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- PDB-5xkv: structure of sperm whale myoglobin F138W -

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Basic information

Entry
Database: PDB / ID: 5xkv
Titlestructure of sperm whale myoglobin F138W
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: 1.4 Å
AuthorsYuan, H.
CitationJournal: Dalton Trans / Year: 2017
Title: Rational design of artificial dye-decolorizing peroxidases using myoglobin by engineering Tyr/Trp in the heme center
Authors: Li, L.L. / Yuan, H. / Liao, F. / He, B. / Gao, S.Q. / Wen, G.B. / Tan, X. / Lin, Y.W.
History
DepositionMay 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

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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)17,8902
Polymers17,2741
Non-polymers6161
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-20 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.766, 48.441, 78.898
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: 17273.986 Da / Num. of mol.: 1 / Fragment: UNP residues 2-154 / Mutation: F138W
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.: 268 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: RIGAKU / Detector: CCD / Date: Dec 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 30559 / % possible obs: 98.9 % / Redundancy: 5.3 % / Rsym value: 0.059 / Net I/σ(I): 23.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.8 % / Num. unique obs: 1312 / Rsym value: 0.487 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HLU

5hlu


Resolution: 1.4→35.54 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.95 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19016 1471 5 %RANDOM
Rwork0.16176 ---
obs0.16326 27687 95.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.364 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.4→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 43 268 1531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191309
X-RAY DIFFRACTIONr_bond_other_d0.0010.021275
X-RAY DIFFRACTIONr_angle_refined_deg2.3261.9971777
X-RAY DIFFRACTIONr_angle_other_deg1.38932942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.855154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96924.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80215238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.108154
X-RAY DIFFRACTIONr_chiral_restr0.1750.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021455
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02301
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_it1.2911.162616
X-RAY DIFFRACTIONr_mcbond_other1.291.161615
X-RAY DIFFRACTIONr_mcangle_it1.8811.747770
X-RAY DIFFRACTIONr_mcangle_other1.881.748771
X-RAY DIFFRACTIONr_scbond_it2.6691.482693
X-RAY DIFFRACTIONr_scbond_other2.6721.482691
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9242.091007
X-RAY DIFFRACTIONr_long_range_B_refined6.31812.6851888
X-RAY DIFFRACTIONr_long_range_B_other5.58911.0891706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 68 -
Rwork0.261 1420 -
obs--66.34 %

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