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- PDB-6g5b: Heme-carbene complex in myoglobin H64V/V68A containing an N-methy... -

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Basic information

Entry
Database: PDB / ID: 6g5b
TitleHeme-carbene complex in myoglobin H64V/V68A containing an N-methylhistidine as the proximal ligand, 1.6 angstrom resolution
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / Myoglobin / Heme / N-methylhistidine
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
ETHYL ACETATE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTinzl, M. / Hayashi, T. / Mori, T. / Hilvert, D.
CitationJournal: Nat Catal / Year: 2018
Title: Capture and characterization of a reactive haem-carbenoid complex in an artificial metalloenzyme
Authors: Hayashi, T. / Tinzl, M. / Mori, T. / Krengel, U. / Proppe, J. / Soetbeer, J. / Klose, D. / Jeschke, G. / Reiher, M. / Hilvert, D.
History
DepositionMar 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)19,0473
Polymers18,3421
Non-polymers7052
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-12 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.873, 47.981, 77.426
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: 18342.160 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-EEE / ETHYL ACETATE / Ethyl acetate


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.02 Å3/Da / Density % sol: 39.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SPG buffer at pH6.8-7.2 containing 28-32% (w/v) 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: Sep 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→48 Å / Num. obs: 20198 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.747 / Num. unique obs: 955 / CC1/2: 0.749 / % possible all: 99.9

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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: 6F17

6f17


Resolution: 1.6→40.785 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.75
RfactorNum. reflection% reflection
Rfree0.2154 1999 9.92 %
Rwork0.1737 --
obs0.1779 20156 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→40.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 49 153 1418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111343
X-RAY DIFFRACTIONf_angle_d1.0251825
X-RAY DIFFRACTIONf_dihedral_angle_d18.894502
X-RAY DIFFRACTIONf_chiral_restr0.051190
X-RAY DIFFRACTIONf_plane_restr0.005226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.3181380.26661256X-RAY DIFFRACTION100
1.64-1.68440.30781430.23941296X-RAY DIFFRACTION100
1.6844-1.73390.29641390.21431263X-RAY DIFFRACTION100
1.7339-1.78990.25511410.20391278X-RAY DIFFRACTION100
1.7899-1.85390.24311400.20021269X-RAY DIFFRACTION100
1.8539-1.92810.23221410.16991284X-RAY DIFFRACTION100
1.9281-2.01580.25531430.17341293X-RAY DIFFRACTION100
2.0158-2.12210.18781410.17281286X-RAY DIFFRACTION100
2.1221-2.25510.20511430.16251287X-RAY DIFFRACTION100
2.2551-2.42920.22051430.16581304X-RAY DIFFRACTION100
2.4292-2.67360.21941440.16751311X-RAY DIFFRACTION100
2.6736-3.06030.19761440.18081305X-RAY DIFFRACTION100
3.0603-3.85520.17491440.16181313X-RAY DIFFRACTION98
3.8552-40.79790.21811550.16241412X-RAY DIFFRACTION100

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