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- PDB-5z7f: Horse Heart Myoglobin Mutant -V68A/I107Y-Sulfide Derivative -

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Basic information

Entry
Database: PDB / ID: 5z7f
TitleHorse Heart Myoglobin Mutant -V68A/I107Y-Sulfide Derivative
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / horse heart myoglobin mutant / V68A/I107Y / sulfide derivative
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / 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
HYDROSULFURIC ACID / PROTOPORPHYRIN IX CONTAINING FE / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsYi, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21271104 China
National Natural Science Foundation of China21671103 China
CitationJournal: To Be Published
Title: Horse Heart Myoglobin Mutant -V68A/I107Y-Sulfide Derivative
Authors: Yi, J.
History
DepositionJan 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9867
Polymers17,0051
Non-polymers9816
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-51 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.003, 28.516, 62.696
Angle α, β, γ (deg.)90.00, 105.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin


Mass: 17005.479 Da / Num. of mol.: 1 / Mutation: V68A,I107Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082

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Non-polymers , 6 types, 62 molecules

#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-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#4: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.77 Å3/Da / Density % sol: 30.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.5-3.0M ammonium sulfate, 0.1M Tris / PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 1.9→60.38 Å / Num. obs: 8914 / % possible obs: 96.98 % / Redundancy: 3.2 % / Net I/σ(I): 15
Reflection shellResolution: 1.9→1.949 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.9→60.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.861 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 452 4.8 %RANDOM
Rwork0.16371 ---
obs0.16674 8914 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.078 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.19 Å2
2---0.14 Å20 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.9→60.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 63 56 1315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191289
X-RAY DIFFRACTIONr_bond_other_d0.0020.021197
X-RAY DIFFRACTIONr_angle_refined_deg1.8452.0081744
X-RAY DIFFRACTIONr_angle_other_deg1.06932783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5945151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.3772554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21315227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.896152
X-RAY DIFFRACTIONr_chiral_restr0.1260.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021410
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02256
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_it1.5671.389607
X-RAY DIFFRACTIONr_mcbond_other1.5551.386606
X-RAY DIFFRACTIONr_mcangle_it2.3272.07757
X-RAY DIFFRACTIONr_mcangle_other2.3312.075758
X-RAY DIFFRACTIONr_scbond_it2.271.738682
X-RAY DIFFRACTIONr_scbond_other2.271.738682
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5132.47988
X-RAY DIFFRACTIONr_long_range_B_refined4.89917.3331548
X-RAY DIFFRACTIONr_long_range_B_other4.86317.2831543
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 29 -
Rwork0.193 598 -
obs--90.22 %

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