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- PDB-6ojt: Crystal structure of Sphingomonas paucimobilis TMY1009 LsdA pheny... -

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Basic information

Entry
Database: PDB / ID: 6ojt
TitleCrystal structure of Sphingomonas paucimobilis TMY1009 LsdA phenylazophenol complex
ComponentsLignostilbene-alpha,beta-dioxygenase isozyme I
KeywordsOXIDOREDUCTASE / aromatic compound / lignostilbene / carotenoid cleavage oxygenase / lignin degradation / bacterial catabolism
Function / homology
Function and homology information


lignostilbene alphabeta-dioxygenase / lignostilbene alpha beta-dioxygenase activity / carotenoid dioxygenase activity / carotene catabolic process / lignin catabolic process / iron ion binding
Similarity search - Function
Carotenoid oxygenase / Retinal pigment epithelial membrane protein
Similarity search - Domain/homology
: / 4-Hydroxyazobenzene / Lignostilbene-alpha,beta-dioxygenase isozyme I
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsKuatsjah, E. / Verstraete, M.M. / Kobylarz, M.J. / Liu, A.K.N. / Murphy, M.E.P. / Eltis, L.D.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)171359 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)04802 Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase.
Authors: Kuatsjah, E. / Verstraete, M.M. / Kobylarz, M.J. / Liu, A.K.N. / Murphy, M.E.P. / Eltis, L.D.
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Lignostilbene-alpha,beta-dioxygenase isozyme I
A: Lignostilbene-alpha,beta-dioxygenase isozyme I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7586
Polymers108,2502
Non-polymers5084
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-16 kcal/mol
Surface area34200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.909, 181.909, 96.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lignostilbene-alpha,beta-dioxygenase isozyme I / LSD-I


Mass: 54124.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Plasmid: pET41b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q53353, lignostilbene alphabeta-dioxygenase
#2: Chemical ChemComp-NSL / 4-Hydroxyazobenzene / 4-[(E)-phenyldiazenyl]phenol


Mass: 198.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.25 Å3/Da / Density % sol: 71.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium fluoride, 17% PEG3350 (v/v), 1 mM phenylazophenol in DMF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3→90.95 Å / Num. obs: 34302 / % possible obs: 92.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 55.44 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.06 / Rrim(I) all: 0.14 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3-3.1550.47945720.8840.2360.53694.4
9.95-90.955.80.06910970.9960.0310.07699.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.18 Å61 Å
Translation6.18 Å61 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimless0.3.5data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→61.004 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 1649 4.84 %
Rwork0.2112 --
obs0.2127 34071 91.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→61.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7628 0 32 2 7662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027890
X-RAY DIFFRACTIONf_angle_d0.5910716
X-RAY DIFFRACTIONf_dihedral_angle_d2.5864620
X-RAY DIFFRACTIONf_chiral_restr0.0461098
X-RAY DIFFRACTIONf_plane_restr0.0051430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.08850.36711350.31892719X-RAY DIFFRACTION94
3.0885-3.18820.29031370.26792728X-RAY DIFFRACTION94
3.1882-3.30210.3241410.26772731X-RAY DIFFRACTION93
3.3021-3.43430.30911250.29932717X-RAY DIFFRACTION93
3.4343-3.59060.3211950.27412094X-RAY DIFFRACTION72
3.5906-3.77990.34841220.28232208X-RAY DIFFRACTION76
3.7799-4.01670.2758950.24642447X-RAY DIFFRACTION82
4.0167-4.32670.20781910.1832856X-RAY DIFFRACTION100
4.3267-4.7620.17331560.15522931X-RAY DIFFRACTION100
4.762-5.45070.21641520.15922939X-RAY DIFFRACTION100
5.4507-6.86580.20551460.18272990X-RAY DIFFRACTION100
6.8658-61.01630.20121540.17483062X-RAY DIFFRACTION100

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