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- PDB-7xcq: X-ray crystal structure of sperm whale myoglobin H64D mutant -

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Basic information

Entry
Database: PDB / ID: 7xcq
TitleX-ray crystal structure of sperm whale myoglobin H64D 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 catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 H64D mutant
Authors: Lin, Y.W.
History
DepositionMar 25, 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)17,9602
Polymers17,3431
Non-polymers6161
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-20 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.740, 49.120, 77.440
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: 17343.088 Da / Num. of mol.: 1 / Mutation: H64D
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.: 193 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
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: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 20645 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.08 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.027 / Net I/σ(I): 19.84
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 6.93 / Num. unique obs: 2037 / CC1/2: 0.99 / Rpim(I) all: 0.151

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MTJ

1mtj


Resolution: 1.6→24.15 Å / SU ML: 0.1167 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1887 1020 4.94 %
Rwork0.178 19625 -
obs0.1785 20645 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.54 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 43 193 1450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781295
X-RAY DIFFRACTIONf_angle_d1.1571754
X-RAY DIFFRACTIONf_chiral_restr0.0702182
X-RAY DIFFRACTIONf_plane_restr0.0054217
X-RAY DIFFRACTIONf_dihedral_angle_d20.092470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.2221380.20122769X-RAY DIFFRACTION100
1.68-1.790.23771360.18942756X-RAY DIFFRACTION100
1.79-1.930.22221540.18922752X-RAY DIFFRACTION99.86
1.93-2.120.21181480.17792772X-RAY DIFFRACTION100
2.12-2.430.19371460.16722793X-RAY DIFFRACTION99.93
2.43-3.060.19251430.18092830X-RAY DIFFRACTION100
3.06-24.150.15721550.17312953X-RAY DIFFRACTION99.97

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