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- PDB-6j83: Crystal structure of TleB with NMVT -

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Basic information

Entry
Database: PDB / ID: 6j83
TitleCrystal structure of TleB with NMVT
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / P450 / indolactam / oxidation / NMVT
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Chem-B9R / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces blastmyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFei, H. / Mori, T. / Abe, I.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Molecular basis for the P450-catalyzed C-N bond formation in indolactam biosynthesis.
Authors: He, F. / Mori, T. / Morita, I. / Nakamura, H. / Alblova, M. / Hoshino, S. / Awakawa, T. / Abe, I.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: 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: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9403
Polymers47,0211
Non-polymers9202
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-26 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.787, 84.761, 113.074
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 Cytochrome P-450


Mass: 47020.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces blastmyceticus (bacteria) / Gene: tleB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A077KEB8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-B9R / N-[(2S)-1-hydroxy-3-(1H-indol-3-yl)propan-2-yl]-N~2~-methyl-L-valinamide


Mass: 303.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES (pH 6.0) containing 1600 mM Na/Ka tartrate and 5% 1, 4-dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.034 Å / Num. obs: 31014 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.983 / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1941 / CC1/2: 0.898 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J82

6j82


Resolution: 1.9→47.034 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.9
RfactorNum. reflection% reflection
Rfree0.2163 2000 6.46 %
Rwork0.1729 --
obs0.1757 30954 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 0 65 331 3493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073235
X-RAY DIFFRACTIONf_angle_d0.9044409
X-RAY DIFFRACTIONf_dihedral_angle_d3.8681976
X-RAY DIFFRACTIONf_chiral_restr0.048495
X-RAY DIFFRACTIONf_plane_restr0.005572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.29571380.22442003X-RAY DIFFRACTION100
1.9475-2.00020.27581420.1992053X-RAY DIFFRACTION100
2.0002-2.0590.26031400.19592025X-RAY DIFFRACTION100
2.059-2.12550.2331420.18412059X-RAY DIFFRACTION100
2.1255-2.20150.24591400.1852023X-RAY DIFFRACTION100
2.2015-2.28960.24561410.18732045X-RAY DIFFRACTION100
2.2896-2.39380.2421420.18022042X-RAY DIFFRACTION100
2.3938-2.520.24971410.17662057X-RAY DIFFRACTION100
2.52-2.67790.21121430.18542065X-RAY DIFFRACTION100
2.6779-2.88460.21081430.17912064X-RAY DIFFRACTION100
2.8846-3.17480.21991430.17472068X-RAY DIFFRACTION100
3.1748-3.63410.20261460.16082113X-RAY DIFFRACTION100
3.6341-4.5780.17311440.14242103X-RAY DIFFRACTION100
4.578-47.04840.18251550.16322234X-RAY DIFFRACTION100

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