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- PDB-6j87: Crystal structure of HinD with NMFT and NO -

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Basic information

Entry
Database: PDB / ID: 6j87
TitleCrystal structure of HinD with NMFT and NO
ComponentsNocardicin N-oxygenase
KeywordsOXIDOREDUCTASE / P450 / indolactam / oxidation / NMFT
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-B9L / PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Nocardicin N-oxygenase
Similarity search - Component
Biological speciesStreptoalloteichus hindustanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)97,8478
Polymers95,8512
Non-polymers1,9966
Water4,540252
1
A: Nocardicin N-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9244
Polymers47,9261
Non-polymers9983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-29 kcal/mol
Surface area16220 Å2
MethodPISA
2
B: Nocardicin N-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9244
Polymers47,9261
Non-polymers9983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-29 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.212, 155.029, 56.556
Angle α, β, γ (deg.)90.00, 115.54, 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-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#4: Chemical ChemComp-B9L / N-[(2S)-1-hydroxy-3-(1H-indol-3-yl)propan-2-yl]-Nalpha-methyl-L-phenylalaninamide


Mass: 351.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 39.43 %
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 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.472 Å / Num. obs: 33169 / % possible obs: 98 % / Redundancy: 2.9 % / CC1/2: 0.987 / Rmerge(I) obs: 0.106 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3239 / CC1/2: 0.693 / % possible all: 98

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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: 2.3→48.472 Å / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 37.49
RfactorNum. reflection% reflection
Rfree0.2586 2049 6.18 %
Rwork0.1781 --
obs0.1965 33139 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6204 0 142 252 6598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086508
X-RAY DIFFRACTIONf_angle_d1.1168908
X-RAY DIFFRACTIONf_dihedral_angle_d18.8982422
X-RAY DIFFRACTIONf_chiral_restr0.0511004
X-RAY DIFFRACTIONf_plane_restr0.0071156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3009-2.35850.39061510.2982287X-RAY DIFFRACTION92
2.3585-2.42220.38171360.29332162X-RAY DIFFRACTION92
2.4222-2.49350.43681450.28622225X-RAY DIFFRACTION92
2.4935-2.5740.4161410.27632229X-RAY DIFFRACTION92
2.574-2.6660.37241420.26052189X-RAY DIFFRACTION92
2.666-2.77270.38641430.24392226X-RAY DIFFRACTION92
2.7727-2.89880.34721430.22522244X-RAY DIFFRACTION92
2.8988-3.05160.35781380.20022215X-RAY DIFFRACTION92
3.0516-3.24280.3011440.18752221X-RAY DIFFRACTION92
3.2428-3.49310.23471420.16882135X-RAY DIFFRACTION88
3.4931-3.84440.23061390.14922186X-RAY DIFFRACTION90
3.8444-4.40030.23421430.12832242X-RAY DIFFRACTION93
4.4003-5.54220.1961470.14022259X-RAY DIFFRACTION93
5.5422-44.41260.25691450.1842295X-RAY DIFFRACTION94

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