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- PDB-4paa: Crystal structure of the mature form of rat DMGDH complexed with ... -

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Basic information

Entry
Database: PDB / ID: 4paa
TitleCrystal structure of the mature form of rat DMGDH complexed with tetrahydrofolate
ComponentsDimethylglycine dehydrogenase
KeywordsOXIDOREDUCTASE / dimethylglycine dehydrogenase / rat / tetrahydrofolate
Function / homology
Function and homology information


dimethylglycine dehydrogenase / dimethylglycine dehydrogenase activity / Choline catabolism / amino-acid betaine catabolic process / choline catabolic process / choline metabolic process / folic acid binding / tetrahydrofolate interconversion / flavin adenine dinucleotide binding / mitochondrial matrix ...dimethylglycine dehydrogenase / dimethylglycine dehydrogenase activity / Choline catabolism / amino-acid betaine catabolic process / choline catabolic process / choline metabolic process / folic acid binding / tetrahydrofolate interconversion / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / cytoplasm
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 / GCVT N-terminal 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 dehydrogenase, mitochondrial / Dimethylglycine dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsLuka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Newcomer, M.E. / Wagner, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK15289 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Folate in demethylation: The crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate.
Authors: Luka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Newcomer, M.E. / Wagner, C.
History
DepositionApr 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / struct_site_gen
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _struct_site_gen.id
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.6Oct 23, 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: Dimethylglycine dehydrogenase
B: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,8706
Polymers190,4082
Non-polymers2,4624
Water4,252236
1
A: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4353
Polymers95,2041
Non-polymers1,2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4353
Polymers95,2041
Non-polymers1,2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.934, 130.661, 171.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 38 - 853 / Label seq-ID: 19 - 834

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Dimethylglycine dehydrogenase / Dimethylglycine dehydrogenase / mitochondrial


Mass: 95204.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dmgdh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5RKL4, UniProt: Q63342*PLUS, dimethylglycine dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M K/Na-tartrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. all: 87235 / Num. obs: 87235 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.061 / Net I/σ(I): 11.7
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 1.9 / % possible all: 90.6

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJ5

1pj5


Resolution: 2.26→40 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.875 / SU B: 8.928 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26739 1743 2 %RANDOM
Rwork0.24075 ---
obs0.24128 85428 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.719 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å20 Å2
2--1.14 Å2-0 Å2
3----1.66 Å2
Refinement stepCycle: 1 / Resolution: 2.26→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12952 0 170 236 13358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01913468
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212692
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.97518302
X-RAY DIFFRACTIONr_angle_other_deg0.882329238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79951630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1123.77610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.306152236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2531586
X-RAY DIFFRACTIONr_chiral_restr0.0640.21962
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115170
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023120
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0482.5166530
X-RAY DIFFRACTIONr_mcbond_other1.0472.5156527
X-RAY DIFFRACTIONr_mcangle_it1.7713.7698156
X-RAY DIFFRACTIONr_mcangle_other1.7713.7698156
X-RAY DIFFRACTIONr_scbond_it0.9982.6196938
X-RAY DIFFRACTIONr_scbond_other0.9982.6196936
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7343.87110146
X-RAY DIFFRACTIONr_long_range_B_refined3.14719.61415462
X-RAY DIFFRACTIONr_long_range_B_other3.13319.6315420
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 51727 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 110 -
Rwork0.353 5423 -
obs--84.42 %

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