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- PDB-4pab: Crystal structure of the precursor form of rat DMGDH complexed wi... -

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Basic information

Entry
Database: PDB / ID: 4pab
TitleCrystal structure of the precursor 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 / 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 / THIOCYANATE ION / (6S)-5,6,7,8-TETRAHYDROFOLATE / Dimethylglycine dehydrogenase / Dimethylglycine dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
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
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.number_atoms_total / _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 1.6Nov 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: Dimethylglycine dehydrogenase
B: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,00814
Polymers195,0822
Non-polymers2,92712
Water12,989721
1
A: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0047
Polymers97,5411
Non-polymers1,4636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0047
Polymers97,5411
Non-polymers1,4636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.182, 107.215, 114.466
Angle α, β, γ (deg.)90.00, 92.16, 90.00
Int Tables number4
Space group name H-MP1211
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: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 38 - 859 / Label seq-ID: 40 - 861

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

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Components

#1: Protein Dimethylglycine dehydrogenase / Dimethylglycine dehydrogenase / mitochondrial


Mass: 97540.859 Da / Num. of mol.: 2 / Mutation: A204V, I267V, T402K, E509R, N746D, N774D
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
#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: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M NaSCN, 20% PEG 3350, 0.1 M Tris pH 7.5

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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: 1.85→48.19 Å / Num. all: 167803 / Num. obs: 167803 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 21.6 Å2 / Rsym value: 0.037 / Net I/σ(I): 22.2
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.5 / % possible all: 90.2

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJ5

1pj5


Resolution: 1.85→48.19 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.995 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23053 3356 2 %RANDOM
Rwork0.20648 ---
obs0.20697 163455 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.572 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å2-0 Å22.73 Å2
2--1.23 Å20 Å2
3----2.76 Å2
Refinement stepCycle: 1 / Resolution: 1.85→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13063 0 194 721 13978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01913621
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212863
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.97718493
X-RAY DIFFRACTIONr_angle_other_deg0.856329635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98751653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03923.681614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.317152274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5621590
X-RAY DIFFRACTIONr_chiral_restr0.0740.21981
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115319
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023151
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_it0.8951.9196606
X-RAY DIFFRACTIONr_mcbond_other0.8751.9146593
X-RAY DIFFRACTIONr_mcangle_it1.3662.8668243
X-RAY DIFFRACTIONr_mcangle_other1.3662.8668242
X-RAY DIFFRACTIONr_scbond_it1.2482.1067015
X-RAY DIFFRACTIONr_scbond_other1.232.1027005
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9743.09710238
X-RAY DIFFRACTIONr_long_range_B_refined4.04416.4916033
X-RAY DIFFRACTIONr_long_range_B_other3.97616.215684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 52989 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 211 -
Rwork0.355 10865 -
obs--86.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8559-0.6281-0.52794.4838-0.46094.33260.04880.6348-0.3853-0.4671-0.02110.00160.3397-0.0658-0.02770.14820.00430.04370.1359-0.05910.071162.942-9.51557.943
21.313-0.0704-0.35780.69190.13512.91470.09520.04140.0868-0.1202-0.0214-0.1703-0.07160.3573-0.07380.0837-0.02940.06590.07610.00170.096569.4260.99572.08
34.8342-0.42411.32981.4577-0.4453.19750.19340.26420.53-0.1522-0.1119-0.3446-0.68520.7571-0.08160.3282-0.21950.17110.224-0.01080.290776.51318.21573.009
40.94640.0172-0.85050.59830.05421.79640.04910.04070.0154-0.00780.02090.0269-0.0888-0.1475-0.06990.02710.0082-0.01880.02490.01770.038245.322-2.67390.799
54.28440.11870.20793.63521.11224.5002-0.0117-0.6669-0.41020.3968-0.0147-0.03270.5998-0.08570.02650.13570.01560.04130.1150.08250.07613.529-9.75356.749
61.31030.0332-0.31250.6858-0.25413.42250.021-0.04940.05610.12320.0140.1733-0.0412-0.4235-0.03510.02860.00520.03220.0621-0.00740.09027.0981.16742.843
75.06630.36931.32791.46890.32633.92030.0739-0.28850.47370.1426-0.04770.3519-0.7858-0.7908-0.02620.29490.21090.10320.19210.00230.26250.36318.55342.055
80.86-0.0887-0.92030.5620.08622.3951-0.0384-0.0701-0.01130.00430.027-0.0240.10680.30580.01150.01960.0159-0.02050.0446-0.00280.032831.171-2.86624.171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 67
2X-RAY DIFFRACTION2A68 - 258
3X-RAY DIFFRACTION3A259 - 360
4X-RAY DIFFRACTION4A361 - 857
5X-RAY DIFFRACTION5B38 - 67
6X-RAY DIFFRACTION6B68 - 258
7X-RAY DIFFRACTION7B259 - 360
8X-RAY DIFFRACTION8B361 - 857

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