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- PDB-6krf: An X-ray structure of ferric F43Y/F46S sperm whale myoglobin in c... -

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Basic information

Entry
Database: PDB / ID: 6krf
TitleAn X-ray structure of ferric F43Y/F46S sperm whale myoglobin in complex with guaiacol
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 / Guaiacol / Myoglobin
Similarity search - Component
Biological speciesPhyseter macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsYuan, H. / Lin, Y.W.
CitationJournal: Acs Catalysis / Year: 2020
Title: A Catalytic Binding Site Together with a Distal Tyr in MyoglobinAffords Catalytic Efficiencies Similar to Natural Peroxidases.
Authors: Zhang, P. / Yuan, H. / Xu, J. / Wang, X.J. / Gao, S.Q. / Tan, X. / Lin, Y.W.
History
DepositionAug 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: 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

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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)17,9313
Polymers17,1911
Non-polymers7412
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-19 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.794, 48.558, 78.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Myoglobin


Mass: 17190.855 Da / Num. of mol.: 1 / Mutation: F43Y, F46S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter macrocephalus (sperm whale) / Gene: MB / Production host: Escherichia coli BL21 (bacteria) / 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: Chemical ChemComp-JZ3 / Guaiacol / 2-methoxyphenol


Mass: 124.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 44.31 %
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 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 13245 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.048 / Net I/σ(I): 19.21
Reflection shellResolution: 1.86→1.91 Å / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.19 / Num. unique obs: 884 / Rpim(I) all: 0.427

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5iks

5iks


Resolution: 1.86→30.78 Å / SU ML: 0.1773 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2587
RfactorNum. reflection% reflection
Rfree0.2052 672 5.07 %
Rwork0.1718 --
obs0.1736 13244 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.64 Å2
Refinement stepCycle: LAST / Resolution: 1.86→30.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 52 197 1462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111318
X-RAY DIFFRACTIONf_angle_d2.71241789
X-RAY DIFFRACTIONf_chiral_restr0.0945186
X-RAY DIFFRACTIONf_plane_restr0.0072223
X-RAY DIFFRACTIONf_dihedral_angle_d7.95851078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-2.010.3161370.22092443X-RAY DIFFRACTION99.5
2.01-2.210.24041440.17832458X-RAY DIFFRACTION99.92
2.21-2.530.25071200.17912503X-RAY DIFFRACTION100
2.53-3.190.22051220.1772526X-RAY DIFFRACTION99.96
3.19-30.780.16341490.15682642X-RAY DIFFRACTION99.93

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