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- PDB-5vzp: Sperm whale myoglobin H64Q with nitric oxide -

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Basic information

Entry
Database: PDB / ID: 5vzp
TitleSperm whale myoglobin H64Q with nitric oxide
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Heme / Myoglobin / nitrosyl / nitric oxide
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 / NITRIC OXIDE / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
Model detailsThis stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale ...This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale myoglobin ferric H64A and N-hydroxyamphetamine.
AuthorsWang, B. / Thomas, L.M. / Richter-Addo, G.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1213674 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
DepositionMay 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 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)18,88816
Polymers17,3551
Non-polymers1,53315
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-41 kcal/mol
Surface area8040 Å2
2
A: Myoglobin
hetero molecules

A: Myoglobin
hetero molecules

A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,66448
Polymers52,0653
Non-polymers4,59945
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area12050 Å2
ΔGint-164 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.132, 90.132, 45.248
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-211-

SO4

21A-211-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin


Mass: 17355.145 Da / Num. of mol.: 1 / Mutation: H64Q
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

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Non-polymers , 6 types, 161 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Chemical
ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, 1 mM EDTA, pH 9 2.5 M Ammonium Sulfate

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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 200K / Detector: PIXEL / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 20200 / % possible obs: 99.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.021 / Rrim(I) all: 0.058 / Χ2: 3.361 / Net I/av σ(I): 68.241 / Net I/σ(I): 32.6 / Num. measured all: 140393
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.814.30.0840.9890.0440.0962.16186.9
1.81-1.8450.0790.9920.0390.0892.358100
1.84-1.885.70.0780.9950.0350.0862.418100
1.88-1.926.60.0760.9950.0320.0832.613100
1.92-1.966.80.0720.9950.030.0792.534100
1.96-26.90.0680.9960.0280.0742.797100
2-2.057.10.0680.9960.0270.0743.124100
2.05-2.117.20.0630.9970.0250.0683.172100
2.11-2.177.40.0620.9970.0240.0663.193100
2.17-2.247.60.0620.9970.0240.0673.355100
2.24-2.327.60.0580.9970.0230.0633.392100
2.32-2.427.60.0590.9970.0220.0633.456100
2.42-2.537.60.0570.9980.0220.0623.606100
2.53-2.667.50.0570.9970.0220.0613.75100
2.66-2.837.60.0560.9970.0220.0613.782100
2.83-3.047.60.0540.9970.0210.0583.83100
3.04-3.357.60.0510.9980.020.0553.949100
3.35-3.837.30.0510.9980.020.0554.025100
3.83-4.837.20.050.9980.020.0544.1399.9
4.83-506.50.0480.9970.020.0524.07798.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MBW

2mbw


Resolution: 1.78→31.95 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.687 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.097
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 1026 5.1 %RANDOM
Rwork0.1525 ---
obs0.1546 19105 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.55 Å2 / Biso mean: 18.933 Å2 / Biso min: 9.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.04 Å20 Å2
2--0.04 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.78→31.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 99 146 1461
Biso mean--27.33 27.21 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191341
X-RAY DIFFRACTIONr_bond_other_d0.0020.021295
X-RAY DIFFRACTIONr_angle_refined_deg2.4432.0231802
X-RAY DIFFRACTIONr_angle_other_deg0.99532984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1855154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5824.54555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92415238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.217154
X-RAY DIFFRACTIONr_chiral_restr0.150.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021449
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02301
X-RAY DIFFRACTIONr_mcbond_it1.9061.5614
X-RAY DIFFRACTIONr_mcbond_other1.7821.497612
X-RAY DIFFRACTIONr_mcangle_it2.3362.239765
LS refinement shellResolution: 1.783→1.829 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 68 -
Rwork0.177 1395 -
all-1463 -
obs--98.99 %

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