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- PDB-2vou: Structure of 2,6-dihydroxypyridine-3-hydroxylase from Arthrobacte... -

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Basic information

Entry
Database: PDB / ID: 2vou
TitleStructure of 2,6-dihydroxypyridine-3-hydroxylase from Arthrobacter nicotinovorans
Components2,6-DIHYDROXYPYRIDINE HYDROXYLASE
KeywordsOXIDOREDUCTASE / AROMATIC HYDROXYLASE / NICOTINE DEGRADATION / FLAVIN MONO-OXYGENASE / FAD-DEPENDENT HYDROXYLASE
Function / homology
Function and homology information


2,6-dihydroxypyridine 3-monooxygenase / 2,6-dihydroxypyridine 3-monooxygenase activity / nicotine catabolic process / FAD binding / flavin adenine dinucleotide binding / protein homodimerization activity
Similarity search - Function
D-Amino Acid Oxidase; Chain A, domain 2 - #60 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / 2,6-dihydroxypyridine 3-monooxygenase
Similarity search - Component
Biological speciesARTHROBACTER NICOTINOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsTreiber, N. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of 2,6-Dihydroxypyridine 3-Hydroxylase from a Nicotine-Degrading Pathway.
Authors: Treiber, N. / Schulz, G.E.
History
DepositionFeb 21, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,6-DIHYDROXYPYRIDINE HYDROXYLASE
B: 2,6-DIHYDROXYPYRIDINE HYDROXYLASE
C: 2,6-DIHYDROXYPYRIDINE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,09812
Polymers130,2883
Non-polymers2,8109
Water6,972387
1
A: 2,6-DIHYDROXYPYRIDINE HYDROXYLASE
hetero molecules

A: 2,6-DIHYDROXYPYRIDINE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7328
Polymers86,8592
Non-polymers1,8736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area1960 Å2
ΔGint-3.9 kcal/mol
Surface area38740 Å2
MethodPISA
2
B: 2,6-DIHYDROXYPYRIDINE HYDROXYLASE
C: 2,6-DIHYDROXYPYRIDINE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7328
Polymers86,8592
Non-polymers1,8736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-10 kcal/mol
Surface area37140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.960, 185.960, 104.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.5075, -0.79698, 0.32751), (-0.79748, 0.29051, -0.5288), (0.3263, -0.52955, -0.78301)
Vector: 150.55136, 138.27512, 110.59136)

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Components

#1: Protein 2,6-DIHYDROXYPYRIDINE HYDROXYLASE / 2 / 6-DIHYDROXYPYRIDINE-3-HYDROXYLASE / DHPH


Mass: 43429.449 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTHROBACTER NICOTINOVORANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q93NG3, 2,6-dihydroxypyridine 3-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 323 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 323 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 323 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 323 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 323 TO SER

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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: 4.02 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 6.6
Details: 0.1 M SODIUM CACODYLATE PH 6.6, 15% (W/V) PEG 8000, 200 MM MAGNESIUM ACETATE, 20% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0008
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0008 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 64088 / % possible obs: 99.7 % / Observed criterion σ(I): 2.4 / Redundancy: 4.9 % / Biso Wilson estimate: 66.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.8 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHARPphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.6→27.92 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 18.65 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3205 5 %RANDOM
Rwork0.185 ---
obs0.186 60887 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.04 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å2-1.49 Å20 Å2
2---2.98 Å20 Å2
3---4.47 Å2
Refinement stepCycle: LAST / Resolution: 2.6→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9014 0 189 387 9590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0219429
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.97412858
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20951164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6623.481428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.143151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6781569
X-RAY DIFFRACTIONr_chiral_restr0.1010.21388
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027290
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.24360
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.26513
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2590
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5581.55894
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93329302
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.52334129
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5154.53556
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: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 233
Rwork0.339 4439
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)
12.62-1.1787-0.80821.22720.5451.80470.44040.40720.3094-0.4829-0.2522-0.0693-0.1628-0.2381-0.1882-0.210.174-0.0068-0.29110.123-0.22436.738597.220938.8299
22.38950.19910.26832.1922-0.47271.64-0.2504-0.45090.17190.6189-0.1396-0.4535-0.52120.24860.390.14650.194-0.1975-0.11490.0759-0.138923.4782141.556445.8678
32.06510.54390.30422.5571-0.1571.7177-0.14930.3414-0.0617-0.7694-0.2394-1.08740.06740.52940.38870.14850.30620.40470.11430.26060.370740.8839136.43747.3697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 394
2X-RAY DIFFRACTION1A1395
3X-RAY DIFFRACTION2B2 - 388
4X-RAY DIFFRACTION2B1389
5X-RAY DIFFRACTION3C2 - 388
6X-RAY DIFFRACTION3C1389

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