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- PDB-3lad: REFINED CRYSTAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM AZOTOBA... -

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Entry
Database: PDB / ID: 3lad
TitleREFINED CRYSTAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM AZOTOBACTER VINELANDII AT 2.2 ANGSTROMS RESOLUTION. A COMPARISON WITH THE STRUCTURE OF GLUTATHIONE REDUCTASE
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
Glucose inhibited division protein A / 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 ...Glucose inhibited division protein A / 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 speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMattevi, A. / Schierbeek, A.J. / Hol, W.G.J.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Refined crystal structure of lipoamide dehydrogenase from Azotobacter vinelandii at 2.2 A resolution. A comparison with the structure of glutathione reductase.
Authors: Mattevi, A. / Schierbeek, A.J. / Hol, W.G.
#1: 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.
#2: Journal: Eur.J.Biochem. / Year: 1988
Title: Lipoamide Dehydrogenase from Azotobacter Vinelandii: Molecular Cloning, Organization and Sequence Analysis of the Gene
Authors: Westphal, A.H. / Dekok, A.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: Crystallization and Preliminary X-Ray Investigation of Lipoamide Dehydrogenase from Azotobacter Vinelandii
Authors: Schierbeek, A.J. / Van Derlaan, J.M. / Groendijk, H. / Wierenga, R.K. / Drenth, J.
History
DepositionDec 11, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)100,5614
Polymers98,9902
Non-polymers1,5712
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-61 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.130, 83.860, 191.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: HIS A 359 - PRO A 360 OMEGA =122.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO A 451
3: HIS B 359 - PRO B 360 OMEGA =324.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: CIS PROLINE - PRO B 451
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.083696, 0.801095, 0.592657), (0.80203, -0.407119, 0.437039), (0.591391, 0.43875, -0.676576)
Vector: -22.602, 26.444, 5.667)
DetailsTHE TRANSFORMATION PROVIDED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. AFTER SUPERPOSITION, THE RMS DIFFERENCE BETWEEN THE POSITIONS OF 472 EQUIVALENT CARBON ALPHA ATOMS IS 0.63 ANGSTROMS.

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Components

#1: Protein DIHYDROLIPOAMIDE DEHYDROGENASE


Mass: 49494.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / References: UniProt: P18925, 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 %(w/v)PEG40001reservoir
250 mMphosphate1reservoir

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Processing

Software
NameClassification
X-PLORmodel building
GROMOSrefinement
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 2.2 Å / σ(F): 2 /
RfactorNum. reflection
obs0.192 44294
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 106 451 7413
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d28.4
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. reflection obs: 44294 / σ(F): 2 / Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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