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- PDB-6j82: Crystal structure of TleB apo -

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Basic information

Entry
Database: PDB / ID: 6j82
TitleCrystal structure of TleB apo
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / P450 / indolactam / oxidation
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces blastmyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsAlblova, M. / Nakamura, 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)47,6372
Polymers47,0211
Non-polymers6161
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-26 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.712, 84.758, 113.124
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 / TleB


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 39.24 %
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: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.05 Å / Num. obs: 20062 / % possible obs: 99.8 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Net I/σ(I): 14.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1650 / CC1/2: 0.866 / % possible all: 97.6

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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: 3WVS

3wvs


Resolution: 2.202→47.048 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.78
RfactorNum. reflection% reflection
Rfree0.2364 1999 9.99 %
Rwork0.1681 --
obs0.1749 20008 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.202→47.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 0 43 243 3383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073212
X-RAY DIFFRACTIONf_angle_d0.8694378
X-RAY DIFFRACTIONf_dihedral_angle_d3.891954
X-RAY DIFFRACTIONf_chiral_restr0.047492
X-RAY DIFFRACTIONf_plane_restr0.006570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2024-2.25740.29231360.1981225X-RAY DIFFRACTION97
2.2574-2.31850.27521400.18991268X-RAY DIFFRACTION100
2.3185-2.38670.28481390.19051255X-RAY DIFFRACTION100
2.3867-2.46370.29991430.18971286X-RAY DIFFRACTION100
2.4637-2.55180.29661370.18881230X-RAY DIFFRACTION100
2.5518-2.65390.24081450.19161308X-RAY DIFFRACTION100
2.6539-2.77470.26291390.18571252X-RAY DIFFRACTION100
2.7747-2.9210.27421430.1861287X-RAY DIFFRACTION100
2.921-3.1040.25551430.1791279X-RAY DIFFRACTION100
3.104-3.34360.24371430.17881296X-RAY DIFFRACTION100
3.3436-3.67990.22631420.15321281X-RAY DIFFRACTION100
3.6799-4.21210.20431460.14721306X-RAY DIFFRACTION100
4.2121-5.30570.17731470.13741328X-RAY DIFFRACTION100
5.3057-47.05860.21311560.16251408X-RAY DIFFRACTION100

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