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- PDB-5ut8: Deoxy form of sperm whale myoglobin H64A -

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Basic information

Entry
Database: PDB / ID: 5ut8
TitleDeoxy form of sperm whale myoglobin H64A
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Heme / Myoglobin / Deoxy / Nitrite / 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-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: 1.78 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)18,5839
Polymers17,2981
Non-polymers1,2858
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.399, 90.399, 45.271
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-203-

SO4

21A-203-

SO4

31A-480-

HOH

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Components

#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
#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.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 294 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 11, 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: 20332 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Χ2: 3.216 / Net I/σ(I): 31.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.814.40.0770.9930.040.0872.38391.9
1.81-1.845.10.0750.9930.0360.0842.6499.8
1.84-1.885.70.0730.9940.0330.0812.652100
1.88-1.926.60.0730.9950.030.0792.752100
1.92-1.966.80.0720.9950.030.0782.963100
1.96-26.90.0670.9960.0280.0732.907100
2-2.057.10.0650.9960.0260.073.134100
2.05-2.117.30.0630.9970.0250.0683.096100
2.11-2.177.40.0610.9960.0240.0663.208100
2.17-2.247.60.0610.9970.0240.0653.273100
2.24-2.327.60.0590.9960.0230.0643.343100
2.32-2.427.70.0590.9970.0230.0633.453100
2.42-2.537.60.0570.9970.0220.0613.258100
2.53-2.667.60.0560.9970.0220.0613.482100
2.66-2.837.60.0550.9970.0210.0593.508100
2.83-3.047.60.0510.9970.020.0543.247100
3.04-3.357.60.0480.9980.0180.0513.197100
3.35-3.837.40.0470.9980.0180.0513.51100
3.83-4.837.20.0480.9980.0190.0513.80999.8
4.83-506.60.0450.9980.0190.0493.6198.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.22data extraction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→32.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.447 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1714 1040 5.1 %RANDOM
Rwork0.1479 ---
obs0.1491 19272 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.38 Å2 / Biso mean: 15.218 Å2 / Biso min: 7.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.78→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 79 201 1492
Biso mean--21.22 23.48 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191318
X-RAY DIFFRACTIONr_bond_other_d0.0010.021275
X-RAY DIFFRACTIONr_angle_refined_deg2.392.0261788
X-RAY DIFFRACTIONr_angle_other_deg1.02932937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0915152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34324.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99115235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.508154
X-RAY DIFFRACTIONr_chiral_restr0.1950.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021430
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02296
LS refinement shellResolution: 1.782→1.828 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 85 -
Rwork0.164 1381 -
all-1466 -
obs--97.21 %

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