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- PDB-8fb0: H64Q Myoglobin in complex with acetamide -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8fb0
TitleH64Q Myoglobin in complex with acetamide
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / heme protein
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
ACETAMIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsPowell, S.M. / Thomas, L.M. / Richter-Addo, G.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J Porphyr Phthalocyanines / Year: 2023
Title: Interactions of metronidazole and chloramphenicol with myoglobin: Crystal structure of a Mb-acetamide product.
Authors: Powell, S.M. / Prather, K.Y. / Nguyen, N. / Thomas, L.M. / Richter-Addo, G.B.
History
DepositionNov 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.2Nov 1, 2023Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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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)18,5999
Polymers17,3551
Non-polymers1,2448
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-57 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.288, 90.288, 45.255
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z

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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 BL21(DE3) (bacteria) / References: UniProt: P02185

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Non-polymers , 5 types, 193 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-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.07 Å3/Da / Density % sol: 59.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2.56-2.76 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 7.4 or 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→45.26 Å / Num. obs: 21044 / % possible obs: 99.8 % / Redundancy: 1.1 % / Biso Wilson estimate: 11.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.32
Reflection shellResolution: 1.76→1.823 Å / Rmerge(I) obs: 0.224 / Num. unique obs: 2046 / CC1/2: 0.999 / % possible all: 98.32

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2MBW

2mbw


Resolution: 1.76→45.26 Å / SU ML: 0.1489 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1937 1057 5.02 %
Rwork0.1632 19980 -
obs0.1648 21037 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.75 Å2
Refinement stepCycle: LAST / Resolution: 1.76→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 79 185 1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741373
X-RAY DIFFRACTIONf_angle_d0.91231864
X-RAY DIFFRACTIONf_chiral_restr0.0465188
X-RAY DIFFRACTIONf_plane_restr0.0047231
X-RAY DIFFRACTIONf_dihedral_angle_d23.4615183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.840.22791120.17972453X-RAY DIFFRACTION97.79
1.84-1.940.19611240.16052492X-RAY DIFFRACTION99.96
1.94-2.060.20791280.17612497X-RAY DIFFRACTION99.96
2.06-2.220.18111440.14842458X-RAY DIFFRACTION99.96
2.22-2.440.21121600.16342463X-RAY DIFFRACTION99.96
2.44-2.790.20841320.16892500X-RAY DIFFRACTION100
2.79-3.520.1811280.17242532X-RAY DIFFRACTION100
3.52-45.260.17581290.15122585X-RAY DIFFRACTION99.89

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