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- PDB-6krc: An X-ray structure of ferric F43Y/F46S sperm whale myoglobin -

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Basic information

Entry
Database: PDB / ID: 6krc
TitleAn X-ray structure of ferric F43Y/F46S 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 macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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)17,8072
Polymers17,1911
Non-polymers6161
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-19 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.776, 48.378, 78.674
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 (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.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 44.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG8000, 0.1 M NaAc, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 31430 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 14.49 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.049 / Net I/σ(I): 14.7
Reflection shellResolution: 1.39→1.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2147 / Rpim(I) all: 0.482 / % possible all: 96.4

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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: 5XKV

5xkv


Resolution: 1.39→30.72 Å / SU ML: 0.1146 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.9515
RfactorNum. reflection% reflection
Rfree0.1727 1567 5 %
Rwork0.1341 --
obs0.1361 31345 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.49 Å2
Refinement stepCycle: LAST / Resolution: 1.39→30.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 43 217 1473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911376
X-RAY DIFFRACTIONf_angle_d2.80391877
X-RAY DIFFRACTIONf_chiral_restr0.16196
X-RAY DIFFRACTIONf_plane_restr0.0071237
X-RAY DIFFRACTIONf_dihedral_angle_d9.85231086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.430.2211160.14512627X-RAY DIFFRACTION96.96
1.43-1.480.18761470.12512648X-RAY DIFFRACTION99.93
1.48-1.540.18471470.11262672X-RAY DIFFRACTION99.93
1.54-1.610.15091330.10662676X-RAY DIFFRACTION99.68
1.61-1.70.14651430.11052679X-RAY DIFFRACTION99.96
1.7-1.80.16211290.11142711X-RAY DIFFRACTION99.96
1.8-1.940.17241570.12042676X-RAY DIFFRACTION99.96
1.94-2.140.16651500.11392703X-RAY DIFFRACTION100
2.14-2.450.16951570.12422717X-RAY DIFFRACTION100
2.45-3.090.16781390.14582774X-RAY DIFFRACTION100
3.09-100.18241490.14652895X-RAY DIFFRACTION99.93

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