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- PDB-4h0b: Complex of G65T Myoglobin with DMSO in its Distal Cavity -

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Basic information

Entry
Database: PDB / ID: 4h0b
TitleComplex of G65T Myoglobin with DMSO in its Distal Cavity
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT
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 / OXYGEN MOLECULE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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: 3OCK
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)18,5839
Polymers17,4101
Non-polymers1,1738
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.499, 90.499, 45.319
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

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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 , 6 types, 274 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
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: 1.26→50 Å / Num. obs: 57188 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.069 / Χ2: 2.434 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.26-1.314.90.16456681.184199.9
1.31-1.365.80.15156651.2981100
1.36-1.425.80.1357351.4441100
1.42-1.495.70.11256681.6331100
1.49-1.595.90.10157132.0511100
1.59-1.715.70.09557242.551100
1.71-1.885.80.0857112.731100
1.88-2.155.70.0757513.441199.9
2.15-2.715.60.06257183.8261100
2.71-505.30.05658354.125199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUISerguidata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→32.02 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1602 / WRfactor Rwork: 0.1297 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.9385 / SU B: 0.712 / SU ML: 0.015 / SU R Cruickshank DPI: 0.032 / SU Rfree: 0.0333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1534 2902 5.1 %RANDOM
Rwork0.1271 ---
obs0.1284 57185 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.73 Å2 / Biso mean: 12.7219 Å2 / Biso min: 3.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.26→32.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 73 266 1551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211314
X-RAY DIFFRACTIONr_angle_refined_deg2.3492.0691783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64224.15153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18415227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.488154
X-RAY DIFFRACTIONr_chiral_restr0.1230.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021958
X-RAY DIFFRACTIONr_mcbond_it2.2241.5765
X-RAY DIFFRACTIONr_mcangle_it3.15921220
X-RAY DIFFRACTIONr_scbond_it5.1083549
X-RAY DIFFRACTIONr_scangle_it6.494.5563
X-RAY DIFFRACTIONr_rigid_bond_restr3.1331314
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 208 -
Rwork0.116 4018 -
all-4226 -
obs--99.72 %

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