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- PDB-4p9s: Crystal structure of the mature form of rat DMGDH -

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Basic information

Entry
Database: PDB / ID: 4p9s
TitleCrystal structure of the mature form of rat DMGDH
ComponentsDimethylglycine dehydrogenase
KeywordsOXIDOREDUCTASE / dimethylglycine dehydrogenase / rat
Function / homology
Function and homology information


dimethylglycine dehydrogenase / dimethylglycine dehydrogenase activity / Choline catabolism / amino-acid betaine catabolic process / choline catabolic process / choline metabolic process / tetrahydrofolate interconversion / folic acid binding / flavin adenine dinucleotide binding / mitochondrial matrix ...dimethylglycine dehydrogenase / dimethylglycine dehydrogenase activity / Choline catabolism / amino-acid betaine catabolic process / choline catabolic process / choline metabolic process / tetrahydrofolate interconversion / folic acid binding / 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 / 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 / Dimethylglycine dehydrogenase / Dimethylglycine dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 4, 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
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / 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_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)191,9794
Polymers190,4082
Non-polymers1,5712
Water1,874104
1
A: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9902
Polymers95,2041
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9902
Polymers95,2041
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.211, 131.442, 171.924
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / 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: 2.3→40 Å / Num. all: 75192 / Num. obs: 75192 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.076 / Net I/σ(I): 13.7
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 6 % / Rsym value: 0.298 / Net I/σ(I) obs: 2.3 / % possible all: 85.5

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Processing

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

1pj5


Resolution: 2.32→40 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.855 / SU B: 11.357 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29479 1517 2 %RANDOM
Rwork0.25304 ---
obs0.25388 73606 89.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.831 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0 Å2
2--1.36 Å2-0 Å2
3----1.68 Å2
Refinement stepCycle: 1 / Resolution: 2.32→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12952 0 106 104 13162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01913400
X-RAY DIFFRACTIONr_bond_other_d0.0040.0212650
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9718208
X-RAY DIFFRACTIONr_angle_other_deg1.002329144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46151630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44723.77610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.158152236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6061586
X-RAY DIFFRACTIONr_chiral_restr0.0760.21958
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115082
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023086
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_it1.9242.9956526
X-RAY DIFFRACTIONr_mcbond_other1.9242.9946525
X-RAY DIFFRACTIONr_mcangle_it3.0034.4888154
X-RAY DIFFRACTIONr_mcangle_other3.0024.4898155
X-RAY DIFFRACTIONr_scbond_it1.873.1416874
X-RAY DIFFRACTIONr_scbond_other1.873.1416875
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0034.63310055
X-RAY DIFFRACTIONr_long_range_B_refined4.64823.5815362
X-RAY DIFFRACTIONr_long_range_B_other4.64623.58315355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 51340 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.32→2.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 94 -
Rwork0.324 4211 -
obs--70.77 %

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