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- PDB-5utc: Deoxy form of sperm whale myoglobin V68A/I107Y -

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Basic information

Entry
Database: PDB / ID: 5utc
TitleDeoxy form of sperm whale myoglobin V68A/I107Y
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Heme / Myoglobin / Nitrite / Nitrosyl / Nitric oxide / deoxy
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionFeb 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Aug 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4767
Polymers17,3871
Non-polymers1,0896
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.454, 30.565, 63.811
Angle α, β, γ (deg.)90.000, 105.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 17387.127 Da / Num. of mol.: 1 / Mutation: V68A, I107Y
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
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.9 Å3/Da / Density % sol: 35.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, 1 mM EDTA, pH 7.4 2.56 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: 1.8→31 Å / Num. obs: 12004 / % possible obs: 99 % / Redundancy: 3 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.031 / Rrim(I) all: 0.056 / Χ2: 4.048 / Net I/σ(I): 39.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.10.070.9860.0540.0892.73794.3
1.83-1.862.40.0670.9860.050.0842.90295.4
1.86-1.92.70.0650.980.0470.0812.81797.7
1.9-1.942.80.0670.9590.0480.0833.40699.3
1.94-1.982.90.0610.990.0430.0763.32899.7
1.98-2.032.90.0640.9920.0440.0783.99999.5
2.03-2.083.10.050.9950.0340.0613.02899.8
2.08-2.1330.050.9910.0340.0613.54499.8
2.13-2.23.10.050.9950.0330.0613.57100
2.2-2.273.20.0460.9950.030.0553.711100
2.27-2.353.20.0480.9940.0310.0583.84399.7
2.35-2.443.20.0460.9950.0310.0563.967100
2.44-2.553.20.0480.9950.0320.0584.3499.8
2.55-2.693.20.0440.9960.0290.0533.9399.7
2.69-2.863.20.050.9930.0330.064.569100
2.86-3.083.10.0520.9070.0350.0635.755100
3.08-3.393.10.0430.9950.0280.0524.52399.8
3.39-3.883.10.0430.9940.0290.0524.46199.8
3.88-4.882.90.0440.9940.030.0535.03199.5
4.88-312.60.0440.9940.0320.0546.29496.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.22data extraction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→26.37 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.176 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.16
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 601 5 %RANDOM
Rwork0.1856 ---
obs0.1887 11396 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.01 Å2 / Biso mean: 23.633 Å2 / Biso min: 11.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0.41 Å2
2--0.96 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.8→26.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 70 91 1375
Biso mean--30.58 29.12 -
Num. residues----152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191315
X-RAY DIFFRACTIONr_bond_other_d0.0010.021274
X-RAY DIFFRACTIONr_angle_refined_deg1.8752.0121780
X-RAY DIFFRACTIONr_angle_other_deg0.92932935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1665151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09224.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79515234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.637154
X-RAY DIFFRACTIONr_chiral_restr0.1570.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021433
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02303
LS refinement shellResolution: 1.799→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 40 -
Rwork0.237 767 -
all-807 -
obs--93.84 %

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