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- PDB-5z7e: Horse Heart Myoglobin Mutant - H93M -

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Basic information

Entry
Database: PDB / ID: 5z7e
TitleHorse Heart Myoglobin Mutant - H93M
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / horse heart myoglobin mutant / H93M
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 1.8 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 - H93M
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)17,8315
Polymers16,9771
Non-polymers8554
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-44 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.082, 28.725, 63.271
Angle α, β, γ (deg.)90.00, 105.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin /


Mass: 16976.562 Da / Num. of mol.: 1 / Mutation: H93M
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
#2: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.81 Å3/Da / Density % sol: 31.94 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→60.89 Å / Num. obs: 10965 / % possible obs: 99.5 % / Redundancy: 3.2 % / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.847 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.8→60.89 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.89 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 525 4.6 %RANDOM
Rwork0.1565 ---
obs0.15837 10965 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.982 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.03 Å2
2---0.55 Å20 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.8→60.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 56 89 1341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191282
X-RAY DIFFRACTIONr_bond_other_d0.0020.021204
X-RAY DIFFRACTIONr_angle_refined_deg1.7832.0111735
X-RAY DIFFRACTIONr_angle_other_deg1.04532799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66425.19252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01815231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.611152
X-RAY DIFFRACTIONr_chiral_restr0.1230.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021403
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02251
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_it1.7012.081611
X-RAY DIFFRACTIONr_mcbond_other1.6912.076610
X-RAY DIFFRACTIONr_mcangle_it2.33.11762
X-RAY DIFFRACTIONr_mcangle_other2.3063.113763
X-RAY DIFFRACTIONr_scbond_it2.7182.408671
X-RAY DIFFRACTIONr_scbond_other2.7052.406669
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9933.471973
X-RAY DIFFRACTIONr_long_range_B_refined4.64225.5831541
X-RAY DIFFRACTIONr_long_range_B_other4.63825.5731541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 42 -
Rwork0.217 798 -
obs--98.59 %

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