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- PDB-5u8w: Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5u8w
TitleDihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NADH
ComponentsDihydrolipoyl dehydrogenase
KeywordsOXIDOREDUCTASE / dihydrolipoamide dehydrogenase / NAD(H) binding
Function / homology
Function and homology information


dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / glycolytic 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 / Pyridine nucleotide-disulphide oxidoreductase ...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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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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)209,40732
Polymers202,0404
Non-polymers7,36728
Water22,1221228
1
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,78117
Polymers101,0202
Non-polymers3,76115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-43 kcal/mol
Surface area33340 Å2
MethodPISA
2
C: Dihydrolipoyl dehydrogenase
D: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,62515
Polymers101,0202
Non-polymers3,60513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-47 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.510, 117.830, 139.730
Angle α, β, γ (deg.)90.00, 94.30, 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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1228 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.71 % / Description: cubes or bricks
Crystal growTemperature: 293 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 PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.79→39.28 Å / Num. obs: 198646 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.3
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.793 / % 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
Resolution: 1.79→34.935 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 17.99
RfactorNum. reflection% reflection
Rfree0.1785 2340 1.18 %
Rwork0.1667 --
obs0.1668 198602 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.79→34.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13640 0 468 1228 15336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414364
X-RAY DIFFRACTIONf_angle_d0.74519602
X-RAY DIFFRACTIONf_dihedral_angle_d13.5558334
X-RAY DIFFRACTIONf_chiral_restr0.0492364
X-RAY DIFFRACTIONf_plane_restr0.0042467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.82650.27811540.248411511X-RAY DIFFRACTION100
1.8265-1.86630.25731330.228411531X-RAY DIFFRACTION100
1.8663-1.90970.23981270.216211448X-RAY DIFFRACTION100
1.9097-1.95740.22111430.201511564X-RAY DIFFRACTION100
1.9574-2.01030.23971400.197211496X-RAY DIFFRACTION100
2.0103-2.06950.21641280.188211510X-RAY DIFFRACTION100
2.0695-2.13630.16931430.175211511X-RAY DIFFRACTION100
2.1363-2.21260.19291370.170711501X-RAY DIFFRACTION100
2.2126-2.30120.17541370.166911562X-RAY DIFFRACTION100
2.3012-2.40590.19481340.164711542X-RAY DIFFRACTION100
2.4059-2.53270.17791370.164611506X-RAY DIFFRACTION100
2.5327-2.69130.16541360.165511540X-RAY DIFFRACTION100
2.6913-2.8990.18811430.163911526X-RAY DIFFRACTION100
2.899-3.19060.18281290.166611578X-RAY DIFFRACTION100
3.1906-3.65190.17061470.161911616X-RAY DIFFRACTION100
3.6519-4.59930.13471320.14411572X-RAY DIFFRACTION100
4.5993-34.94140.1791400.162611748X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.8159-0.8349-0.71092.32880.21082.062-0.05640.4809-0.2853-0.43320.1473-0.03710.02230.06040.02230.3831-0.04190.05280.3876-0.20510.405528.718817.580339.1318
21.72152.62590.93026.6992.74351.7666-0.07570.10370.37560.02570.05320.043-0.0409-0.07060.07840.24660.00240.02290.22310.02420.266420.387749.40553.6286
36.9405-5.7547-4.79487.55264.27514.0064-0.03510.3394-0.038-0.37680.1181-0.033-0.05250.0942-0.03530.2668-0.05910.01330.3215-0.03250.170523.51232.324538.5956
40.50440.33940.42451.1594-0.04590.867-0.0910.3788-0.788-0.33530.09550.10380.2068-0.00060.45470.3978-0.05430.02270.2892-0.23110.490620.256111.961844.064
52.88590.32430.51281.459-0.12160.52780.0368-0.18890.0050.08630.02260.05830.0638-0.0062-0.04880.27310.00820.03750.1932-0.00680.264716.069634.5965.1728
61.59320.4490.23750.65490.0120.6188-0.04670.0679-0.40750.03420.1324-0.12170.20690.1018-0.05890.34080.0250.0040.2213-0.0260.383726.50719.393857.5678
72.8116-2.15390.83536.4025-1.50761.46770.0241-0.1622-0.10190.2575-0.0065-0.00520.03710.0343-0.05810.2554-0.0056-0.00040.1756-0.00670.219640.664937.68270.1506
81.51480.3838-0.06664.36440.36681.36110.04860.0154-0.04460.0907-0.0127-0.2679-0.07850.137-0.00610.2611-0.0020.010.1904-0.00930.284847.737540.86664.4591
93.3937-0.70761.26732.8718-0.79562.1782-0.0137-0.2220.21560.12870.04550.1195-0.0317-0.0707-0.02460.2493-0.00130.03160.1905-0.06020.289754.475762.234771.3281
104.19734.05572.08683.82542.12332.2315-0.18680.36370.4569-0.15110.10640.3047-0.11770.01030.07950.28270.0043-0.00770.24370.06210.317626.99857.198149.3333
116.1755-1.64974.81341.391-1.86455.3126-0.0606-0.35780.5639-0.017-0.08610.11960.0647-0.25350.09660.23790.0050.03840.1571-0.03410.340739.482762.352267.464
121.99980.57610.49651.06090.33690.4588-0.20230.1410.5621-0.10990.09650.0323-0.15520.04750.04560.28450.00040.01690.19640.01680.439352.244269.555759.0828
131.0913-0.21360.14184.3848-0.16230.8005-0.13150.6640.4214-0.60530.1134-0.2899-0.12460.1865-0.07020.4392-0.1009-0.01340.49480.13410.353344.763761.257336.1937
141.77720.36190.39630.85030.33890.6722-0.08710.30620.2506-0.11790.1076-0.1013-0.02990.14220.16540.2598-0.01880.04680.20830.02620.316757.783159.92453.2471
153.5373-0.55720.24351.4359-0.31181.0565-0.17510.5198-0.151-0.19390.1296-0.14740.10020.0788-0.00170.2847-0.03660.06580.3137-0.08330.239447.260838.943941.3766
161.59750.0358-0.37680.8622-0.54820.596-0.10940.3457-0.434-0.03990.0448-0.08160.1992-0.10170.02930.2731-0.02530.0510.2682-0.10580.337944.810332.354347.9406
171.53930.2954-0.5581.4696-0.51452.5403-0.0174-0.20710.12090.0482-0.07840.0426-0.32030.03820.09710.31770.0109-0.03120.3141-0.06160.211847.4206-4.3095-18.7111
180.18160.00240.04551.184-0.18992.28830.0121-0.44140.16080.1820.06230.1824-0.3901-0.20420.17950.34260.0680.05410.7366-0.14750.373239.3531-8.669115.0066
192.22190.5852-1.85630.475-1.25584.511-0.05660.01770.16880.1077-0.00720.1254-0.6357-0.4651-0.01390.37160.02260.00590.3492-0.13540.342.11930.348-4.832
201.98880.38870.94450.9297-0.19342.293-0.00280.15730.2361-0.0698-0.14570.0528-0.297-0.15260.0790.40490.0738-0.03510.3391-0.050.271242.2464-4.6169-30.1713
212.82780.8528-1.64931.0104-1.13422.95890.09170.33270.048-0.03190.0970.2604-0.0693-0.6913-0.0980.36120.0172-0.03540.4645-0.05210.334734.6763-17.6518-14.0182
222.978-0.56460.9511.9719-0.24071.86230.0741-0.3669-0.2334-0.01550.03850.13350.1559-0.268-0.10250.2979-0.04190.02270.54730.00060.310634.9756-24.28385.1031
231.465-0.2449-0.88210.433-0.69192.7760.0236-0.1814-0.2449-0.17050.00980.26370.3096-0.2049-0.04730.3609-0.0667-0.0450.4426-0.0530.403632.2896-25.0488-10.1124
240.4178-0.110.56660.548-1.38152.91160.0966-0.04680.0367-0.086-0.105-0.02390.20760.39460.09440.3310.0532-0.00180.4279-0.05560.263954.9841-18.8079-12.9253
252.7342-0.0016-0.26231.28630.10712.21530.0406-0.318-0.22150.1209-0.0793-0.09440.19460.2905-0.00430.35250.0587-0.00780.5397-0.02430.296762.9599-24.342310.5323
262.332-1.72411.83534.2724-0.67832.120.0296-0.6106-0.28970.5134-0.40.0356-0.08770.49780.01340.4312-0.1012-0.03111.07360.15120.308672.9814-20.642133.3372
270.69030.4339-1.19920.5579-0.40152.8341-0.2039-0.60130.1830.32370.12730.2508-0.5426-0.3349-0.18060.55370.07720.0270.6988-0.23670.420745.6706-2.064321.4691
285.7247-1.7742-3.24432.70752.30382.6163-0.1001-1.2253-0.52580.5739-0.05750.20.0362-0.01010.38210.4465-0.08260.02430.8977-0.02880.274458.4411-17.793232.5481
290.91840.397-0.28630.3474-0.04650.96960.2101-1.22950.25570.4897-0.26880.0151-0.39790.70340.97810.6335-0.1928-0.1581.3816-0.07810.229470.4331-6.559536.3834
301.7567-0.0620.09060.2448-0.08260.93870.365-0.79121.0180.3494-0.2714-0.0903-0.90730.46472.34680.7646-0.3555-0.11310.8897-0.36010.540368.87298.66828.0021
311.1334-0.69921.15272.4927-1.75092.16140.1014-0.4195-0.07670.0335-0.3937-0.31-0.08910.65610.18680.3557-0.0712-0.03030.91340.04150.361378.5631-12.267519.6186
323.74680.6675-1.57822.2164-0.2992.4262-0.1676-0.03820.5799-0.1191-0.08110.0008-0.3720.18190.19840.3573-0.042-0.04510.4242-0.03620.281163.41841.39542.1508
335.39820.0298-3.92783.7778-0.50994.1782-0.0692-0.06190.4147-0.1172-0.129-0.2789-0.16250.36930.3850.3363-0.0783-0.03630.566-0.03940.296369.7699-2.70571.3204
344.2536-0.18441.21732.4143-0.15821.5971-0.05020.15040.0224-0.3064-0.1242-0.0107-0.0170.28990.16820.3087-0.0148-0.00120.4814-0.05930.219563.6324-8.3893-2.3448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 114 )
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 171 )
5X-RAY DIFFRACTION5chain 'A' and (resid 172 through 252 )
6X-RAY DIFFRACTION6chain 'A' and (resid 253 through 370 )
7X-RAY DIFFRACTION7chain 'A' and (resid 371 through 424 )
8X-RAY DIFFRACTION8chain 'A' and (resid 425 through 474 )
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 54 )
10X-RAY DIFFRACTION10chain 'B' and (resid 55 through 88 )
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 114 )
12X-RAY DIFFRACTION12chain 'B' and (resid 115 through 203 )
13X-RAY DIFFRACTION13chain 'B' and (resid 204 through 252 )
14X-RAY DIFFRACTION14chain 'B' and (resid 253 through 370 )
15X-RAY DIFFRACTION15chain 'B' and (resid 371 through 424 )
16X-RAY DIFFRACTION16chain 'B' and (resid 425 through 474 )
17X-RAY DIFFRACTION17chain 'C' and (resid 3 through 54 )
18X-RAY DIFFRACTION18chain 'C' and (resid 55 through 88 )
19X-RAY DIFFRACTION19chain 'C' and (resid 89 through 114 )
20X-RAY DIFFRACTION20chain 'C' and (resid 115 through 144 )
21X-RAY DIFFRACTION21chain 'C' and (resid 145 through 171 )
22X-RAY DIFFRACTION22chain 'C' and (resid 172 through 252 )
23X-RAY DIFFRACTION23chain 'C' and (resid 253 through 302 )
24X-RAY DIFFRACTION24chain 'C' and (resid 303 through 370 )
25X-RAY DIFFRACTION25chain 'C' and (resid 371 through 474 )
26X-RAY DIFFRACTION26chain 'D' and (resid 4 through 54 )
27X-RAY DIFFRACTION27chain 'D' and (resid 55 through 88 )
28X-RAY DIFFRACTION28chain 'D' and (resid 89 through 114 )
29X-RAY DIFFRACTION29chain 'D' and (resid 115 through 203 )
30X-RAY DIFFRACTION30chain 'D' and (resid 204 through 302 )
31X-RAY DIFFRACTION31chain 'D' and (resid 303 through 370 )
32X-RAY DIFFRACTION32chain 'D' and (resid 371 through 402 )
33X-RAY DIFFRACTION33chain 'D' and (resid 403 through 424 )
34X-RAY DIFFRACTION34chain 'D' and (resid 425 through 474 )

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