.32238290.7251100
1.2-1.235.70.30138230.7231100
1.23-1.255.80.26238580.7581100
1.25-1.285.80.23538050.7561100
1.28-1.325.90.20738310.7811100
1.32-1.355.90.19238450.8131100
1.35-1.3960.16838290.8651100
1.39-1.4460.15838300.9351100
1.44-1.4960.12838531.011100
1.49-1.556.10.10638221.0271100
1.55-1.626.10.08838670.981100
1.62-1.76.20.07938201.1091100
1.7-1.816.80.07938781.4641100
1.81-1.9512.20.06938291.5821100
1.95-2.1512.60.05138851.5181100
2.15-2.4612.60.04538691.61100
2.46-3.0912.60.0438831.7271100
3.09-5012.20.03639781.868199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUISerguidata collection
RefinementResolution: 1.14→39.13 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.1613 / WRfactor Rwork: 0.1404 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.9433 / SU B: 0.589 / SU ML: 0.013 / SU R Cruickshank DPI: 0.0249 / SU Rfree: 0.0257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1526 3859 5 %RANDOM
Rwork0.1329 73021 --
obs0.1339 76880 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.92 Å2 / Biso mean: 12.9702 Å2 / Biso min: 4.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.14→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 78 233 1530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221338
X-RAY DIFFRACTIONr_angle_refined_deg2.3432.0771809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1555153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6524.15153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42215244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.777154
X-RAY DIFFRACTIONr_chiral_restr0.1180.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02965
X-RAY DIFFRACTIONr_mcbond_it2.0211.5764
X-RAY DIFFRACTIONr_mcangle_it3.04521222
X-RAY DIFFRACTIONr_scbond_it5.3453574
X-RAY DIFFRACTIONr_scangle_it7.1674.5587
X-RAY DIFFRACTIONr_rigid_bond_restr3.05231338
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 276 -
Rwork0.217 5275 -
all-5551 -
obs--98.44 %

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