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- PDB-5uta: Sperm whale myoglobin H64Q with nitrite -

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Basic information

Entry
Database: PDB / ID: 5uta
TitleSperm whale myoglobin H64Q with nitrite
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Heme / Myoglobin / 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 / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 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)18,80816
Polymers17,3551
Non-polymers1,45315
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.388, 90.388, 45.244
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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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 , 5 types, 109 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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: NO2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 94 / 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: 60.29 %
Crystal growTemperature: 294 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 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 19390 / % possible obs: 99.9 % / Redundancy: 16.8 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.017 / Rrim(I) all: 0.07 / Χ2: 6.126 / Net I/σ(I): 41.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.81-1.8412.60.1160.9950.0340.1214.467100
1.84-1.8715.20.1150.9970.0310.124.396100
1.87-1.9116.50.1040.9970.0270.1084.444100
1.91-1.9516.60.0990.9970.0250.1034.788100
1.95-1.9916.70.0980.9980.0250.1015.21199.9
1.99-2.0417.60.0860.9980.0210.0895.101100
2.04-2.0917.70.0810.9980.020.0845.396100
2.09-2.1517.80.0770.9980.0190.0795.617100
2.15-2.2117.40.080.9980.020.0826.101100
2.21-2.2818.50.0720.9990.0170.0745.91100
2.28-2.3617.70.0710.9990.0170.0736.0699.9
2.36-2.4617.70.0690.9990.0170.0716.13599.9
2.46-2.5717.60.0670.9990.0160.0696.12999.9
2.57-2.717.30.0690.9980.0170.0726.71499.9
2.7-2.87180.0670.9990.0160.0696.674100
2.87-3.0917.90.0650.9990.0160.0677.158100
3.09-3.4117.60.060.9990.0150.0626.886100
3.41-3.916.90.0610.9980.0150.0637.40299.9
3.9-4.9115.60.0670.9980.0170.0698.16100
4.91-5013.30.0740.9850.0230.0789.76198.2

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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: 1.81→32 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.856 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.104
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 979 5.1 %RANDOM
Rwork0.1595 ---
obs0.1617 18200 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.46 Å2 / Biso mean: 22.987 Å2 / Biso min: 11.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.03 Å20 Å2
2--0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.81→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 95 94 1404
Biso mean--29.58 29.87 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191348
X-RAY DIFFRACTIONr_bond_other_d0.0020.021309
X-RAY DIFFRACTIONr_angle_refined_deg2.1352.0181811
X-RAY DIFFRACTIONr_angle_other_deg0.96233019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0035158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81824.54555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03415243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.44154
X-RAY DIFFRACTIONr_chiral_restr0.1580.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021459
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02303
LS refinement shellResolution: 1.809→1.856 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 69 -
Rwork0.204 1276 -
all-1345 -
obs--97.25 %

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