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- PDB-1pj7: Structure of dimethylglycine oxidase of Arthrobacter globiformis ... -

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Basic information

Entry
Database: PDB / ID: 1pj7
TitleStructure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folinic acid
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
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 / Chem-FFO / Dimethylglycine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 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
Revision 1.3Oct 3, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)91,3574
Polymers90,0751
Non-polymers1,2823
Water14,016778
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)365,43016
Polymers360,3024
Non-polymers5,12812
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)70.621, 223.740, 119.371
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-3331-

HOH

21A-3354-

HOH

DetailsDMGO is a tetramer (dimer of dimers) formed by applying 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-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7
#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.: 778 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG 2000MME, 0.2M 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 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: 2.1→20 Å / Num. all: 46564 / Num. obs: 46564 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.2
Reflection shellResolution: 2.1→2.15 Å / % possible all: 84.5
Reflection
*PLUS
Reflection shell
*PLUS
Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1PJ6

1pj6


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.568 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22172 2482 5.1 %RANDOM
Rwork0.15934 ---
all0.16253 46564 --
obs0.16253 46564 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: 33.336 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 88 778 7103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0216478
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9698837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5225826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.77115971
X-RAY DIFFRACTIONr_chiral_restr0.1280.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024961
X-RAY DIFFRACTIONr_nbd_refined0.2280.23321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2722
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3530.234
X-RAY DIFFRACTIONr_mcbond_it1.0371.54100
X-RAY DIFFRACTIONr_mcangle_it1.78626557
X-RAY DIFFRACTIONr_scbond_it3.23832378
X-RAY DIFFRACTIONr_scangle_it4.964.52280
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.274 163
Rwork0.201 3178
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.837
LS refinement shell
*PLUS
Rfactor Rwork: 0.2

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