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- PDB-8j4k: X-ray crystal structure of F46C myoglobin with a covalently linke... -

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Basic information

Entry
Database: PDB / ID: 8j4k
TitleX-ray crystal structure of F46C myoglobin with a covalently linked phenol group
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / MYOGLOBIN MUTANT
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: 1.46 Å
AuthorsYuan, H. / Lin, 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 F46C myoglobin with a covalently linked phenol group
Authors: Yuan, H. / Lin, Y.W.
History
DepositionApr 20, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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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)18,1283
Polymers17,3221
Non-polymers8062
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.719, 48.172, 78.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: Chemical ChemComp-9UU / 1-(4-hydroxyphenyl)pyrrole-2,5-dione


Mass: 189.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8000

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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 EIGER2 S 9M / Detector: PIXEL / Date: Dec 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 27141 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 4.51 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.047 / Net I/σ(I): 16
Reflection shellResolution: 1.46→1.54 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3856 / CC1/2: 0.878 / Rpim(I) all: 0.248

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→41.12 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.745 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20039 1335 4.9 %RANDOM
Rwork0.14985 ---
obs0.15236 25749 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.904 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0 Å2
2---0.23 Å20 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.46→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 57 228 1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0121337
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2131.6831813
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9085159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56323.44858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5115241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.596154
X-RAY DIFFRACTIONr_chiral_restr0.1160.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021001
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7210.499630
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2440.75791
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4520.837707
X-RAY DIFFRACTIONr_scbond_other
LS refinement shellResolution: 1.46→1.495 Å
RfactorNum. reflection% reflection
Rfree0.275 88 -
Rwork0.255 1842 -
obs--98.07 %

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