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- PDB-8xc2: The X-ray structure of F46C myoglobin with a covalently linked Ni... -

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Basic information

Entry
Database: PDB / ID: 8xc2
TitleThe X-ray structure of F46C myoglobin with a covalently linked Ni-complex
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 domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NICKEL (II) ION / : / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLin, Y.W. / Yuan, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The X-ray structure of F46C myoglobin with a covalently linked Ni-complex
Authors: Lin, Y.W. / Yuan, H.
History
DepositionDec 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 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)18,4535
Polymers17,1911
Non-polymers1,2624
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-32 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.827, 49.215, 76.748
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: 17190.920 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-Y6C / 4-oxidanylidene-4-(1,10-phenanthrolin-5-ylamino)but-2-enoic acid


Mass: 293.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.19 Å3/Da / Density % sol: 43.78 %
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: Oct 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 496250 / % possible obs: 99.88 % / Redundancy: 11.6 % / Biso Wilson estimate: 16.12 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.016 / Net I/σ(I): 29.18
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4.97 / Num. unique obs: 2441 / Rpim(I) all: 0.157 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→22.7 Å / SU ML: 0.1194 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.8224
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1863 2445 5.25 %
Rwork0.1766 44170 -
obs0.1771 46615 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.69 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 88 216 1515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01581394
X-RAY DIFFRACTIONf_angle_d1.69021898
X-RAY DIFFRACTIONf_chiral_restr0.0942189
X-RAY DIFFRACTIONf_plane_restr0.0106237
X-RAY DIFFRACTIONf_dihedral_angle_d24.0853537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.23931450.24422625X-RAY DIFFRACTION99.75
1.53-1.560.25331370.20452539X-RAY DIFFRACTION99.93
1.56-1.60.18561390.1972666X-RAY DIFFRACTION99.68
1.6-1.640.21161430.19462554X-RAY DIFFRACTION99.89
1.64-1.680.1991470.19742615X-RAY DIFFRACTION99.86
1.68-1.730.22841440.18532586X-RAY DIFFRACTION99.85
1.73-1.790.19561480.18412580X-RAY DIFFRACTION100
1.79-1.850.18311370.17832609X-RAY DIFFRACTION99.96
1.85-1.930.17991420.17362614X-RAY DIFFRACTION99.89
1.93-2.020.19151480.17932596X-RAY DIFFRACTION100
2.02-2.120.17071450.1752621X-RAY DIFFRACTION100
2.12-2.260.16791470.16742580X-RAY DIFFRACTION100
2.26-2.430.17041420.17222603X-RAY DIFFRACTION99.89
2.43-2.670.18841430.17392608X-RAY DIFFRACTION100
2.67-3.060.19681440.17922603X-RAY DIFFRACTION100
3.06-3.850.1911490.16182580X-RAY DIFFRACTION99.96
3.85-22.70.17051450.17572591X-RAY DIFFRACTION99.6

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