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- PDB-1zy8: The crystal structure of dihydrolipoamide dehydrogenase and dihyd... -
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Basic information
Entry | Database: PDB / ID: 1zy8 | |||||||||
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Title | The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein (didomain) subcomplex of human pyruvate dehydrogenase complex. | |||||||||
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![]() | OXIDOREDUCTASE / human / dihydrolipoamide dehydrogenase / E3 / dihydrolipoyl dehydrogenase / dihydrolipoamide dehydrogenase binding protein / E3-binding protein / pyruvate dehydrogenase complex / alpha-keto acid complex / flavin adenine dinucleotide cofactor | |||||||||
Function / homology | ![]() acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / Glycine degradation / PDH complex synthesizes acetyl-CoA from PYR / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / acetyl-CoA biosynthetic process from pyruvate / Lysine catabolism / Regulation of pyruvate dehydrogenase (PDH) complex ...acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / Glycine degradation / PDH complex synthesizes acetyl-CoA from PYR / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / acetyl-CoA biosynthetic process from pyruvate / Lysine catabolism / Regulation of pyruvate dehydrogenase (PDH) complex / branched-chain amino acid catabolic process / oxoglutarate dehydrogenase complex / pyruvate dehydrogenase complex / Branched-chain amino acid catabolism / motile cilium / sperm capacitation / Signaling by Retinoic Acid / acyltransferase activity / mitochondrial electron transport, NADH to ubiquinone / gastrulation / Mitochondrial protein degradation / regulation of membrane potential / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / proteolysis / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ciszak, E.M. / Makal, A. / Hong, Y.S. / Vettaikkorumakankauv, A.K. / Korotchkina, L.G. / Patel, M.S. | |||||||||
![]() | ![]() Title: How Dihydrolipoamide Dehydrogenase-binding Protein Binds Dihydrolipoamide Dehydrogenase in the Human Pyruvate Dehydrogenase Complex. Authors: Ciszak, E.M. / Makal, A. / Hong, Y.S. / Vettaikkorumakankauv, A.K. / Korotchkina, L.G. / Patel, M.S. | |||||||||
History |
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Remark 7 | TLS DEFINITIONS USED IN A FEW FINAL ROUNDS OF REFINEMENT: TLS DETAILS NUMBER OF TLS GROUPS : 14 TLS ...TLS DEFINITIONS USED IN A FEW FINAL ROUNDS OF REFINEMENT: TLS DETAILS NUMBER OF TLS GROUPS : 14 TLS GROUP : 1 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 1 A 474 RESIDUE RANGE : B 1 B 474 ORIGIN FOR THE GROUP (A): 86.1202 99.6574 31.9079 T TENSOR T11: 0.0962 T22: 0.0966 T33: 0.1192 T12: -0.0077 T13: -0.0131 T23: 0.0092 L TENSOR L11: 0.3111 L22: 0.4258 L33: 0.1516 L12: 0.1598 L13: 0.0144 L23: -0.0850 S TENSOR S11: -0.0115 S12: -0.0013 S13: -0.0442 S21: -0.0584 S22: 0.0562 S23: -0.0301 S31: 0.0119 S32: -0.0028 S33: -0.0447 TLS GROUP : 2 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : C 1 C 474 RESIDUE RANGE : D 1 D 474 ORIGIN FOR THE GROUP (A): -17.3563 162.0474 24.0414 T TENSOR T11: 0.1129 T22: 0.1419 T33: 0.0669 T12: -0.0044 T13: 0.0029 T23: -0.0133 L TENSOR L11: 0.1933 L22: 0.2406 L33: 0.1909 L12: 0.1034 L13: 0.0140 L23: 0.1195 S TENSOR S11: 0.0146 S12: -0.0580 S13: 0.0224 S21: -0.0312 S22: 0.0100 S23: 0.0049 S31: -0.0371 S32: 0.0017 S33: -0.0246 TLS GROUP : 3 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : E 1 E 474 RESIDUE RANGE : F 1 F 474 ORIGIN FOR THE GROUP (A): 22.9044 111.2218 24.5784 T TENSOR T11: 0.0926 T22: 0.1239 T33: 0.0984 T12: -0.0045 T13: -0.0026 T23: 0.0204 L TENSOR L11: 0.2617 L22: 0.1605 L33: 0.2782 L12: -0.1073 L13: 0.1000 L23: -0.0903 S TENSOR S11: 0.0241 S12: 0.0053 S13: -0.0823 S21: 0.0159 S22: -0.0348 S23: -0.0010 S31: -0.0103 S32: 0.0048 S33: 0.0108 TLS GROUP : 4 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : G 1 G 474 RESIDUE RANGE : H 1 H 474 ORIGIN FOR THE GROUP (A): 44.3574 163.4538 42.3307 T TENSOR T11: 0.1103 T22: 0.1371 T33: 0.0439 T12: -0.0280 T13: 0.0094 T23: -0.0217 L TENSOR L11: 0.4296 L22: 0.2204 L33: 0.3207 L12: -0.0547 L13: -0.1238 L23: 0.1761 S TENSOR S11: -0.0052 S12: -0.0646 S13: -0.0272 S21: 0.0212 S22: -0.0436 S23: -0.0070 S31: 0.0411 S32: -0.0242 S33: 0.0488 TLS GROUP : 5 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : I 1 I 474 RESIDUE RANGE : J 1 J 474 ORIGIN FOR THE GROUP (A): 102.2937 125.8036 89.1832 T TENSOR T11: 0.2667 T22: 0.0152 T33: 0.0375 T12: 0.0568 T13: -0.0185 T23: 0.0066 L TENSOR L11: 0.2782 L22: 0.8217 L33: 0.2621 L12: -0.1916 L13: 0.0687 L23: -0.2564 S TENSOR S11: -0.0730 S12: 0.0522 S13: 0.0029 S21: 0.3286 S22: 0.0470 S23: -0.0232 S31: -0.1408 S32: -0.0309 S33: 0.0260 TLS GROUP : 6 NUMBER OF COMPONENTS GROUP : 1 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : K 130 K 172 ORIGIN FOR THE GROUP (A): 67.1227 121.3561 45.9160 T TENSOR T11: 0.1206 T22: 0.1259 T33: 0.1307 T12: 0.0719 T13: 0.0885 T23: -0.0059 L TENSOR L11: 5.4752 L22: 0.8436 L33: 4.8189 L12: 2.9672 L13: 2.3986 L23: -1.4737 S TENSOR S11: 0.0022 S12: -0.4169 S13: 0.3266 S21: 0.0591 S22: 0.0481 S23: 1.1399 S31: -0.2283 S32: 0.4191 S33: -0.0503 TLS GROUP : 7 NUMBER OF COMPONENTS GROUP : 1 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : L 130 L 172 ORIGIN FOR THE GROUP (A): -40.4707 181.2114 13.2992 T TENSOR T11: 0.1419 T22: 0.1369 T33: 0.1289 T12: 0.0481 T13: -0.0159 T23: 0.0322 L TENSOR L11: 5.4827 L22: 5.6926 L33: -0.0158 L12: 1.7497 L13: 0.5351 L23: -0.2493 S TENSOR S11: 0.0362 S12: -0.3140 S13: 0.2294 S21: -0.2651 S22: -0.3943 S23: 0.6852 S31: -0.5508 S32: -0.4283 S33: 0.3581 TLS GROUP : 8 NUMBER OF COMPONENTS GROUP : 1 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : M 130 M 172 ORIGIN FOR THE GROUP (A): -3.6551 116.8287 41.5098 T TENSOR T11: 0.1389 T22: 0.1388 T33: 0.1388 T12: 0.0001 T13: 0.0000 T23: 0.0000 L TENSOR L11: 5.6808 L22: -3.8181 L33: 7.8371 L12: -0.0512 L13: 2.2408 L23: 0.1207 S TENSOR S11: -0.2257 S12: -0.4904 S13: -1.0279 S21: 0.0234 S22: 0.1101 S23: 0.2179 S31: -0.0685 S32: -0.4809 S33: 0.1155 TLS GROUP : 9 NUMBER OF COMPONENTS GROUP : 1 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : N 130 N 172 ORIGIN FOR THE GROUP (A): 29.2149 178.9735 18.8928 T TENSOR T11: 0.1424 T22: 0.1378 T33: 0.1408 T12: 0.0092 T13: 0.0552 T23: -0.0197 L TENSOR L11: 1.9301 L22: 6.1973 L33: 7.1735 L12: -1.7731 L13: -0.9269 L23: 0.3456 S TENSOR S11: 0.2165 S12: 0.0825 S13: -0.1547 S21: -0.3692 S22: -0.1953 S23: 0.1543 S31: -0.6799 S32: -0.2946 S33: -0.0211 TLS GROUP : 10 NUMBER OF COMPONENTS GROUP : 1 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : O 130 O 172 ORIGIN FOR THE GROUP (A): 93.0687 148.0909 110.0533 T TENSOR T11: 0.1389 T22: 0.1389 T33: 0.1389 T12: -0.0003 T13: 0.0000 T23: -0.0001 L TENSOR L11: -5.5074 L22: 3.4674 L33: 3.4261 L12: -3.1769 L13: 0.0324 L23: 0.8680 S TENSOR S11: -0.3717 S12: -0.3302 S13: 0.5220 S21: 0.2067 S22: 0.5225 S23: 0.5672 S31: 0.1152 S32: -0.1844 S33: -0.1508 TLS GROUP : 11 NUMBER OF COMPONENTS GROUP : 1 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : P 130 P 172 ORIGIN FOR THE GROUP (A): 67.9552 106.9793 57.0398 T TENSOR T11: 0.1388 T22: 0.1390 T33: 0.1388 T12: -0.0001 T13: -0.0001 T23: 0.0000 L TENSOR L11: -0.5002 L22: 8.9919 L33: 8.3677 L12: 3.0593 L13: -6.6157 L23: -8.5085 S TENSOR S11: 0.0751 S12: -0.1005 S13: 0.1267 S21: 0.7428 S22: 0.1565 S23: 0.1710 S31: -0.4400 S32: -0.5036 S33: -0.2315 TLS GROUP : 12 NUMBER OF COMPONENTS GROUP : 1 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : Q 130 Q 172 ORIGIN FOR THE GROUP (A): -48.1656 169.0876 24.0358 T TENSOR T11: 0.1389 T22: 0.1389 T33: 0.1388 T12: -0.0002 T13: 0.0001 T23: 0.0000 L TENSOR L11: -0.8070 L22: 10.9262 L33: 4.3786 L12: 1.1688 L13: 2.2047 L23: -4.4870 S TENSOR S11: -0.0252 S12: 0.0282 S13: 0.5892 S21: 0.0604 S22: -0.1147 S23: 0.3524 S31: -0.0507 S32: -0.7846 S33: 0.1399 TLS GROUP : 13 NUMBER OF COMPONENTS GROUP : 1 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : R 130 R 172 ORIGIN FOR THE GROUP (A): -8.8810 106.7716 26.7941 T TENSOR T11: 0.1389 T22: 0.1387 T33: 0.1389 T12: -0.0001 T13: 0.0000 T23: 0.0002 L TENSOR L11: -1.6405 L22: -3.9522 L33: 14.0992 L12: 8.8584 L13: -0.0833 L23: -1.1462 S TENSOR S11: -0.0573 S12: -0.0086 S13: 0.8503 S21: -0.5033 S22: 0.2338 S23: -0.0232 S31: 0.1421 S32: -0.7948 S33: -0.1765 TLS GROUP : 14 NUMBER OF COMPONENTS GROUP : 1 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : S 130 S 172 ORIGIN FOR THE GROUP (A): 30.1901 190.0453 32.8045 T TENSOR T11: 0.1388 T22: 0.1387 T33: 0.1388 T12: -0.0002 T13: 0.0005 T23: 0.0000 L TENSOR L11: 4.7041 L22: 4.1759 L33: 6.7881 L12: -2.0061 L13: 3.3509 L23: -1.0774 S TENSOR S11: -0.1093 S12: 0.7393 S13: 0.1751 S21: -0.1106 S22: -0.3777 S23: 1.0177 S31: -0.7533 S32: -0.4869 S33: 0.4871 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.7 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Number of models | 2 |
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Components
#1: Protein | Mass: 50236.484 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 24449.850 Da / Num. of mol.: 5 / Fragment: didomain (lipoyl and E3-binding domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-FAD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 6000, diammonium citrate, potassium phosphate buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 188229 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.164 |
Reflection shell | Resolution: 2.59→2.68 Å / Redundancy: 2 % / Rmerge(I) obs: 0.357 / Num. unique obs: 12561 / % possible all: 59.5 |
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Processing
Software |
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Refinement | Method to determine structure: de novo chain building for E3-binding protein Starting model: PDB entries: 3LAD and 1JEH Resolution: 2.59→45.64 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.857 / SU B: 18.042 / SU ML: 0.332 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.979 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE REFINEMENT WAS DONE USING CNS THROUGHOUT THE ENTIRE MODEL BUILDING. TLS REFINEMENT WAS USED IN A FEW FINAL CYCLES. THE TLS GROUP DEFINITIONS ARE LISTED IN REMARK 7. CHAINS K-N HAVE ...Details: THE REFINEMENT WAS DONE USING CNS THROUGHOUT THE ENTIRE MODEL BUILDING. TLS REFINEMENT WAS USED IN A FEW FINAL CYCLES. THE TLS GROUP DEFINITIONS ARE LISTED IN REMARK 7. CHAINS K-N HAVE ALTERNATE POSITIONS WHICH ARE REPRESENTED IN THE 2 MODELS IN THIS FILE. NOTE THAT THE CHAINS P-S IN THE TLS GROUP DEFINITIONS CORRESPOND TO THE CHAINS K-N IN MODEL 2 OF THE STRUCTURE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.188 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→45.64 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.59 Å / Num. reflection Rwork: 12897 / Total num. of bins used: 10 |