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- PDB-4qau: Crystal structure of F43Y mutant of sperm whale myoglobin -

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Basic information

Entry
Database: PDB / ID: 4qau
TitleCrystal structure of F43Y mutant of sperm whale myoglobin
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / alpha helix boundle / F43Y 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 / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.597 Å
AuthorsLin, Y. / Tan, X. / Li, W.
CitationJournal: Chembiochem / Year: 2015
Title: A Novel Tyrosine-Heme C-O Covalent Linkage in F43Y Myoglobin: A New Post-translational Modification of Heme Proteins
Authors: Yan, D.-J. / Li, W. / Xiang, Y. / Wen, G.-B. / Lin, Y.-W. / Tan, X.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)17,9992
Polymers17,3821
Non-polymers6161
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.871, 48.400, 78.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin


Mass: 17382.148 Da / Num. of mol.: 1 / Mutation: F43Y
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.: 205 / Source method: isolated from a natural source / Formula: H2O

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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: 43.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate, 30% w/v Polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2013 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5967→30.78 Å / Num. obs: 20569 / % possible obs: 10.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.357 / Rsym value: 0.077 / Net I/σ(I): 26.9
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.5967-1.72119.7
1.72-1.9119.7
1.9-2.09114.6
2.09-2.39114.9
2.39-3.01115.3
3.01-50115.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX1.7.1_743refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4it8

4it8


Resolution: 1.597→30.774 Å / SU ML: 0.33 / σ(F): 0.13 / Phase error: 18.11 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2045 1999 9.91 %
Rwork0.1773 --
obs0.18 20170 96.55 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.065 Å2 / ksol: 0.398 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3224 Å2-0 Å20 Å2
2---2.9052 Å2-0 Å2
3---5.2275 Å2
Refinement stepCycle: LAST / Resolution: 1.597→30.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 43 205 1465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071295
X-RAY DIFFRACTIONf_angle_d1.1021755
X-RAY DIFFRACTIONf_dihedral_angle_d16.051483
X-RAY DIFFRACTIONf_chiral_restr0.069182
X-RAY DIFFRACTIONf_plane_restr0.004213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5967-1.63660.25181300.1934117790
1.6366-1.68080.22141380.1738126495
1.6808-1.73030.21351400.1746126295
1.7303-1.78610.24291370.1739125996
1.7861-1.850.20681390.1788126195
1.85-1.9240.211380.1743125595
1.924-2.01160.21641420.1724128695
2.0116-2.11760.18891400.1755128197
2.1176-2.25020.16661440.1626131498
2.2502-2.42390.18431470.1713133199
2.4239-2.66770.18721480.18091345100
2.6677-3.05340.21491500.1907135999
3.0534-3.84580.20661500.16931364100
3.8458-30.77950.21331560.1843141396

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