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- PDB-1pj5: Crystal structure of dimethylglycine oxidase of Arthrobacter glob... -

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Basic information

Entry
Database: PDB / ID: 1pj5
TitleCrystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with acetate
ComponentsN,N-dimethylglycine oxidase
KeywordsOXIDOREDUCTASE / Channelling / FAD binding / folate binding / amine oxidase
Function / homology
Function and homology information


dimethylglycine oxidase / dimethylglycine oxidase activity / nucleotide binding
Similarity search - Function
FAD dependent oxidoreductase, central domain / FAD dependent oxidoreductase central domain / Aminomethyltransferase beta-barrel domains / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain ...FAD dependent oxidoreductase, central domain / FAD dependent oxidoreductase central domain / Aminomethyltransferase beta-barrel domains / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / Aminomethyltransferase folate-binding domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / Gyrase A; domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Dimethylglycine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.61 Å
AuthorsLeys, D. / Basran, J. / Scrutton, N.S.
CitationJournal: Embo J. / Year: 2003
Title: Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase.
Authors: Leys, D. / Basran, J. / Scrutton, N.S.
History
DepositionJun 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N,N-dimethylglycine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9434
Polymers90,0751
Non-polymers8683
Water31,3461740
1
A: N,N-dimethylglycine oxidase
hetero molecules

A: N,N-dimethylglycine oxidase
hetero molecules

A: N,N-dimethylglycine oxidase
hetero molecules

A: N,N-dimethylglycine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,77216
Polymers360,3024
Non-polymers3,47012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)71.381, 226.680, 120.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-2280-

HOH

21A-2649-

HOH

31A-2661-

HOH

41A-2833-

HOH

51A-3478-

HOH

61A-3544-

HOH

71A-3612-

HOH

81A-3725-

HOH

DetailsThe molecule is a tetramer (dimer of dimers) generated by the 222 point symmetry of the C222 spacegroup.

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Components

#1: Protein N,N-dimethylglycine oxidase


Mass: 90075.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AGP8, dimethylglycine oxidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1740 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15 % PEG 2000MME, 0.2 M MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
215 %PEG5000 MME1reservoir
30.2 M1reservoirpH7.5MgCl2
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2002
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 114767 / Num. obs: 114767 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.4
Reflection shellResolution: 1.6→1.65 Å / % possible all: 96.8
Reflection
*PLUS
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.61→14.99 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.572 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19825 6074 5 %RANDOM
Rwork0.15997 ---
all0.1619 114766 --
obs0.1619 114766 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.994 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.61→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6299 0 58 1740 8097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216507
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9658866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.794151004
X-RAY DIFFRACTIONr_chiral_restr0.1180.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024985
X-RAY DIFFRACTIONr_nbd_refined0.2140.23058
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.21156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.2111
X-RAY DIFFRACTIONr_mcbond_it0.9711.54099
X-RAY DIFFRACTIONr_mcangle_it1.6826560
X-RAY DIFFRACTIONr_scbond_it2.77332408
X-RAY DIFFRACTIONr_scangle_it4.534.52306
LS refinement shellResolution: 1.61→1.646 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 364
Rwork0.287 7086
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.578
LS refinement shell
*PLUS
Rfactor Rfree: 0.3 / Rfactor Rwork: 0.28

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