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- PDB-5vzo: Sperm whale myoglobin H64A with nitric oxide -

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Basic information

Entry
Database: PDB / ID: 5vzo
TitleSperm whale myoglobin H64A with nitric oxide
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Heme / Myoglobin / nitrosyl / nitric oxide
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / 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 / 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

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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)18,73915
Polymers17,2981
Non-polymers1,44114
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-42 kcal/mol
Surface area8150 Å2
2
A: Myoglobin
hetero molecules

A: Myoglobin
hetero molecules

A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,21745
Polymers51,8943
Non-polymers4,32342
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 area11320 Å2
ΔGint-168 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.222, 90.222, 45.310
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-206-

SO4

21A-206-

SO4

31A-455-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin /


Mass: 17298.094 Da / Num. of mol.: 1 / Mutation: H64A
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, 180 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 0.1 M Tris-Hcl, 1 mM EDTA, pH 9 2.3 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 17, 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: 20265 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.024 / Rrim(I) all: 0.06 / Χ2: 2.48 / Net I/av σ(I): 54.952 / Net I/σ(I): 23.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.813.60.0910.9870.0550.1071.51893.5
1.81-1.844.20.0870.990.0480.0991.67499.8
1.84-1.884.80.0870.9920.0440.0981.726100
1.88-1.925.60.0830.9940.0390.0921.776100
1.92-1.965.80.0810.9940.0370.0891.957100
1.96-25.80.0740.9940.0330.0811.977100
2-2.0560.0720.9950.0310.0782.177100
2.05-2.116.10.0690.9960.030.0752.424100
2.11-2.176.20.0650.9960.0280.0712.359100
2.17-2.246.40.0650.9960.0270.072.516100
2.24-2.326.40.0610.9960.0260.0662.581100
2.32-2.426.50.060.9960.0250.0652.588100
2.42-2.536.40.0610.9960.0260.0662.787100
2.53-2.666.40.060.9960.0260.0652.853100
2.66-2.836.40.0580.9970.0250.0632.781100
2.83-3.046.40.0550.9950.0240.062.842100
3.04-3.356.40.050.9970.0210.0542.751100
3.35-3.836.30.0470.9970.020.0522.87199.7
3.83-4.836.10.0490.9970.0210.0543.16999.8
4.83-505.60.0460.9980.0210.0513.01197.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 1.78→29.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.633 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.094
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 1034 5.1 %RANDOM
Rwork0.1487 ---
obs0.1506 19212 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.55 Å2 / Biso mean: 16.282 Å2 / Biso min: 7.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.06 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.78→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 93 166 1471
Biso mean--25.93 24.31 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191354
X-RAY DIFFRACTIONr_bond_other_d0.0020.021307
X-RAY DIFFRACTIONr_angle_refined_deg2.1862.0171824
X-RAY DIFFRACTIONr_angle_other_deg0.97933014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1235158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38224.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35815241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.787154
X-RAY DIFFRACTIONr_chiral_restr0.1510.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021477
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02307
X-RAY DIFFRACTIONr_mcbond_it1.371.256624
X-RAY DIFFRACTIONr_mcbond_other1.3191.254622
X-RAY DIFFRACTIONr_mcangle_it1.8371.874781
LS refinement shellResolution: 1.783→1.829 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 87 -
Rwork0.179 1409 -
all-1496 -
obs--99.8 %

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