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- PDB-9ijo: X-ray crystal structure of F46C myoglobin with a covalently linke... -

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Basic information

Entry
Database: PDB / ID: 9ijo
TitleX-ray crystal structure of F46C myoglobin with a covalently linked 4-methyl-2,2'-bipyridine group in complex with Cu2+
ComponentsMyoglobin
KeywordsMETAL BINDING PROTEIN / heme protein / myoglobin / copper binding
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
: / COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsLin, Y.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: X-ray crystal structure of F46C myoglobin with a covalently linked 4-methyl-2,2'-bipyridine group in complex with Cu2+
Authors: Lin, Y.W.
History
DepositionJun 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: 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)18,1864
Polymers17,3221
Non-polymers8643
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-34 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.989, 77.523, 39.751
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 BL21(DE3) (bacteria) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1D9G / 4-methyl-2-(4-methylpyridin-2-yl)pyridine


Mass: 184.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, PEG 8000, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.53→30.87 Å / Num. obs: 22848 / % possible obs: 97.07 % / Redundancy: 12.2 % / Biso Wilson estimate: 10.77 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.08
Reflection shellResolution: 1.53→1.585 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.49 / Num. unique obs: 2210 / % possible all: 95.41

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XC9

7xc9


Resolution: 1.53→30.87 Å / SU ML: 0.1473 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.1598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.194 1095 4.8 %
Rwork0.1672 21716 -
obs0.1685 22811 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.17 Å2
Refinement stepCycle: LAST / Resolution: 1.53→30.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 58 197 1458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711301
X-RAY DIFFRACTIONf_angle_d0.97861765
X-RAY DIFFRACTIONf_chiral_restr0.051182
X-RAY DIFFRACTIONf_plane_restr0.0059218
X-RAY DIFFRACTIONf_dihedral_angle_d13.5856170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.60.22391350.18032568X-RAY DIFFRACTION94.54
1.6-1.680.22331240.1672654X-RAY DIFFRACTION95.73
1.68-1.790.18791390.16992642X-RAY DIFFRACTION95.93
1.79-1.930.21611390.17122678X-RAY DIFFRACTION97
1.93-2.120.19811400.16032690X-RAY DIFFRACTION96.85
2.12-2.430.18021330.16212762X-RAY DIFFRACTION98
2.43-3.060.20961440.17312774X-RAY DIFFRACTION98.28
3.06-30.870.17411410.16492948X-RAY DIFFRACTION99.26

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