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- PDB-5oj9: Structure of Mb NMH -

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Basic information

Entry
Database: PDB / ID: 5oj9
TitleStructure of Mb NMH
ComponentsMyoglobin
KeywordsOXIDOREDUCTASE / myoglobin / NMH / N-methylhistidine / heme
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / 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 / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.483 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)19,0262
Polymers18,4091
Non-polymers6161
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-20 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.712, 47.786, 77.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin /


Mass: 18409.229 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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 Å3/Da / Density % sol: 38.4 %
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: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 46776 / % possible obs: 99 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/av σ(I): 9.18 / Net I/σ(I): 9.2
Reflection shellResolution: 1.48→1.57 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.995 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7528 / CC1/2: 0.723 / % possible all: 98.9

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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: 5C6Y

5c6y


Resolution: 1.483→40.673 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.53
RfactorNum. reflection% reflection
Rfree0.232 1252 5 %
Rwork0.1997 --
obs0.2013 25020 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.483→40.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 43 132 1396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061305
X-RAY DIFFRACTIONf_angle_d0.8581770
X-RAY DIFFRACTIONf_dihedral_angle_d18.144473
X-RAY DIFFRACTIONf_chiral_restr0.058183
X-RAY DIFFRACTIONf_plane_restr0.004219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4832-1.54260.37971360.33092579X-RAY DIFFRACTION99
1.5426-1.61280.34261370.28762580X-RAY DIFFRACTION99
1.6128-1.69780.31931350.25432590X-RAY DIFFRACTION100
1.6978-1.80420.25541380.22172633X-RAY DIFFRACTION100
1.8042-1.94350.26061380.20252618X-RAY DIFFRACTION100
1.9435-2.13910.24911390.18832618X-RAY DIFFRACTION100
2.1391-2.44860.21251400.18332654X-RAY DIFFRACTION100
2.4486-3.08480.22571410.19432686X-RAY DIFFRACTION100
3.0848-40.68830.19621480.18092810X-RAY DIFFRACTION100

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