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- PDB-6j88: Crystal structure of HinD with benzo[b]thiophen analog -

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Basic information

Entry
Database: PDB / ID: 6j88
TitleCrystal structure of HinD with benzo[b]thiophen analog
ComponentsNocardicin N-oxygenase
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
Chem-B9O / PROTOPORPHYRIN IX CONTAINING FE / Nocardicin N-oxygenase
Similarity search - Component
Biological speciesStreptoalloteichus hindustanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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: Nocardicin N-oxygenase
B: Nocardicin N-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7256
Polymers95,8512
Non-polymers1,8744
Water2,180121
1
A: Nocardicin N-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8633
Polymers47,9261
Non-polymers9372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-25 kcal/mol
Surface area16040 Å2
MethodPISA
2
B: Nocardicin N-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8633
Polymers47,9261
Non-polymers9372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-25 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.933, 150.354, 55.860
Angle α, β, γ (deg.)90.00, 115.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nocardicin N-oxygenase


Mass: 47925.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus hindustanus (bacteria)
Gene: SAMN05444320_102263 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M4Y7D5
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-B9O / N-[(2S)-1-(1-benzothiophen-3-yl)-3-hydroxypropan-2-yl]-N~2~-methyl-L-valinamide


Mass: 320.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24N2O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES (pH 6.5) containing 1200 mM (NH4)2HPO4 and 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.35→47.631 Å / Num. obs: 29547 / % possible obs: 98.1 % / Redundancy: 3 % / CC1/2: 0.947 / Rmerge(I) obs: 0.182 / Net I/σ(I): 3.1
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2923 / CC1/2: 0.456 / % possible all: 98.1

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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: 2.35→47.631 Å / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 24.48
RfactorNum. reflection% reflection
Rfree0.2392 2005 6.79 %
Rwork0.1657 --
obs0.1855 29518 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→47.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6204 0 130 121 6455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096496
X-RAY DIFFRACTIONf_angle_d1.2588896
X-RAY DIFFRACTIONf_dihedral_angle_d4.6593914
X-RAY DIFFRACTIONf_chiral_restr0.0631006
X-RAY DIFFRACTIONf_plane_restr0.0091154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3505-2.40920.28661450.21291957X-RAY DIFFRACTION92
2.4092-2.47440.32531310.21611930X-RAY DIFFRACTION91
2.4744-2.54720.28641390.2061990X-RAY DIFFRACTION92
2.5472-2.62940.2621370.20951919X-RAY DIFFRACTION90
2.6294-2.72340.26051440.20411955X-RAY DIFFRACTION91
2.7234-2.83240.27951410.19321957X-RAY DIFFRACTION92
2.8324-2.96130.25091470.18151992X-RAY DIFFRACTION92
2.9613-3.11740.28291390.17871964X-RAY DIFFRACTION92
3.1174-3.31260.27931430.18051959X-RAY DIFFRACTION92
3.3126-3.56830.25851410.17241977X-RAY DIFFRACTION92
3.5683-3.92730.22671460.16571962X-RAY DIFFRACTION91
3.9273-4.49520.23211430.14611977X-RAY DIFFRACTION91
4.4952-5.6620.20591410.15982000X-RAY DIFFRACTION92
5.662-47.64040.24151410.19711991X-RAY DIFFRACTION91

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