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- PDB-7ehx: X-ray crystal strcture of F46C/L49C sperm whale myoglobin with an... -

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Basic information

Entry
Database: PDB / ID: 7ehx
TitleX-ray crystal strcture of F46C/L49C sperm whale myoglobin with an intramolecular disulfide bond
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.
CitationJournal: To Be Published
Title: X-ray crystal strcture of F46C/L49C sperm whale myoglobin with an intramolecular disulfide bond
Authors: Lin, Y.W.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 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 1.2Oct 30, 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
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-18 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.956, 49.620, 76.802
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: 17312.104 Da / Num. of mol.: 1 / Mutation: F46C, L49C
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.: 195 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% peg 8000,

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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: Jan 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14702 / % possible obs: 99.6 % / Redundancy: 11.3 % / Biso Wilson estimate: 20.58 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.024 / Rsym value: 0.063 / Net I/σ(I): 31.7
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 5 / Num. unique obs: 704 / Rpim(I) all: 0.177 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MCY

1mcy


Resolution: 1.8→23.61 Å / SU ML: 0.2621 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 751 5.13 %
Rwork0.1949 13883 -
obs0.1965 14634 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 43 195 1448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00971333
X-RAY DIFFRACTIONf_angle_d1.28261814
X-RAY DIFFRACTIONf_chiral_restr0.0642188
X-RAY DIFFRACTIONf_plane_restr0.009228
X-RAY DIFFRACTIONf_dihedral_angle_d22.8422178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.32771500.25262619X-RAY DIFFRACTION95.61
1.94-2.130.2511420.2112765X-RAY DIFFRACTION99.97
2.13-2.440.23611580.19232758X-RAY DIFFRACTION100
2.44-3.070.21351580.22803X-RAY DIFFRACTION99.97
3.07-23.610.20761430.17932938X-RAY DIFFRACTION99.84

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