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- PDB-5ojb: Structure of MbQ NMH -

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Basic information

Entry
Database: PDB / ID: 5ojb
TitleStructure of MbQ NMH
ComponentsMyoglobin
KeywordsOXIDOREDUCTASE / myoglobin / NMH / N-methylhistidine / heme
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / 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 / IMIDAZOLE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.543 Å
AuthorsHayashi, T. / Pott, M. / Mori, T. / Mittl, P. / Green, A. / Hivert, D.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: A Noncanonical Proximal Heme Ligand Affords an Efficient Peroxidase in a Globin Fold.
Authors: Pott, M. / Hayashi, T. / Mori, T. / Mittl, P.R.E. / Green, A.P. / Hilvert, D.
History
DepositionJul 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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)19,0653
Polymers18,3791
Non-polymers6862
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-13 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.134, 91.134, 39.687
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Myoglobin /


Mass: 18379.178 Da / Num. of mol.: 1
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-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG (pH 7.0), 30% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 54004 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.83
Reflection shellResolution: 1.54→1.64 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.285 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 8534 / CC1/2: 0.552 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OJ9

5oj9


Resolution: 1.543→45.567 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 26.36
RfactorNum. reflection% reflection
Rfree0.2329 2699 5.01 %
Rwork0.2006 --
obs0.2021 53926 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.543→45.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 48 76 1347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071381
X-RAY DIFFRACTIONf_angle_d0.9351877
X-RAY DIFFRACTIONf_dihedral_angle_d4.4441375
X-RAY DIFFRACTIONf_chiral_restr0.045192
X-RAY DIFFRACTIONf_plane_restr0.005235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.543-1.5710.41541310.3582478X-RAY DIFFRACTION91
1.571-1.60120.3361420.31712698X-RAY DIFFRACTION100
1.6012-1.63390.31531450.31332744X-RAY DIFFRACTION100
1.6339-1.66940.30251410.30472655X-RAY DIFFRACTION100
1.6694-1.70830.30281430.28732734X-RAY DIFFRACTION100
1.7083-1.7510.33811440.27482732X-RAY DIFFRACTION100
1.751-1.79830.30561420.26232699X-RAY DIFFRACTION100
1.7983-1.85130.27211410.24642684X-RAY DIFFRACTION100
1.8513-1.9110.22821440.2252720X-RAY DIFFRACTION100
1.911-1.97930.26061440.22872711X-RAY DIFFRACTION100
1.9793-2.05860.26381420.22392686X-RAY DIFFRACTION100
2.0586-2.15230.22531430.19422703X-RAY DIFFRACTION100
2.1523-2.26570.24771420.18952731X-RAY DIFFRACTION100
2.2657-2.40770.23731420.192686X-RAY DIFFRACTION100
2.4077-2.59360.22661440.19822740X-RAY DIFFRACTION100
2.5936-2.85450.26561440.20712709X-RAY DIFFRACTION100
2.8545-3.26750.21161450.19852695X-RAY DIFFRACTION100
3.2675-4.11630.20721400.17462703X-RAY DIFFRACTION100
4.1163-45.58690.18951400.16612719X-RAY DIFFRACTION100

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