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- PDB-8j4l: X-ray crystal structure of F46C myoglobin with a covalently linke... -

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Basic information

Entry
Database: PDB / ID: 8j4l
TitleX-ray crystal structure of F46C myoglobin with a covalently linked triazole 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
1H-1,2,3-triazole-5-thiol / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 triazole group
Authors: Yuan, H. / Lin, Y.W.
History
DepositionApr 20, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 1, 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)18,0403
Polymers17,3221
Non-polymers7182
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-19 kcal/mol
Surface area7980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.928, 50.130, 76.208
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 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: Chemical ChemComp-EBJ / 1H-1,2,3-triazole-5-thiol


Mass: 101.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3N3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 44.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG8000

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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 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 27514 / % possible obs: 98.84 % / Redundancy: 8.9 % / Biso Wilson estimate: 12.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.031 / Net I/σ(I): 14.48
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.3441 / Mean I/σ(I) obs: 3.76 / Num. unique obs: 2442 / CC1/2: 0.92 / Rpim(I) all: 0.1532 / % possible all: 89.35

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→31.23 Å / SU ML: 0.1499 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.4982
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2007 1326 4.82 %
Rwork0.1571 26186 -
obs0.1592 27512 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.26 Å2
Refinement stepCycle: LAST / Resolution: 1.45→31.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 49 225 1485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01961312
X-RAY DIFFRACTIONf_angle_d3.08171780
X-RAY DIFFRACTIONf_chiral_restr0.0973185
X-RAY DIFFRACTIONf_plane_restr0.0103221
X-RAY DIFFRACTIONf_dihedral_angle_d23.5233493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.510.22911380.15792599X-RAY DIFFRACTION90.36
1.51-1.580.21811470.15422912X-RAY DIFFRACTION100
1.58-1.660.23941420.14632909X-RAY DIFFRACTION99.9
1.66-1.760.2031430.14092867X-RAY DIFFRACTION99.87
1.76-1.90.18821500.14162940X-RAY DIFFRACTION99.9
1.9-2.090.1831410.14242932X-RAY DIFFRACTION99.81
2.09-2.390.17871520.14352942X-RAY DIFFRACTION99.9
2.39-3.020.20211710.17312953X-RAY DIFFRACTION99.97
3.02-31.230.20661420.16743132X-RAY DIFFRACTION99.85

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