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- PDB-5l46: Crystal structure of human dimethylglycine-dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 5l46
TitleCrystal structure of human dimethylglycine-dehydrogenase
ComponentsDimethylglycine dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / electron transfer / covalent flavinylation / one-carbon metabolism
Function / homology
Function and homology information


dimethylglycine dehydrogenase / dimethylglycine dehydrogenase activity / amino-acid betaine catabolic process / Choline catabolism / choline catabolic process / choline metabolic process / electron transfer activity / oxidoreductase activity / mitochondrial matrix / mitochondrion ...dimethylglycine dehydrogenase / dimethylglycine dehydrogenase activity / amino-acid betaine catabolic process / Choline catabolism / choline catabolic process / choline metabolic process / electron transfer activity / oxidoreductase activity / mitochondrial matrix / mitochondrion / RNA binding / 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, folate-binding domain / 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, 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, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsHromic, A. / Pavkov-Keller, T. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW901 Austria
CitationJournal: Febs J. / Year: 2016
Title: Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant.
Authors: Augustin, P. / Hromic, A. / Pavkov-Keller, T. / Gruber, K. / Macheroux, P.
History
DepositionMay 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dimethylglycine dehydrogenase, mitochondrial
B: Dimethylglycine dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,1904
Polymers188,6192
Non-polymers1,5712
Water1086
1
A: Dimethylglycine dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0952
Polymers94,3101
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dimethylglycine dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0952
Polymers94,3101
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.377, 119.868, 86.466
Angle α, β, γ (deg.)90.00, 92.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dimethylglycine dehydrogenase, mitochondrial / / ME2GLYDH


Mass: 94309.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DMGDH / Plasmid: pPICK-PDI / Production host: Komagataella phaffii (fungus) / Strain (production host): KM71H / References: UniProt: Q9UI17, dimethylglycine dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.32 Å3/Da / Density % sol: 47.01 % / Description: long needles
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 7.5
Details: 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M of each amino acid and 0.1 M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 3.09→58.651 Å / Num. obs: 30495 / % possible obs: 97.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 47.09 Å2 / CC1/2: 0.958 / Rmerge(I) obs: 0.2058 / Net I/σ(I): 4.81
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.6573 / Mean I/σ(I) obs: 1.53 / % possible all: 93.81

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PAA

4paa


Resolution: 3.09→58.651 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.78
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 1524 5 %random
Rwork0.179 ---
obs0.1835 30482 97.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.1 Å2
Refinement stepCycle: LAST / Resolution: 3.09→58.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12782 0 106 6 12894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113218
X-RAY DIFFRACTIONf_angle_d1.37317951
X-RAY DIFFRACTIONf_dihedral_angle_d17.0564887
X-RAY DIFFRACTIONf_chiral_restr0.0541933
X-RAY DIFFRACTIONf_plane_restr0.0072298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0899-3.18960.32421310.25742490X-RAY DIFFRACTION93
3.1896-3.30360.33081390.23172642X-RAY DIFFRACTION99
3.3036-3.43580.32121390.23022651X-RAY DIFFRACTION98
3.4358-3.59220.30221370.21822593X-RAY DIFFRACTION97
3.5922-3.78150.27241390.1982639X-RAY DIFFRACTION98
3.7815-4.01840.29141400.18572656X-RAY DIFFRACTION98
4.0184-4.32860.26711390.16182642X-RAY DIFFRACTION99
4.3286-4.7640.25671390.14792634X-RAY DIFFRACTION97
4.764-5.45290.21971400.14672659X-RAY DIFFRACTION99
5.4529-6.86840.28251400.17192658X-RAY DIFFRACTION98
6.8684-58.66110.20141410.13722694X-RAY DIFFRACTION98

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