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- PDB-5kd1: Sperm whale myoglobin H64A with nitrosoamphetamine -

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Basic information

Entry
Database: PDB / ID: 5kd1
TitleSperm whale myoglobin H64A with nitrosoamphetamine
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / heme / myoglobin / nitrosoalkane / nitrosoamphetamine / 2-nitroso-1-phenylpropane / N-hydroxyamphetamine / C-nitroso
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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
[(2R)-2-nitrosopropyl]benzene / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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. / Guan, Y. / 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: Nitric Oxide / Year: 2017
Title: Nitrosoamphetamine binding to myoglobin and hemoglobin: Crystal structure of the H64A myoglobin-nitrosoamphetamine adduct.
Authors: Wang, B. / Powell, S.M. / Guan, Y. / Xu, N. / Thomas, L.M. / Richter-Addo, G.B.
History
DepositionJun 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)18,77712
Polymers17,1671
Non-polymers1,61011
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Myoglobin
hetero molecules

A: Myoglobin
hetero molecules

A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,33236
Polymers51,5013
Non-polymers4,83133
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area10010 Å2
ΔGint-243 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.500, 90.500, 45.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-203-

SO4

21A-203-

SO4

31A-472-

HOH

41A-477-

HOH

Detailsmonomer according to gel filtration

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin


Mass: 17166.898 Da / Num. of mol.: 1 / Mutation: H65A, D122N
Source method: isolated from a genetically manipulated source
Details: ALA A 64 UNP P02185 HIS 65 ENGINEERED MUTATION ASN A 122 UNP P02185 ASP 123 VARIANT
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, 203 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.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-3QM / [(2R)-2-nitrosopropyl]benzene / 2-nitroso-1-phenylpropane


Mass: 149.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 296 K / Method: batch mode
Details: 100 mM 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 RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→29.65 Å / Num. obs: 23468 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 23.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.191 / % possible all: 99.8

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Processing

Software
NameClassification
REFMACrefinement
CrystalCleardata collection
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MBW

2mbw


Resolution: 1.7→29.36 Å / SU B: 1.329 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.177 1206 5.1 %RANDOM
Rwork0.148 ---
obs0.149 22261 99.9 %-
Displacement parametersBiso mean: 16.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 105 192 1508

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