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- PDB-2e2y: Crystal Structure of F43W/H64D/V68I Myoglobin -

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Basic information

Entry
Database: PDB / ID: 2e2y
TitleCrystal Structure of F43W/H64D/V68I Myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / 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 / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOhki, T. / Ueno, T. / Hikage, T. / Suzuki, A. / Yamane, T. / Watanabe, Y.
CitationJournal: Acc.Chem.Res. / Year: 2007
Title: Reactivities of oxo and peroxo intermediates studied by hemoprotein mutants
Authors: Watanabe, Y. / Nakajima, H. / Ueno, T.
History
DepositionNov 18, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)18,3926
Polymers17,3951
Non-polymers9975
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.651, 90.651, 45.447
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-1164-

HOH

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Components

#1: Protein Myoglobin /


Mass: 17395.166 Da / Num. of mol.: 1 / Mutation: F43W, H64D, V68I, D122N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0KIY8, UniProt: P02185*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.2M Ammonium Sulfate, 20mM Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 22, 2005 / Details: Confocal Millor
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→80 Å / Num. all: 28345 / Num. obs: 28285 / % possible obs: 99.8 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.056 / Net I/σ(I): 23.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 10.7 / Num. unique all: 2792 / Rsym value: 0.347 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LUE

1lue


Resolution: 1.6→39.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.253 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19543 1428 5 %RANDOM
Rwork0.16821 ---
obs0.16959 26855 99.81 %-
all-28285 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.649 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 64 226 1511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221375
X-RAY DIFFRACTIONr_angle_refined_deg1.1792.071873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3475169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31124.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19315262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.244153
X-RAY DIFFRACTIONr_chiral_restr0.0760.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021002
X-RAY DIFFRACTIONr_nbd_refined0.1990.2693
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.230
X-RAY DIFFRACTIONr_mcbond_it0.721.5810
X-RAY DIFFRACTIONr_mcangle_it1.11921263
X-RAY DIFFRACTIONr_scbond_it1.8373641
X-RAY DIFFRACTIONr_scangle_it2.814.5600
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 98 -
Rwork0.244 1966 -
obs-1966 99.28 %

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