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- PDB-3gsi: Crystal structure of D552A dimethylglycine oxidase mutant of Arth... -

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Basic information

Entry
Database: PDB / ID: 3gsi
TitleCrystal structure of D552A dimethylglycine oxidase mutant of Arthrobacter globiformis in complex with tetrahydrofolate
ComponentsN,N-dimethylglycine oxidase
KeywordsOXIDOREDUCTASE / Channelling / FAD binding / folinic acid / folate binding / amine oxidation
Function / homology
Function and homology information


dimethylglycine oxidase / dimethylglycine oxidase activity / nucleotide binding / cytosol
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
FLAVIN-ADENINE DINUCLEOTIDE / (6S)-5,6,7,8-TETRAHYDROFOLATE / Dimethylglycine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsTralau, T. / Lafite, P. / Levy, C. / Combe, J.P. / Scrutton, N.S. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: An internal reaction chamber in dimethylglycine oxidase provides efficient protection from exposure to toxic formaldehyde.
Authors: Tralau, T. / Lafite, P. / Levy, C. / Combe, J.P. / Scrutton, N.S. / Leys, D.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,9974
Polymers89,7421
Non-polymers1,2553
Water19,4561080
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)363,99016
Polymers358,9694
Non-polymers5,02112
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
Buried area8490 Å2
ΔGint-29.5 kcal/mol
Surface area113920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.215, 224.548, 119.382
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-1296-

HOH

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Components

#1: Protein N,N-dimethylglycine oxidase


Mass: 89742.125 Da / Num. of mol.: 1 / Mutation: D552A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: dmg / Plasmid: pEH1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9AGP8, dimethylglycine oxidase
#2: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FAD / 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


Mass: 18.015 Da / Num. of mol.: 1080 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG MME 5000, 0.1M Hepes pH 7.5, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2→39.809 Å / Num. obs: 62960 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameClassification
DNAdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→39.794 Å / SU ML: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.2015 3193 5.07 %
Rwork0.1502 --
obs0.1529 62960 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.433 Å2 / ksol: 0.362 e/Å3
Refinement stepCycle: LAST / Resolution: 2→39.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 86 1080 7436
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02990.22541210.168253795
2.0299-2.06160.25611220.166254195
2.0616-2.09540.21931360.1598253795
2.0954-2.13150.21981460.153247895
2.1315-2.17030.21921380.1493253795
2.1703-2.2120.21571440.1472252196
2.212-2.25720.22611520.1519251495
2.2572-2.30620.21971400.1465253595
2.3062-2.35990.20191440.1453253396
2.3599-2.41890.22661360.1433252195
2.4189-2.48430.19061220.1538256896
2.4843-2.55740.24541230.1544257296
2.5574-2.63990.23711580.1546255596
2.6399-2.73420.23421310.161258596
2.7342-2.84370.22151260.1659260197
2.8437-2.9730.22291350.1645261698
2.973-3.12970.21041260.1666264998
3.1297-3.32570.20611560.15782664100
3.3257-3.58240.16431560.13772689100
3.5824-3.94260.16041470.1272696100
3.9426-4.51240.1591470.11782722100
4.5124-5.68250.16281450.13492755100
5.6825-39.80170.19791420.1603284198

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