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- PDB-5u8u: Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5u8u
TitleDihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa
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 / response to oxidative stress / 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 / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGlasser, N.R. / Wang, B.X. / Hoy, J.A. / Newman, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
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 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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 1.6Oct 23, 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)208,22947
Polymers202,0404
Non-polymers6,18943
Water42,9302383
1
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,07623
Polymers101,0202
Non-polymers3,05621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-20 kcal/mol
Surface area34140 Å2
MethodPISA
2
C: Dihydrolipoyl dehydrogenase
D: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,15424
Polymers101,0202
Non-polymers3,13422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-6 kcal/mol
Surface area34280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.320, 116.280, 136.590
Angle α, β, γ (deg.)90.00, 94.73, 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, UniProt: Q9I3D1*PLUS, 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2383 / 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: 2.57 Å3/Da / Density % sol: 52.07 % / Description: bricks or cubes
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: PEG 3350, HEPES, KCl, microseeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 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: 1.35→38.76 Å / Num. obs: 443473 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.3
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.736 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.659 / % possible all: 99.5

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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: 1.35→38.755 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 15.74
RfactorNum. reflection% reflection
Rfree0.1565 5212 1.18 %
Rwork0.1325 --
obs0.1328 443380 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→38.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13770 0 368 2383 16521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214484
X-RAY DIFFRACTIONf_angle_d1.21319705
X-RAY DIFFRACTIONf_dihedral_angle_d18.3225054
X-RAY DIFFRACTIONf_chiral_restr0.0852359
X-RAY DIFFRACTIONf_plane_restr0.0092500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.2741750.253314550X-RAY DIFFRACTION99
1.3653-1.38140.3121890.240414460X-RAY DIFFRACTION99
1.3814-1.39830.27021660.234114505X-RAY DIFFRACTION100
1.3983-1.4160.24561710.217114542X-RAY DIFFRACTION100
1.416-1.43460.26621470.198414603X-RAY DIFFRACTION100
1.4346-1.45420.19051860.185814494X-RAY DIFFRACTION100
1.4542-1.4750.22741830.166614530X-RAY DIFFRACTION100
1.475-1.4970.18831740.160614600X-RAY DIFFRACTION100
1.497-1.52040.21031750.152914602X-RAY DIFFRACTION100
1.5204-1.54540.19711600.146914547X-RAY DIFFRACTION100
1.5454-1.5720.17881820.136314589X-RAY DIFFRACTION100
1.572-1.60060.14491580.123214584X-RAY DIFFRACTION100
1.6006-1.63140.16191760.119814608X-RAY DIFFRACTION100
1.6314-1.66470.15621810.117614610X-RAY DIFFRACTION100
1.6647-1.70090.13461850.111114513X-RAY DIFFRACTION100
1.7009-1.74040.14381640.106514633X-RAY DIFFRACTION100
1.7404-1.7840.1441770.102714580X-RAY DIFFRACTION100
1.784-1.83220.1461740.102414614X-RAY DIFFRACTION100
1.8322-1.88610.13691690.105514618X-RAY DIFFRACTION100
1.8861-1.9470.13051830.104914617X-RAY DIFFRACTION100
1.947-2.01660.15611680.10514605X-RAY DIFFRACTION100
2.0166-2.09730.13531760.103914622X-RAY DIFFRACTION100
2.0973-2.19270.12311680.101914670X-RAY DIFFRACTION100
2.1927-2.30830.13561730.107414598X-RAY DIFFRACTION100
2.3083-2.45290.12991810.112514651X-RAY DIFFRACTION100
2.4529-2.64230.15061690.122114671X-RAY DIFFRACTION100
2.6423-2.90810.15091780.131814660X-RAY DIFFRACTION100
2.9081-3.32870.16151730.137414704X-RAY DIFFRACTION100
3.3287-4.19310.14781740.141714702X-RAY DIFFRACTION100
4.1931-38.77110.17231770.158714886X-RAY DIFFRACTION100

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