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- PDB-5u8v: Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa... -

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Basic information

Entry
Database: PDB / ID: 5u8v
TitleDihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NAD+
ComponentsDihydrolipoyl dehydrogenase
KeywordsOXIDOREDUCTASE / dihydrolipoamide dehydrogenase / NAD(H) binding
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 aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGlasser, N.R. / Wang, B.X. / Hoy, J.A. / Newman, D.K.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The Pyruvate and alpha-Ketoglutarate Dehydrogenase Complexes of Pseudomonas aeruginosa Catalyze Pyocyanin and Phenazine-1-carboxylic Acid Reduction via the Subunit Dihydrolipoamide Dehydrogenase.
Authors: Glasser, N.R. / Wang, B.X. / Hoy, J.A. / Newman, D.K.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
C: Dihydrolipoyl dehydrogenase
D: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,33644
Polymers202,0404
Non-polymers8,29640
Water37,9222105
1
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,16822
Polymers101,0202
Non-polymers4,14820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15170 Å2
ΔGint-20 kcal/mol
Surface area33640 Å2
MethodPISA
2
C: Dihydrolipoyl dehydrogenase
D: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,16822
Polymers101,0202
Non-polymers4,14820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15220 Å2
ΔGint-16 kcal/mol
Surface area34230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.610, 116.690, 136.860
Angle α, β, γ (deg.)90.00, 94.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dihydrolipoyl dehydrogenase


Mass: 50510.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: lpdG, PA14_43970 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H2Z9F5, 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: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2105 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: PEG 3350, HEPES, KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→38.901 Å / Num. obs: 361955 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.5
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 13 % / Rmerge(I) obs: 1.672 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.608 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LPF

1lpf


Resolution: 1.45→38.901 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 16.82
RfactorNum. reflection% reflection
Rfree0.1736 4260 1.18 %
Rwork0.1521 --
obs0.1524 361890 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→38.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13756 0 448 2105 16309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414536
X-RAY DIFFRACTIONf_angle_d0.76719810
X-RAY DIFFRACTIONf_dihedral_angle_d18.2755040
X-RAY DIFFRACTIONf_chiral_restr0.0672374
X-RAY DIFFRACTIONf_plane_restr0.0042495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.23721510.237711854X-RAY DIFFRACTION100
1.4665-1.48370.24231420.22511851X-RAY DIFFRACTION100
1.4837-1.50180.22821430.217411913X-RAY DIFFRACTION100
1.5018-1.52080.26531490.215611898X-RAY DIFFRACTION100
1.5208-1.54090.25731320.211611882X-RAY DIFFRACTION100
1.5409-1.5620.21591360.197911955X-RAY DIFFRACTION100
1.562-1.58430.23831400.185511790X-RAY DIFFRACTION100
1.5843-1.60790.22751290.177111968X-RAY DIFFRACTION100
1.6079-1.6330.22971460.1711917X-RAY DIFFRACTION100
1.633-1.65980.19791600.161211810X-RAY DIFFRACTION100
1.6598-1.68840.19171380.153511972X-RAY DIFFRACTION100
1.6884-1.71910.1591360.147911883X-RAY DIFFRACTION100
1.7191-1.75220.19721430.146811853X-RAY DIFFRACTION100
1.7522-1.7880.21281470.145211907X-RAY DIFFRACTION100
1.788-1.82690.16891470.143911959X-RAY DIFFRACTION100
1.8269-1.86940.16691360.144511867X-RAY DIFFRACTION100
1.8694-1.91610.18771360.143811919X-RAY DIFFRACTION100
1.9161-1.96790.18451500.139911869X-RAY DIFFRACTION100
1.9679-2.02580.17941340.138611921X-RAY DIFFRACTION100
2.0258-2.09120.16551460.136811947X-RAY DIFFRACTION100
2.0912-2.16590.15371400.133111925X-RAY DIFFRACTION100
2.1659-2.25260.15211380.130511919X-RAY DIFFRACTION100
2.2526-2.35510.1481440.133511927X-RAY DIFFRACTION100
2.3551-2.47930.1541450.136411944X-RAY DIFFRACTION100
2.4793-2.63460.16811380.141311966X-RAY DIFFRACTION100
2.6346-2.8380.14941430.146811935X-RAY DIFFRACTION100
2.838-3.12340.16131360.152411997X-RAY DIFFRACTION100
3.1234-3.57510.18921480.155211915X-RAY DIFFRACTION100
3.5751-4.50320.14181430.149612028X-RAY DIFFRACTION100
4.5032-38.91460.19571440.166912139X-RAY DIFFRACTION100

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