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- PDB-6z4r: sperm whale myoglobin mutant (H64V V64A) bearing the non-canonica... -

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Basic information

Entry
Database: PDB / ID: 6z4r
Titlesperm whale myoglobin mutant (H64V V64A) bearing the non-canonical amino acid 3-thienylalanine as axial heme ligand
ComponentsMyoglobin
KeywordsMETAL BINDING PROTEIN / Globin / Heme protein / Enzyme
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
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsTinzl, M. / Hilvert, D. / Mittl, P.R.E.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Noncanonical Heme Ligands Steer Carbene Transfer Reactivity in an Artificial Metalloenzyme*.
Authors: Pott, M. / Tinzl, M. / Hayashi, T. / Ota, Y. / Dunkelmann, D. / Mittl, P.R.E. / Hilvert, D.
History
DepositionMay 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Sep 13, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)17,8712
Polymers17,2541
Non-polymers6161
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-19 kcal/mol
Surface area7630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.063, 47.260, 76.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Myoglobin


Mass: 17254.016 Da / Num. of mol.: 1 / Mutation: H64V V68A H93(3ThiA)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter macrocephalus (sperm whale) / Gene: MB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SPG buffer 28-32% PEG 1500 180 nL protein 10 mg/mL + 20 nL seed 100 nL well solution
PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000031 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 20069 / % possible obs: 99.3 % / Redundancy: 6.77 % / CC1/2: 0.996 / Net I/σ(I): 8.16
Reflection shellResolution: 1.96→2.08 Å / Num. unique obs: 3194 / CC1/2: 0.731 / % possible all: 98

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.16_3549model building
PHENIX1.16_3549phasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G5T

6g5t


Resolution: 1.96→40.16 Å / SU ML: 0.2898 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5172
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2683 990 4.96 %
Rwork0.2192 18976 -
obs0.2216 19966 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.31 Å2
Refinement stepCycle: LAST / Resolution: 1.96→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 43 63 1322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411293
X-RAY DIFFRACTIONf_angle_d1.08731751
X-RAY DIFFRACTIONf_chiral_restr0.0405183
X-RAY DIFFRACTIONf_plane_restr0.0047215
X-RAY DIFFRACTIONf_dihedral_angle_d19.8101472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.060.38011410.34982679X-RAY DIFFRACTION97.71
2.06-2.190.3511430.31222716X-RAY DIFFRACTION98.89
2.19-2.360.32911410.29872682X-RAY DIFFRACTION98.29
2.36-2.60.29031430.2282708X-RAY DIFFRACTION99.65
2.6-2.970.2611450.20562729X-RAY DIFFRACTION99.62
2.97-3.740.20031380.18272727X-RAY DIFFRACTION99.93
3.74-40.160.25171390.18422735X-RAY DIFFRACTION99.65

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