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- PDB-6m8f: Engineered sperm whale myoglobin-based carbene transferase -

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Basic information

Entry
Database: PDB / ID: 6m8f
TitleEngineered sperm whale myoglobin-based carbene transferase
ComponentsMyoglobin
KeywordsTRANSFERASE / Metalloprotein / myoglobin / carbene transferase / cyclopropanation / 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 / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
sucrose / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsBacik, J.P. / Ando, N. / Fasan, R.
CitationJournal: Acs Catalysis / Year: 2019
Title: Origin of high stereocontrol in olefin cyclopropanation catalyzed by an engineered carbene transferase.
Authors: Tinoco, A. / Wei, Y. / Bacik, J.P. / Carminati, D.M. / Moore, E.J. / Ando, N. / Zhang, Y. / Fasan, R.
History
DepositionAug 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5456
Polymers17,2981
Non-polymers1,2475
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.780, 90.780, 45.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-492-

HOH

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Components

#1: Protein Myoglobin


Mass: 17298.094 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: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 224 / 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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: A crystal was grown by mixing 1 ul of reservoir buffer (2 M ammonium sulfate, 0.2 M Tris pH 8.6) with 1 ul of protein in buffer (20 mM Tris pH 8.0, 1 mM EDTA). The crystal was cryoprotected ...Details: A crystal was grown by mixing 1 ul of reservoir buffer (2 M ammonium sulfate, 0.2 M Tris pH 8.6) with 1 ul of protein in buffer (20 mM Tris pH 8.0, 1 mM EDTA). The crystal was cryoprotected by soaking it in a drop containing reservoir buffer supplemented with 25% sucrose for 5 minutes prior to being flash-cooled in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 1.1→39.43 Å / Num. obs: 76057 / % possible obs: 87.7 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.025 / Net I/σ(I): 13.5
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.448 / Num. unique obs: 5028 / CC1/2: 0.617 / Rpim(I) all: 0.407 / % possible all: 40.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JW8

1jw8


Resolution: 1.1→32.163 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1458 3765 4.95 %
Rwork0.1263 --
obs0.1273 76038 87.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→32.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 81 224 1521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081408
X-RAY DIFFRACTIONf_angle_d1.1341919
X-RAY DIFFRACTIONf_dihedral_angle_d29.707524
X-RAY DIFFRACTIONf_chiral_restr0.076203
X-RAY DIFFRACTIONf_plane_restr0.006230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11390.3356350.322595X-RAY DIFFRACTION20
1.1139-1.12860.3029480.27531107X-RAY DIFFRACTION36
1.1286-1.14410.2604670.26851433X-RAY DIFFRACTION47
1.1441-1.16040.2407970.23311735X-RAY DIFFRACTION58
1.1604-1.17770.23741250.2132072X-RAY DIFFRACTION68
1.1777-1.19610.22261150.19542286X-RAY DIFFRACTION75
1.1961-1.21570.21231110.18772479X-RAY DIFFRACTION82
1.2157-1.23670.22171450.17172667X-RAY DIFFRACTION87
1.2367-1.25920.20091710.15692840X-RAY DIFFRACTION94
1.2592-1.28340.14821590.13522978X-RAY DIFFRACTION98
1.2834-1.30960.15891340.12752989X-RAY DIFFRACTION98
1.3096-1.33810.14851650.11793059X-RAY DIFFRACTION100
1.3381-1.36920.12241560.11073040X-RAY DIFFRACTION100
1.3692-1.40350.13751270.11123069X-RAY DIFFRACTION100
1.4035-1.44140.11811410.11283072X-RAY DIFFRACTION100
1.4414-1.48380.11321490.10663047X-RAY DIFFRACTION100
1.4838-1.53170.14261610.0993072X-RAY DIFFRACTION100
1.5317-1.58650.11581390.10063082X-RAY DIFFRACTION100
1.5865-1.650.11691900.10843012X-RAY DIFFRACTION100
1.65-1.72510.13811480.10683065X-RAY DIFFRACTION100
1.7251-1.8160.14611500.11043098X-RAY DIFFRACTION100
1.816-1.92980.12211590.11053042X-RAY DIFFRACTION100
1.9298-2.07880.12071720.11493063X-RAY DIFFRACTION100
2.0788-2.28790.12471510.10593077X-RAY DIFFRACTION100
2.2879-2.61880.13111830.11313056X-RAY DIFFRACTION100
2.6188-3.29890.15132090.12913063X-RAY DIFFRACTION100
3.2989-32.17650.16121580.14343175X-RAY DIFFRACTION100

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