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- PDB-1ojt: STRUCTURE OF DIHYDROLIPOAMIDE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1ojt
TitleSTRUCTURE OF DIHYDROLIPOAMIDE DEHYDROGENASE
ComponentsSURFACE PROTEIN
KeywordsOXIDOREDUCTASE / REDOX-ACTIVE CENTER / GLYCOLYSIS / NAD / FLAVOPROTEIN / FAD / P64K
Function / homology
Function and homology information


dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / 2-oxoglutarate metabolic process / flavin adenine dinucleotide binding
Similarity search - Function
Dihydrolipoamide dehydrogenase / : / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 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 ...Dihydrolipoamide dehydrogenase / : / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 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 / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / 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 speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR / Resolution: 2.75 Å
AuthorsLi De La Sierra, I. / Prange, T. / Pernot, L.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Molecular structure of the lipoamide dehydrogenase domain of a surface antigen from Neisseria meningitidis.
Authors: Li de la Sierra, I. / Pernot, L. / Prange, T. / Saludjian, P. / Schiltz, M. / Fourme, R. / Padron, G.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Investigation of a Recombinant Outer Membrane Protein from Neisseria Meningitidis
Authors: Li De La Sierra, I. / Prange, T. / Fourme, R. / Padron, G. / Fuentes, P. / Musacchio, A. / Madrazo, J.
#2: 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.
#3: 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.
History
DepositionSep 6, 1996Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SURFACE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5242
Polymers50,7381
Non-polymers7861
Water2,072115
1
A: SURFACE PROTEIN
hetero molecules

A: SURFACE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0474
Polymers101,4762
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area11180 Å2
ΔGint-66 kcal/mol
Surface area35040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)138.050, 138.050, 79.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SURFACE PROTEIN


Mass: 50737.961 Da / Num. of mol.: 1 / Fragment: DIHYDROLIPOAMIDE DEHYDROGENASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: M-6 OBTAINED FROM A GENOMIC / Gene (production host): M-6 OBTAINED FROM A GENOMIC / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q51225
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ORIGINAL RECOMBINANT PROTEIN CONTAINS THE TWO DOMAINS E2 AND E3 OF THE DEHYDROGENASE ...THE ORIGINAL RECOMBINANT PROTEIN CONTAINS THE TWO DOMAINS E2 AND E3 OF THE DEHYDROGENASE MULTIENZYMATIC COMPLEX, LINKED BY A SPACER RICH IN ALA AND PRO. THIS SPACER IS CLEAVED DURING PURIFICATION. ONLY E3 CRYSTALLIZES. COMPARED TO THE DLDH OF PSEUDOMONAS PUTIDA, IT CONTAINS AN ADDITIONAL LOOP (RESIDUES 231 - 263) WHICH CONSTITUTES THE ANTIGENIC SITE. THE LIPOAMIDE BINDING DOMAIN (E2) IS ABSENT.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Description: MIR USED 2 DERIVATIVES, ONE MERCURY (TAMM) IN 3 SITES, AND ONE XENON (PRESSURE = 15 BAR) IN 2 SITES. THE TWO MR AND MIR MAPS WERE COMBINED WITH SIGMAA PROGRAM (CCP4) AND SOLVENT ...Description: MIR USED 2 DERIVATIVES, ONE MERCURY (TAMM) IN 3 SITES, AND ONE XENON (PRESSURE = 15 BAR) IN 2 SITES. THE TWO MR AND MIR MAPS WERE COMBINED WITH SIGMAA PROGRAM (CCP4) AND SOLVENT FLATTENED WITH DM (CCP4) AND SOLOMON PROGRAMS.
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: BRIGHT YELLOW CRYSTALS WERE GROWN IN 24-WELL LINBRO PLATES USING HANGING DROP DIFFUSION METHOD AT ROOM TEMPERATURE. RESERVOIR: 1 ML CONTAINING 0.1M POTASSIUM PHOSPHATE AND 2M AMMONIUM ...Details: BRIGHT YELLOW CRYSTALS WERE GROWN IN 24-WELL LINBRO PLATES USING HANGING DROP DIFFUSION METHOD AT ROOM TEMPERATURE. RESERVOIR: 1 ML CONTAINING 0.1M POTASSIUM PHOSPHATE AND 2M AMMONIUM SULFATE (PH 7.0). PRISM CRYSTALS TYPICALLY IN TWO WEEKS AT ROOM TEMPERATURE., vapor diffusion - hanging drop THE E3 DOMAIN (117-601) CRYSTALLIZES IN AMMONIUM SULFATE. IT INCLUDES A FAD COFACTOR BUT NOT THE NADH. THE E3 DOMAIN (117-601) CRYSTALLIZES IN AMMONIUM SULFATE. IT INCLUDE A FAD COFACTOR BUT NOT THE NADH.
Temp details: room temp
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Details: Li De La Sierra, I., (1994) J.Mol.Biol., 235, 1154.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
20.02 MTris-HCl1drop
30.006 MEDTA1drop
40.15 M1dropNaCl
50.1 Mpotassium phosphate1reservoir
62 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Type: LURE / Wavelength: 0.91
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Details: MULTILAYER MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 11724 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 18
Reflection shellResolution: 2.7→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4 / % possible all: 70

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Processing

Software
NameVersionClassification
MOSFLM(+ CCP4)data reduction
SCALEIT(CCP4)data reduction
SHARPphasing
PROLSQrefinement
CCP4data reduction
CCP4(SCALEIT)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MIR
Starting model: DLDH OF PSEUDOMONAS PUTIDA, PDB ENTRY 1LVL.

1lvl


Resolution: 2.75→18 Å / Details: X-PLOR ALSO WAS USED. /
RfactorNum. reflection
Rfree0.232 -
obs0.173 15850
Refinement stepCycle: LAST / Resolution: 2.75→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 53 115 3724
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.055
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_chiral_restr0.08
X-RAY DIFFRACTIONp_singtor_nbd0.23
X-RAY DIFFRACTIONp_multtor_nbd0.33
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.24
X-RAY DIFFRACTIONp_planar_tor2.3
X-RAY DIFFRACTIONp_staggered_tor24
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / Rfactor all: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS

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