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

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Basic information

Entry
Database: PDB / ID: 2bvh
TitleCrystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 2 (P21)
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: 2.9 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)198,8148
Polymers195,6724
Non-polymers3,1424
Water00
1
A: 6-HYDROXY-D-NICOTINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7042
Polymers48,9181
Non-polymers7861
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: 6-HYDROXY-D-NICOTINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7042
Polymers48,9181
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: 6-HYDROXY-D-NICOTINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7042
Polymers48,9181
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.320, 90.940, 104.440
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.53507, 0.0859, 0.84043), (0.23497, -0.94043, 0.24572), (0.81147, 0.32896, 0.48302)119.21603, 62.40942, -79.0088
3given(0.99721, -0.05173, 0.05379), (-0.04677, 0.99487, 0.08973), (-0.05816, 0.08697, -0.99451)138.75499, -1.89308, 27.0474
4given(0.46817, -0.19496, -0.86186), (0.09795, -0.95789, 0.2699), (-0.87819, -0.21078, -0.42936)25.78508, 66.93747, 105.60591

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Components

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


Mass: 48918.074 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 433 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 433 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 433 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 433 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 433 TO SER ENGINEERED RESIDUE IN CHAIN D, 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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.36 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9787
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.9→44.3 Å / Num. obs: 42084 / % possible obs: 98.9 % / Observed criterion σ(I): 4 / Redundancy: 3.1 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.7
Reflection shellResolution: 2.89→3.06 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6.2 / % possible all: 95.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→44.3 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2955351.72 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.297 2134 5 %RANDOM
Rwork0.274 ---
obs0.274 42286 99.7 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 14.437 Å2 / ksol: 0.290134 e/Å3
Displacement parametersBiso mean: 47.61 Å2
Baniso -1Baniso -2Baniso -3
1--9.08 Å20 Å218.78 Å2
2--2.22 Å20 Å2
3---6.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.9→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13596 0 212 0 13808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.553
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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