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- PDB-7qr6: Stilbene dioxygenase (NOV1) from Novosphingobium aromaticivorans:... -

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Basic information

Entry
Database: PDB / ID: 7qr6
TitleStilbene dioxygenase (NOV1) from Novosphingobium aromaticivorans: Ser283Phe mutant
ComponentsDioxygenase
KeywordsOXIDOREDUCTASE / Iron / Dioxygenase / Biocatalysis / Carotenoid Cleavage Oxygenases / Non-heme iron proteins / Biorefinery / Lignin valorization / Thermostability
Function / homologycarotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / metal ion binding / : / OXYGEN MOLECULE / Dioxygenase
Function and homology information
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAlvigini, L. / Mattevi, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission837890 (SMARTBOX)European Union
CitationJournal: Biochemistry / Year: 2023
Title: Rationally Guided Improvement of NOV1 Dioxygenase for the Conversion of Lignin-Derived Isoeugenol to Vanillin.
Authors: De Simone, M. / Alvigini, L. / Alonso-Cotchico, L. / Brissos, V. / Caroli, J. / Lucas, M.F. / Monza, E. / Melo, E.P. / Mattevi, A. / Martins, L.O.
History
DepositionJan 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dioxygenase
B: Dioxygenase
C: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,8979
Polymers166,6343
Non-polymers2646
Water27015
1
A: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6323
Polymers55,5451
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6323
Polymers55,5451
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6323
Polymers55,5451
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.471, 187.984, 105.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHELEULEUAA10 - 48710 - 487
21PHEPHELEULEUBB10 - 48710 - 487
12PHEPHELEULEUAA10 - 48710 - 487
22PHEPHELEULEUCC10 - 48710 - 487
13PROPROALAALABB5 - 4885 - 488
23PROPROALAALACC5 - 4885 - 488

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Dioxygenase


Mass: 55544.574 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199
Gene: Saro_0802
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: Q2GA76, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: sitting drop vapour diffusion, 0.16 M MgCl2, 0.08 M Tris/HCl pH 8.5, 18% wt/vol PEG 4000, and 20% vol/vol glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999977 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999977 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 36348 / % possible obs: 91.9 % / Redundancy: 3.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.079 / Rrim(I) all: 0.146 / Rsym value: 0.092 / Net I/σ(I): 6.1
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.917 / Num. unique obs: 4697 / CC1/2: 0.302 / Rpim(I) all: 0.627 / Rrim(I) all: 1.121 / Rsym value: 0.731 / % possible all: 97.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J55

5j55


Resolution: 2.9→49.04 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.872 / SU B: 24.56 / SU ML: 0.437 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1698 4.7 %RANDOM
Rwork0.2141 ---
obs0.2178 34650 91.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 175.35 Å2 / Biso mean: 67.13 Å2 / Biso min: 34.13 Å2
Baniso -1Baniso -2Baniso -3
1-6.1 Å2-0 Å2-0 Å2
2---3.77 Å2-0 Å2
3----2.33 Å2
Refinement stepCycle: final / Resolution: 2.9→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11322 0 9 15 11346
Biso mean--55.55 50.08 -
Num. residues----1422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311689
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710381
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.64515859
X-RAY DIFFRACTIONr_angle_other_deg1.1961.57824093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.04651421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77822.23677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.446151838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7491578
X-RAY DIFFRACTIONr_chiral_restr0.060.21457
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022662
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A146610.15
12B146610.15
21A142240.18
22C142240.18
31B143420.17
32C143420.17
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 135 -
Rwork0.341 2703 -
all-2838 -
obs--97.39 %

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