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- PDB-5utb: Met form of sperm whale myoglobin V68A/I107Y -

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Basic information

Entry
Database: PDB / ID: 5utb
TitleMet form of sperm whale myoglobin V68A/I107Y
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Heme / Myoglobin / Nitrite / Nitrosyl / Nitric oxide
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / 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 / 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
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)18,3846
Polymers17,3871
Non-polymers9975
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.437, 30.778, 64.043
Angle α, β, γ (deg.)90.000, 105.470, 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 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 35.32 %
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: Oct 20, 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: 12651 / % possible obs: 99.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Χ2: 4.165 / Net I/σ(I): 43.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.813.60.0670.9910.0390.0782.79192.2
1.81-1.844.30.0710.9940.0380.0813.157100
1.84-1.884.90.0720.9930.0360.0813.447100
1.88-1.925.60.0670.9960.0310.0743.524100
1.92-1.965.90.0640.9960.0280.073.503100
1.96-260.0650.9970.0280.0713.711100
2-2.056.10.0620.9960.0270.0673.78100
2.05-2.116.40.060.9970.0260.0664.195100
2.11-2.176.30.0570.9970.0250.0624.079100
2.17-2.246.50.0570.9970.0240.0624.113100
2.24-2.326.70.0530.9980.0220.0574.114100
2.32-2.426.60.0510.9970.0210.0564.017100
2.42-2.536.60.0530.9970.0220.0574.48899.8
2.53-2.666.60.0550.9970.0230.064.406100
2.66-2.836.60.0540.9980.0230.0594.747100
2.83-3.046.50.0510.9970.0220.0564.50499.8
3.04-3.356.50.0490.9970.020.0534.191100
3.35-3.836.30.0480.9980.020.0524.301100
3.83-4.836.20.050.9970.0220.0554.944100
4.83-505.50.0490.9960.0240.0555.84698.8

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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: 1.78→33.19 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.319 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.026
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 618 4.9 %RANDOM
Rwork0.1597 ---
obs0.1616 12024 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.72 Å2 / Biso mean: 20.972 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1-3.49 Å20 Å23.01 Å2
2--1.41 Å20 Å2
3----4.91 Å2
Refinement stepCycle: final / Resolution: 1.78→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 64 99 1376
Biso mean--23.2 26.05 -
Num. residues----152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191309
X-RAY DIFFRACTIONr_bond_other_d0.0020.021269
X-RAY DIFFRACTIONr_angle_refined_deg1.9072.0111773
X-RAY DIFFRACTIONr_angle_other_deg0.94132924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1665151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01324.07454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.536154
X-RAY DIFFRACTIONr_chiral_restr0.1510.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021427
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02301
LS refinement shellResolution: 1.778→1.824 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 40 -
Rwork0.177 826 -
all-866 -
obs--95.37 %

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