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- PDB-7vw4: The X-ray structure of sperm whale F46C/L61C myoglobin double mutant -

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Basic information

Entry
Database: PDB / ID: 7vw4
TitleThe X-ray structure of sperm whale F46C/L61C myoglobin double mutant
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / SPERM WHALE 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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLin, Y.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The X-ray structure of sperm whale F46C/L61C myoglobin double mutant
Authors: Lin, Y.W.
History
DepositionNov 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)17,9292
Polymers17,3121
Non-polymers6161
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-21 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.944, 48.016, 76.847
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: 17312.102 Da / Num. of mol.: 1 / Mutation: F46C, L61C
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.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, Sodium cacodylate trihydrate pH 6.5, Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→24.01 Å / Num. obs: 27268 / % possible obs: 95.63 % / Redundancy: 13.2 % / Biso Wilson estimate: 22.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08057 / Rpim(I) all: 0.02286 / Net I/σ(I): 25.39
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.6268 / Mean I/σ(I) obs: 6.15 / Num. unique obs: 2600 / Rpim(I) all: 0.1739 / % possible all: 94.34

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 101M

101m


Resolution: 1.8→24.01 Å / SU ML: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.0506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2264 1915 7.55 %
Rwork0.179 23443 -
obs0.1826 25358 95.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.52 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 43 135 1381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321316
X-RAY DIFFRACTIONf_angle_d1.55951790
X-RAY DIFFRACTIONf_chiral_restr0.0995185
X-RAY DIFFRACTIONf_plane_restr0.0083224
X-RAY DIFFRACTIONf_dihedral_angle_d23.5161480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.32921340.23381645X-RAY DIFFRACTION94.58
1.85-1.890.26491350.21841673X-RAY DIFFRACTION95.31
1.89-1.950.29381370.21091711X-RAY DIFFRACTION98.14
1.95-2.010.2961440.21131702X-RAY DIFFRACTION96.35
2.01-2.090.2471410.20961685X-RAY DIFFRACTION96.72
2.09-2.170.28641280.20681628X-RAY DIFFRACTION94.92
2.17-2.270.22911340.19821653X-RAY DIFFRACTION93.95
2.27-2.390.24861420.18691701X-RAY DIFFRACTION97.51
2.39-2.540.24521350.18791694X-RAY DIFFRACTION97.39
2.54-2.730.25351340.1871673X-RAY DIFFRACTION95.71
2.73-30.22161380.18911645X-RAY DIFFRACTION93.16
3.01-3.440.21491380.16381698X-RAY DIFFRACTION98.18
3.44-4.330.17211370.1431667X-RAY DIFFRACTION95
4.33-24.010.20411380.16551668X-RAY DIFFRACTION95.66

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