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- PDB-6z4t: sperm whale myoglobin mutant (H64V V64A) bearing the non-canonica... -

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Basic information

Entry
Database: PDB / ID: 6z4t
Titlesperm whale myoglobin mutant (H64V V64A) bearing the non-canonical amino acid 2-Amino-3-(thiazol-5-yl)propanoic acid as axial heme ligand
ComponentsMyoglobin
KeywordsMETAL BINDING PROTEIN / Globin / Heme protein / Enzyme
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 / Globin family profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Myoglobin
Similarity search - Component
Biological speciesPhyseter macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 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 / Non-polymer description / 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 / entity_poly / pdbx_struct_conn_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.formula / _chem_comp.formula_weight / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
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)17,8893
Polymers17,2411
Non-polymers6482
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-19 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.009, 47.327, 76.897
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: 17240.977 Da / Num. of mol.: 1 / Mutation: H64V V68A H93(5ThzA)
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SPG 28-32% PEG 1500 180 nL protein 10mg/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: 1.000023 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000023 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 77274 / % possible obs: 94.2 % / Redundancy: 3.09 % / CC1/2: 0.999 / Net I/σ(I): 12.22
Reflection shellResolution: 1.23→1.3 Å / Num. unique obs: 9194 / CC1/2: 0.382

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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: 1.23→40.31 Å / SU ML: 0.1479 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1875 3828 4.96 %
Rwork0.15 73367 -
obs0.1519 77195 94.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.99 Å2
Refinement stepCycle: LAST / Resolution: 1.23→40.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 45 193 1453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561370
X-RAY DIFFRACTIONf_angle_d0.88471871
X-RAY DIFFRACTIONf_chiral_restr0.0639197
X-RAY DIFFRACTIONf_plane_restr0.0041233
X-RAY DIFFRACTIONf_dihedral_angle_d19.0408527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.250.3772720.39131360X-RAY DIFFRACTION46.43
1.25-1.260.36791020.35671902X-RAY DIFFRACTION66.49
1.26-1.280.38271030.32542135X-RAY DIFFRACTION74.06
1.28-1.30.31871300.30642438X-RAY DIFFRACTION83.38
1.3-1.320.31661340.2792672X-RAY DIFFRACTION93.04
1.32-1.340.3031390.2692753X-RAY DIFFRACTION95.07
1.34-1.360.27751450.24182745X-RAY DIFFRACTION97.7
1.36-1.380.24851470.23032850X-RAY DIFFRACTION97.12
1.38-1.410.24481530.21842876X-RAY DIFFRACTION99.31
1.41-1.440.28521540.20212867X-RAY DIFFRACTION99.18
1.44-1.460.22831450.19332814X-RAY DIFFRACTION99.3
1.46-1.50.18841530.18142874X-RAY DIFFRACTION99.21
1.5-1.530.25581500.16122874X-RAY DIFFRACTION99.67
1.53-1.570.21751520.15082887X-RAY DIFFRACTION99.93
1.57-1.610.17091540.13372850X-RAY DIFFRACTION99.67
1.61-1.660.21011510.13152891X-RAY DIFFRACTION99.84
1.66-1.710.15931470.13482864X-RAY DIFFRACTION99.74
1.71-1.770.18211490.13112886X-RAY DIFFRACTION99.64
1.77-1.850.15341510.13212862X-RAY DIFFRACTION99.83
1.85-1.930.18351540.12922870X-RAY DIFFRACTION99.54
1.93-2.030.17361500.12062873X-RAY DIFFRACTION99.77
2.03-2.160.16851490.12052889X-RAY DIFFRACTION99.61
2.16-2.330.17421460.11892854X-RAY DIFFRACTION99.67
2.33-2.560.16571530.13472876X-RAY DIFFRACTION99.51
2.56-2.930.17691500.13392872X-RAY DIFFRACTION99.47
2.93-3.690.15591430.12822862X-RAY DIFFRACTION99.31
3.69-40.310.17071520.15272871X-RAY DIFFRACTION99.44

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