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- PDB-1dxl: Dihydrolipoamide dehydrogenase of glycine decarboxylase from Pisu... -

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Basic information

Entry
Database: PDB / ID: 1dxl
TitleDihydrolipoamide dehydrogenase of glycine decarboxylase from Pisum Sativum
ComponentsDIHYDROLIPOAMIDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DIHYDROLIPOAMIDE DEHYDROGENASE / MULTIENZYME COMPLEX PROTEIN / PYRUVATE DEHYDROGENASE COMPLEX / GLYCINE DECARBOXYLASE COMPLEX / FLAVOPROTEIN
Function / homology
Function and homology information


glycine decarboxylation via glycine cleavage system / glycine cleavage complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / oxoglutarate dehydrogenase complex / 2-oxoglutarate metabolic process / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion
Similarity search - Function
Dihydrolipoamide dehydrogenase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Dihydrolipoamide dehydrogenase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesPISUM SATIVUM (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsFaure, M. / Cohen-Addad, C. / Bourguignon, J. / Macherel, D. / Neuburger, M. / Douce, R.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: Interaction between the Lipoamide-Containing H-Protein and the Lipoamide Dehydrogenase (L-Protein) of the Glycine Decarboxylase Multienzyme System. 2. Crystal Structure of H- and L-Proteins
Authors: Faure, M. / Bourguignon, J. / Neuburger, M. / Macherel, D. / Sieker, L. / Ober, R. / Kahn, R. / Cohen-Addad, C. / Douce, R.
#1: Journal: Biochem.J. / Year: 1996
Title: Glycine Decarboxylase and Pyruvate Dehydrogenase Complexes Share the Same Dihydrolipoamide Dehydrogenase in Pea Leaf Mitochondria: Evidence from Mass Spectrometry and Primary-Structure Analysis
Authors: Bourguignon, J. / Merand, V. / Rawsthorne, S. / Forest, E. / Douce, R.
History
DepositionJan 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2000Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROLIPOAMIDE DEHYDROGENASE
B: DIHYDROLIPOAMIDE DEHYDROGENASE
C: DIHYDROLIPOAMIDE DEHYDROGENASE
D: DIHYDROLIPOAMIDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,3788
Polymers199,2364
Non-polymers3,1424
Water1,874104
1
A: DIHYDROLIPOAMIDE DEHYDROGENASE
B: DIHYDROLIPOAMIDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1894
Polymers99,6182
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-51.6 kcal/mol
Surface area44680 Å2
MethodPQS
2
C: DIHYDROLIPOAMIDE DEHYDROGENASE
D: DIHYDROLIPOAMIDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1894
Polymers99,6182
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-51.3 kcal/mol
Surface area45210 Å2
MethodPQS
Unit cell
Length a, b, c (Å)100.560, 108.330, 202.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.561818, -0.313054, -0.76574), (-0.330398, -0.763691, 0.554628), (-0.758418, 0.564599, 0.325623)76.6425, 37.4478, 28.2936
2given(-0.056013, 0.094754, -0.993924), (-0.083306, 0.991572, 0.099225), (0.994949, 0.088358, -0.047647)-50.7683, -35.5089, 49.5664
3given(0.753692, -0.355954, -0.55249), (-0.618841, -0.667443, -0.414192), (-0.221322, 0.654077, -0.723325)79.6334, 107.9737, 63.0491
DetailsBIOLOGICAL_UNIT: HOMODIMERTHE ASYMETRIC UNIT CONTAINS 2 DIMERS (AB AND CD)

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Components

#1: Protein
DIHYDROLIPOAMIDE DEHYDROGENASE / LIPOAMIDE DEHYDROGENASE / L PROTEIN / E3 / DLDH / GLYCINE CLEAVAGE SYSTEM L PROTEIN


Mass: 49808.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PISUM SATIVUM (garden pea) / Tissue: LEAF / Cellular location: MITOCHONDRIA / Organelle: MITOCHONDRIA / Plasmid: PET3A / Cellular location (production host): INCLUSION BODIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P31023, dihydrolipoyl dehydrogenase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / 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
Sequence detailsTHE SWISSPROT ENTRY P31023 GIVES THE SEQUENCE FROM BOURGUIGNON J., MACHEREL D., NEUBURGER M., DOUCE ...THE SWISSPROT ENTRY P31023 GIVES THE SEQUENCE FROM BOURGUIGNON J., MACHEREL D., NEUBURGER M., DOUCE R. EUR. J. BIOCHEM. 204 865 (1992) WHICH HAS ASN480. THE KNOWN CONFLICT AT POSITION 480 OF ASN -> HIS IS THE SEQUENCE USED IN THIS STRUCTURE FROM TURNER S.R., IRELAND R., RAWSTHORNE S., J. BIOL. CHEM. 267 7745 (1992)

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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: 2.76 Å3/Da / Density % sol: 45 %
Crystal growpH: 5
Details: 15 % PEG MME 5K, 100 MM MES PH 5, 0.45 % HEPTYL-B-D-THIOGLUCOPYRANOSIDE, 2MM POTASSIUM LIPOATE.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
212 %(w/v)mPEG50001reservoir
30.1 MMES1reservoir
40.45 %heptyl-beta-D-thioglucopyranoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9475
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 1998 / Details: MULTILAYER MIRRORS
RadiationMonochromator: DIAMOND C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9475 Å / Relative weight: 1
ReflectionResolution: 3.15→30 Å / Num. obs: 33527 / % possible obs: 87 % / Redundancy: 3.4 % / Biso Wilson estimate: 87.2 Å2 / Rsym value: 0.063 / Net I/σ(I): 8.6
Reflection shellResolution: 3.15→3.32 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.254 / % possible all: 77.3
Reflection
*PLUS
% possible obs: 86.7 % / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 77.3 % / Rmerge(I) obs: 0.254

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Processing

Software
NameVersionClassification
CNS0.4refinement
MOSFLMdata reduction
SCALAdata scaling
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LAD

3lad


Resolution: 3.15→15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1953239.04 / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.323 1650 5 %RANDOM
Rwork0.226 ---
obs0.226 33219 86.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54 Å2 / ksol: 0.225025 e/Å3
Displacement parametersBiso mean: 75 Å2
Baniso -1Baniso -2Baniso -3
1-4.63 Å20 Å20 Å2
2---11.76 Å20 Å2
3---7.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.94 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.15→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13900 0 212 104 14216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.15→3.35 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.514 228 4.7 %
Rwork0.376 4630 -
obs--76.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FAD.PARFAD.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.325
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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