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- PDB-1lvl: THE REFINED STRUCTURE OF PSEUDOMONAS PUTIDA LIPOAMIDE DEHYDROGENA... -

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Basic information

Entry
Database: PDB / ID: 1lvl
TitleTHE REFINED STRUCTURE OF PSEUDOMONAS PUTIDA LIPOAMIDE DEHYDROGENASE COMPLEXED WITH NAD+ AT 2.45 ANGSTROMS RESOLUTION
ComponentsDIHYDROLIPOAMIDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / 2-oxoglutarate metabolic process / flavin adenine dinucleotide binding / cytoplasm
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsMattevi, A. / Hol, W.G.J.
Citation
Journal: Proteins / Year: 1992
Title: The refined crystal structure of Pseudomonas putida lipoamide dehydrogenase complexed with NAD+ at 2.45 A resolution.
Authors: Mattevi, A. / Obmolova, G. / Sokatch, J.R. / Betzel, C. / Hol, W.G.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: The Refined Crystal Structure of Lipoamide Dehydrogenase from Azotobacter Vinelandii at 2.2 Angstroms Resolution. A Comparison with the Structure of Glutathione Reductase
Authors: Mattevi, A. / Schierbeek, A.J. / Hol, W.G.J.
#2: Journal: Eur.J.Biochem. / Year: 1989
Title: Sequence Analysis of the Lpdv Gene for Lipoamide Dehydrogenase of Branched-Chain-Oxoacid Dehydrogenase of Pseudomonas Putida
Authors: Burns, G. / Brown, T. / Hatter, K. / Sokatch, J.R.
History
DepositionDec 16, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650HELIX EACH HELIX IS LABELED BY TWO DIGITS. THE FIRST INDICATES THE DOMAIN WHERE THE HELIX IS ...HELIX EACH HELIX IS LABELED BY TWO DIGITS. THE FIRST INDICATES THE DOMAIN WHERE THE HELIX IS LOCATED AND THE SECOND ONE GIVES ITS SEQUENTIAL NUMBER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROLIPOAMIDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5303
Polymers48,0811
Non-polymers1,4492
Water3,423190
1
A: DIHYDROLIPOAMIDE DEHYDROGENASE
hetero molecules

A: DIHYDROLIPOAMIDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0616
Polymers96,1632
Non-polymers2,8984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544x,-y-1,-z-11
Buried area12510 Å2
ΔGint-85 kcal/mol
Surface area33060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.320, 108.120, 151.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUES PRO 347 AND PRO 438 ARE CIS PROLINES.
DetailsTHE CRYSTALS CONTAIN ONE MONOMER PER ASYMMETRIC UNIT. THE SECOND SUBUNIT OF THE DIMER IS GENERATED BY THE TWOFOLD ROTATION ABOUT THE A AXIS: 1.00 0.00 0.00 0.00 0.00 -1.00 0.00 -108.118 0.00 0.00 -1.00 -151.077

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Components

#1: Protein DIHYDROLIPOAMIDE DEHYDROGENASE


Mass: 48081.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / References: UniProt: P09063, dihydrolipoyl dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPSEUDOMONAS PUTIDA IS THE ONLY KNOWN ORGANISM WHICH PRODUCES THREE DIFFERENT LIPOAMIDE ...PSEUDOMONAS PUTIDA IS THE ONLY KNOWN ORGANISM WHICH PRODUCES THREE DIFFERENT LIPOAMIDE DEHYDROGENASES. ONE (LIPDH VAL) OF THEM IS SPECIFIC FOR THE BRANCHED CHAIN OXOACIDDEHYDROGENASE COMPLEX. LIPDH VAL IS A DIMER OF TWO IDENTICAL SUBUNITS. EACH CHAIN IS COMPOSED OF 458 RESIDUES AND ONE MOLECULE OF FAD. THE PROTEIN WAS COCRYSTALLIZED WITH NAD+.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMNAD+1drop
316 %(w/v)PEG60001drop
450 mMHEPES1drop
50.5 mMEDTA1drop
60.02 %1dropNaN3
715 %PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 12 Å / Num. obs: 18731 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 2.5 Å / Rmerge(I) obs: 0.189

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Processing

Software
NameClassification
GROMOSrefinement
TNTrefinement
RefinementResolution: 2.45→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.215 18085
Refinement stepCycle: LAST / Resolution: 2.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 97 190 3659
Refinement
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 10 Å / Num. reflection all: 18085 / σ(I): 0 / Rfactor all: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.022
X-RAY DIFFRACTIONo_angle_deg4
X-RAY DIFFRACTIONo_dihedral_angle_d28
X-RAY DIFFRACTIONo_dihedral_angle_deg
X-RAY DIFFRACTIONo_plane_restr0.03

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