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- PDB-6zyl: non-heme monooxygenase; ThoJ apo -

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Basic information

Entry
Database: PDB / ID: 6zyl
Titlenon-heme monooxygenase; ThoJ apo
ComponentsUncharacterized protein
KeywordsMETAL BINDING PROTEIN / non-heme deoxygenate / ThoJ
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding / L(+)-TARTARIC ACID / Phytanoyl-CoA dioxygenase
Function and homology information
Biological speciesStreptomyces malaysiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKoehnke, J. / Sikandar, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO4116_3_1 Germany
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Non-Heme Monooxygenase ThoJ Catalyzes Thioholgamide beta-Hydroxylation.
Authors: Sikandar, A. / Lopatniuk, M. / Luzhetskyy, A. / Koehnke, J.
History
DepositionAug 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7282
Polymers33,5781
Non-polymers1501
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint2 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.517, 80.517, 130.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-635-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 33578.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces malaysiense (bacteria) / Gene: VT52_024865
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1J4PXK4
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.72 Å3/Da / Density % sol: 66.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 150 mM Sodium tartrate, 28% (w/v) PEG 3350, 10% (v/v) 2.0 M NDSB-221

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.09→42.85 Å / Num. obs: 26006 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.996 / Net I/σ(I): 9.8
Reflection shellResolution: 2.09→2.15 Å / Num. unique obs: 1981 / CC1/2: 0.788

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data reduction
SCALAdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NCJ

5ncj


Resolution: 2.09→42.85 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 1259 4.85 %
Rwork0.1768 --
obs0.1782 25949 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 10 242 2247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042062
X-RAY DIFFRACTIONf_angle_d0.6632813
X-RAY DIFFRACTIONf_dihedral_angle_d5.198286
X-RAY DIFFRACTIONf_chiral_restr0.042316
X-RAY DIFFRACTIONf_plane_restr0.004373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.170.26281450.22982694X-RAY DIFFRACTION100
2.17-2.270.23561420.2122695X-RAY DIFFRACTION100
2.27-2.390.24161490.19752685X-RAY DIFFRACTION100
2.39-2.540.22781120.18272736X-RAY DIFFRACTION100
2.54-2.740.20881470.18732707X-RAY DIFFRACTION100
2.74-3.010.23591470.18472724X-RAY DIFFRACTION100
3.01-3.450.18891330.17032760X-RAY DIFFRACTION100
3.45-4.350.18051460.15062783X-RAY DIFFRACTION100
4.35-42.850.19671380.17322906X-RAY DIFFRACTION98

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