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- PDB-2bvf: Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacte... -

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Basic information

Entry
Database: PDB / ID: 2bvf
TitleCrystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 3 (P1)
Components6-HYDROXY-D-NICOTINE OXIDASE
KeywordsOXIDASE / AUTOFLAVINYLATION / ENANTIOMERIC SUBSTRATES / FLAVOENZYMES / NICOTINE DEGRADATION
Function / homology
Function and homology information


(R)-6-hydroxynicotine oxidase / (R)-6-hydroxynicotine oxidase activity / nicotine catabolic process / alkaloid metabolic process / FAD binding / cytoplasm
Similarity search - Function
: / Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 ...: / Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / (R)-6-hydroxynicotine oxidase
Similarity search - Component
Biological speciesARTHROBACTER NICOTINOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsKoetter, J.W.A. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of 6-Hydroxy-D-Nicotine Oxidase from Arthrobacter Nicotinovorans.
Authors: Koetter, J.W.A. / Schulz, G.E.
History
DepositionJun 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-HYDROXY-D-NICOTINE OXIDASE
B: 6-HYDROXY-D-NICOTINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4074
Polymers97,8362
Non-polymers1,5712
Water19,6361090
1
A: 6-HYDROXY-D-NICOTINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7042
Polymers48,9181
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 6-HYDROXY-D-NICOTINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7042
Polymers48,9181
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.527, 62.398, 73.351
Angle α, β, γ (deg.)89.56, 85.29, 73.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 6-HYDROXY-D-NICOTINE OXIDASE


Mass: 48918.074 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FAD COVALENTLY BOUND TO H 72 / Source: (gene. exp.) ARTHROBACTER NICOTINOVORANS (bacteria) / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GAG1, (R)-6-hydroxynicotine oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1090 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 433 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 433 TO SER
Has protein modificationY
Sequence detailsMUTATION C433S

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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: 2.7 Å3/Da / Density % sol: 53.6 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.843
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.9→70 Å / Num. obs: 76158 / % possible obs: 95.9 % / Observed criterion σ(I): 4 / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.19
Reflection shellResolution: 1.91→1.99 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→73.13 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.496 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2286 3 %RANDOM
Rwork0.169 ---
obs0.17 73871 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.84 Å21.87 Å2
2---1.23 Å21.18 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.92→73.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6798 0 106 1090 7994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227059
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9859606
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67523.725306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.803151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5821556
X-RAY DIFFRACTIONr_chiral_restr0.2240.21072
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025422
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.23884
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24912
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2994
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6841.54579
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11927140
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.78132825
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8014.52466
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 152 -
Rwork0.233 4922 -
obs--86.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.72270.2298-1.01311.3899-0.5371.66890.022-0.0933-0.00510.0371-0.04340.00920.0190.19980.0214-0.0665-0.0024-0.0101-0.0589-0.0047-0.083942.94450.61254.214
21.33380.4828-0.49231.3612-0.4920.9759-0.06460.005-0.0658-0.01120.12830.23080.04440.0108-0.0637-0.08310.01990.0353-0.13360.01310.034220.34438.98763.803
31.0771-0.0513-0.84251.2775-0.4312.1123-0.0357-0.20510.06110.11570.042-0.0315-0.03140.1855-0.0062-0.0706-0.0227-0.0527-0.0161-0.0359-0.079563.7266.97122.827
41.26210.0443-0.62031.3162-0.99142.1735-0.03490.11540.2008-0.19650.10750.00010.0256-0.1475-0.0725-0.0419-0.0273-0.0547-0.0859-0.0191-0.06764.22774.592-3.277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 205
2X-RAY DIFFRACTION1A412 - 457
3X-RAY DIFFRACTION2A206 - 411
4X-RAY DIFFRACTION3B4 - 205
5X-RAY DIFFRACTION3B412 - 457
6X-RAY DIFFRACTION4B206 - 411

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