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- PDB-5zzf: X-ray structure of F43Y/H64D sperm whale myoglobin -

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Basic information

Entry
Database: PDB / ID: 5zzf
TitleX-ray structure of F43Y/H64D sperm whale myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / myoglobin
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYuan, H. / Lin, Y.W.
CitationJournal: Acs Catalysis / Year: 2018
Title: A Rationally Designed Myoglobin Exhibits a Catalytic Dehalogenation Efficiency More than 1000-Fold That of a Native Dehaloperoxidase
Authors: Yin, L.L. / Yuan, H. / Liu, C. / He, B. / Gao, S.Q. / Wen, G.B. / Tan, X. / Lin, Y.W.
History
DepositionJun 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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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)17,8442
Polymers17,2281
Non-polymers6161
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-20 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.841, 49.327, 77.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin


Mass: 17227.893 Da / Num. of mol.: 1 / Mutation: F43Y/H64D
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
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% w/v Polyethylene glycol 8000, 0.1 M Sodium cacodylate trihydrate pH 6.5, 0.2 M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 20810 / % possible obs: 99 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rsym value: 0.056 / Net I/σ(I): 16.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3 / Num. unique obs: 1019 / Rpim(I) all: 0.183 / Rsym value: 0.39 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JHO

2jho


Resolution: 1.6→31.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.559 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20989 1068 5.1 %RANDOM
Rwork0.16648 ---
obs0.16865 19690 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.911 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2--0.04 Å20 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.6→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 43 226 1484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191353
X-RAY DIFFRACTIONr_bond_other_d0.0020.021309
X-RAY DIFFRACTIONr_angle_refined_deg3.6051.9981843
X-RAY DIFFRACTIONr_angle_other_deg1.15133024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18124.57659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15315243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.289154
X-RAY DIFFRACTIONr_chiral_restr0.2190.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021534
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02312
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5651.259639
X-RAY DIFFRACTIONr_mcbond_other1.5611.26636
X-RAY DIFFRACTIONr_mcangle_it2.3321.892806
X-RAY DIFFRACTIONr_mcangle_other2.3321.892806
X-RAY DIFFRACTIONr_scbond_it2.6331.572714
X-RAY DIFFRACTIONr_scbond_other2.6351.573712
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.982.2291035
X-RAY DIFFRACTIONr_long_range_B_refined6.24612.8671897
X-RAY DIFFRACTIONr_long_range_B_other5.9211.7981770
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 87 -
Rwork0.223 1402 -
obs--98.22 %

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