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- PDB-7xc9: X-ray crystal structure of sperm whale myoglobin F46C mutant -

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Basic information

Entry
Database: PDB / ID: 7xc9
TitleX-ray crystal structure of sperm whale myoglobin F46C mutant
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLin, Y.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: X-ray crystal structure of sperm whale myoglobin F46C mutant
Authors: Lin, Y.W.
History
DepositionMar 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)17,9392
Polymers17,3221
Non-polymers6161
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-19 kcal/mol
Surface area7960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.789, 49.251, 77.574
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: 17322.117 Da / Num. of mol.: 1 / Mutation: F46C
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.: 144 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: peg 3350

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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 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 12433 / % possible obs: 99.19 % / Redundancy: 12.3 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.032 / Net I/σ(I): 18.47
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.95 / Num. unique obs: 1147 / CC1/2: 0.95 / Rpim(I) all: 0.117

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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: 1DO3

1do3


Resolution: 1.9→27.77 Å / SU ML: 0.1618 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 18.2723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2094 1244 10.01 %
Rwork0.173 11189 -
obs0.1766 12433 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 43 144 1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151292
X-RAY DIFFRACTIONf_angle_d1.38961750
X-RAY DIFFRACTIONf_chiral_restr0.0723182
X-RAY DIFFRACTIONf_plane_restr0.0092216
X-RAY DIFFRACTIONf_dihedral_angle_d19.8462469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.980.21251280.16621157X-RAY DIFFRACTION94.76
1.98-2.070.23381340.17791202X-RAY DIFFRACTION99.04
2.07-2.170.23771380.16931239X-RAY DIFFRACTION100
2.17-2.310.21371350.1751222X-RAY DIFFRACTION99.71
2.31-2.490.23981390.16731250X-RAY DIFFRACTION100
2.49-2.740.2211390.1811246X-RAY DIFFRACTION100
2.74-3.140.25821390.18581254X-RAY DIFFRACTION99.79
3.14-3.950.18041410.1711276X-RAY DIFFRACTION100
3.95-27.770.16981510.16631343X-RAY DIFFRACTION99.87

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