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- PDB-6cf0: Sperm Whale Myoglobin H64V Mutant with Nitrite -

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Basic information

Entry
Database: PDB / ID: 6cf0
TitleSperm Whale Myoglobin H64V Mutant with Nitrite
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / Myoglobin / nitrite / sperm whale
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 domain 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 speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsPowell, S.M. / Wang, B. / Thomas, L.M. / Richter-Addo, G.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biochemistry / Year: 2018
Title: Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets.
Authors: Wang, B. / Shi, Y. / Tejero, J. / Powell, S.M. / Thomas, L.M. / Gladwin, M.T. / Shiva, S. / Zhang, Y. / Richter-Addo, G.B.
History
DepositionFeb 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)18,59511
Polymers17,3261
Non-polymers1,26910
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-28 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.150, 90.150, 45.324
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin


Mass: 17326.148 Da / Num. of mol.: 1 / Mutation: H64V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02185

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Non-polymers , 5 types, 165 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-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsD122N mutation is a result from an error in sequencing by the Rivera lab; see Quillin, et al., J. ...D122N mutation is a result from an error in sequencing by the Rivera lab; see Quillin, et al., J. Mol. Biol. 1993, 234, p140-155

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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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 2.64 M ammonium sulfate, 100 mM Tris-Cl, 1 mM EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.641→78.07 Å / Num. obs: 20847 / % possible obs: 100 % / Redundancy: 4.7 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.12 / Χ2: 1.162 / Net I/σ(I): 5
Reflection shellResolution: 1.641→1.684 Å / Num. unique all: 1537

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MGJ

2mgj


Resolution: 1.64→78.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.131 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19325 959 4.6 %RANDOM
Rwork0.16543 ---
obs0.16669 19887 80.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.575 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.64→78.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 83 155 1452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191352
X-RAY DIFFRACTIONr_bond_other_d0.0020.021276
X-RAY DIFFRACTIONr_angle_refined_deg2.1422.0151827
X-RAY DIFFRACTIONr_angle_other_deg1.12632961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75524.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65815240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.473154
X-RAY DIFFRACTIONr_chiral_restr0.1520.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021468
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02268
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_it1.5131.377626
X-RAY DIFFRACTIONr_mcbond_other1.5121.375625
X-RAY DIFFRACTIONr_mcangle_it2.1852.05786
X-RAY DIFFRACTIONr_mcangle_other2.1942.054787
X-RAY DIFFRACTIONr_scbond_it3.5181.93726
X-RAY DIFFRACTIONr_scbond_other2.9031.785718
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1792.4981030
X-RAY DIFFRACTIONr_long_range_B_refined5.75218.1191676
X-RAY DIFFRACTIONr_long_range_B_other5.75218.1361677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.641→1.684 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.393 12 -
obs--0.62 %

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