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- PDB-1lpf: THREE-DIMENSIONAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM PSEUD... -

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Entry
Database: PDB / ID: 1lpf
TitleTHREE-DIMENSIONAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM PSEUDOMONAS FLUORESCENS AT 2.8 ANGSTROMS RESOLUTION. ANALYSIS OF REDOX AND THERMOSTABILITY PROPERTIES
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 / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsMattevi, A. / Hol, W.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Three-dimensional structure of lipoamide dehydrogenase from Pseudomonas fluorescens at 2.8 A resolution. Analysis of redox and thermostability properties.
Authors: Mattevi, A. / Obmolova, G. / Kalk, K.H. / van Berkel, W.J. / 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: J.Gen.Microbiol. / Year: 1989
Title: Molecular Cloning and Sequence Determination of the Gene Encoding Lipoamide Dehydrogenase from Pseudomonas Fluorescens
Authors: Benen, J.A.E. / Van Berkel, W.J.H. / Van Dongen, W.M.A.M. / Muller, F. / Dekok, A.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: X-Ray Structure of Lipoamide Dehydrogenase from Azotobacter Vinelandii Determined by a Combination of Molecular and Isomorphous Replacement Techniques
Authors: Schierbeek, A.J. / Swarte, M.B.A. / Dijkstra, B.W. / Vriend, G. / Read, R.J. / Hol, W.G.J. / Drenth, J. / Betzel, C.
History
DepositionOct 26, 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: 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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 GIVES ITS SEQUENTIAL NUMBER. THE DIGITS ARE SEPARATED BY THE CHAIN IDENTIFIER. BECAUSE THE HELIX IDENTIFIERS ARE RESTRICTED TO THREE CHARACTERS, HELIX 4-10 AND 4-11 OF BOTH CHAINS ARE LABELED 4A1, 4AA, 4B1 AND 4BA.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7364
Polymers100,1652
Non-polymers1,5712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-63 kcal/mol
Surface area33840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.600, 66.400, 164.300
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES PRO 360 AND PRO 451 IN BOTH CHAINS ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.192992, -0.39284, -0.899128), (-0.39067, -0.871354, 0.29685), (-0.900073, 0.293972, -0.321635)
Vector: -58.801, 2.82, -79.197)
DetailsTHE TWO INDEPENDENTLY REFINED SUBUNITS ARE RELATED BY THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW. THIS TRANSFORMATION WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. AFTER SUPERPOSITION, THE RMS DIFFERENCE BETWEEN THE POSITIONS OF 3490 EQUIVALENT ATOMS IS 0.14 ANGSTROMS.

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Components

#1: Protein DIHYDROLIPOAMIDE DEHYDROGENASE


Mass: 50082.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / References: UniProt: P14218, dihydrolipoyl 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
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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
29 %(w/v)PEG60001drop
350 mMHEPES1drop
40.5 mMEDTA1drop
50.02 %(w/v)1dropNaN3
69 %PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 100 Å / Num. obs: 23546 / % possible obs: 78.2 % / Num. measured all: 40000 / Rmerge(I) obs: 0.0435
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 40.7 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→10 Å / σ(F): 0
Details: DURING REFINEMENT, RESIDUES 42, 163, 387, AND 388 OF EACH CHAIN WERE IDENTIFIED AS THR. THEY ARE, IN FACT, VAL, SER, ALA, AND ALA, RESPECTIVELY. FOR THESE RESIDUES, IN THIS ENTRY, THE SIDE ...Details: DURING REFINEMENT, RESIDUES 42, 163, 387, AND 388 OF EACH CHAIN WERE IDENTIFIED AS THR. THEY ARE, IN FACT, VAL, SER, ALA, AND ALA, RESPECTIVELY. FOR THESE RESIDUES, IN THIS ENTRY, THE SIDE CHAIN ATOMS BEYOND CB HAVE BEEN REMOVED AND THE RESIDUES ARE PRESENTED WITH THEIR CORRECT RESIDUE NAMES. THIS MATTER IS BEING INVESTIGATED BY THE DEPOSITORS.
RfactorNum. reflection
Rwork0.192 -
obs0.192 23164
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6858 0 106 0 6964
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Num. reflection all: 23164 / σ(F): 0 / Rfactor all: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg

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