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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
TitleThe crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein (didomain) subcomplex of human pyruvate dehydrogenase complex.
Components
  • Dihydrolipoyl dehydrogenase, mitochondrial
  • Pyruvate dehydrogenase protein X component, mitochondrial
KeywordsOXIDOREDUCTASE / 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
Function and homology information


acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / OADH complex synthesizes glutaryl-CoA from 2-OA / oxoadipate dehydrogenase complex / Glycine degradation / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD ...acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / OADH complex synthesizes glutaryl-CoA from 2-OA / oxoadipate dehydrogenase complex / Glycine degradation / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of MSUD / PDH complex synthesizes acetyl-CoA from PYR / Branched-chain ketoacid dehydrogenase kinase deficiency / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate decarboxylation to acetyl-CoA / branched-chain amino acid catabolic process / pyruvate dehydrogenase complex / oxoglutarate dehydrogenase complex / Branched-chain amino acid catabolism / 2-oxoglutarate metabolic process / motile cilium / sperm capacitation / Signaling by Retinoic Acid / pyruvate metabolic process / 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
E3-binding domain / Dihydrolipoamide Transferase / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / : / Dihydrolipoamide dehydrogenase / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site ...E3-binding domain / Dihydrolipoamide Transferase / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / : / Dihydrolipoamide dehydrogenase / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 / Chloramphenicol acetyltransferase-like 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 / Few Secondary Structures / Irregular / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Pyruvate dehydrogenase protein X component, mitochondrial / Dihydrolipoyl dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / de novo chain building for E3-binding protein / Resolution: 2.59 Å
AuthorsCiszak, E.M. / Makal, A. / Hong, Y.S. / Vettaikkorumakankauv, A.K. / Korotchkina, L.G. / Patel, M.S.
CitationJournal: J.Biol.Chem. / Year: 2006
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
DepositionJun 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 23, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _atom_site.label_asym_id / _database_2.pdbx_DOI ..._atom_site.label_asym_id / _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 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 7TLS 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 viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrolipoyl dehydrogenase, mitochondrial
B: Dihydrolipoyl dehydrogenase, mitochondrial
C: Dihydrolipoyl dehydrogenase, mitochondrial
D: Dihydrolipoyl dehydrogenase, mitochondrial
E: Dihydrolipoyl dehydrogenase, mitochondrial
F: Dihydrolipoyl dehydrogenase, mitochondrial
G: Dihydrolipoyl dehydrogenase, mitochondrial
H: Dihydrolipoyl dehydrogenase, mitochondrial
I: Dihydrolipoyl dehydrogenase, mitochondrial
J: Dihydrolipoyl dehydrogenase, mitochondrial
K: Pyruvate dehydrogenase protein X component, mitochondrial
L: Pyruvate dehydrogenase protein X component, mitochondrial
M: Pyruvate dehydrogenase protein X component, mitochondrial
N: Pyruvate dehydrogenase protein X component, mitochondrial
O: Pyruvate dehydrogenase protein X component, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)632,47025
Polymers624,61415
Non-polymers7,85610
Water8,863492
1
A: Dihydrolipoyl dehydrogenase, mitochondrial
B: Dihydrolipoyl dehydrogenase, mitochondrial
K: Pyruvate dehydrogenase protein X component, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4945
Polymers124,9233
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Dihydrolipoyl dehydrogenase, mitochondrial
D: Dihydrolipoyl dehydrogenase, mitochondrial
L: Pyruvate dehydrogenase protein X component, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4945
Polymers124,9233
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Dihydrolipoyl dehydrogenase, mitochondrial
F: Dihydrolipoyl dehydrogenase, mitochondrial
M: Pyruvate dehydrogenase protein X component, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4945
Polymers124,9233
Non-polymers1,5712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Dihydrolipoyl dehydrogenase, mitochondrial
H: Dihydrolipoyl dehydrogenase, mitochondrial
N: Pyruvate dehydrogenase protein X component, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4945
Polymers124,9233
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Dihydrolipoyl dehydrogenase, mitochondrial
J: Dihydrolipoyl dehydrogenase, mitochondrial
O: Pyruvate dehydrogenase protein X component, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4945
Polymers124,9233
Non-polymers1,5712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.790, 186.910, 217.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Number of models2

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Components

#1: Protein
Dihydrolipoyl dehydrogenase, mitochondrial / Dihydrolipoamide dehydrogenase / Glycine cleavage system L protein


Mass: 50236.484 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLD, GCSL, LAD, PHE3 / Plasmid: PROEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1_blue / References: UniProt: P09622, dihydrolipoyl dehydrogenase
#2: Protein
Pyruvate dehydrogenase protein X component, mitochondrial / Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex / Lipoyl- ...Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex / Lipoyl-containing pyruvate dehydrogenase complex component X / E3-binding protein / E3BP / proX


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.) Homo sapiens (human) / Gene: PDHX, PDX1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O00330
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.9 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: de novo chain building for E3-binding protein
Starting model: PDB entries: 3LAD and 1JEH

3lad

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.27592 8336 5 %RANDOM
Rwork0.208 ---
all0.275 188162 --
obs0.275 158086 88.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.188 Å2
Baniso -1Baniso -2Baniso -3
1--4.08 Å20 Å20 Å2
2---1.18 Å20 Å2
3---5.26 Å2
Refinement stepCycle: LAST / Resolution: 2.59→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36865 0 530 492 37887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02139308
X-RAY DIFFRACTIONr_angle_refined_deg2.1161.9853171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09955110
X-RAY DIFFRACTIONr_chiral_restr0.1160.26141
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0228798
X-RAY DIFFRACTIONr_nbd_refined0.30.318822
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.52465
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3280.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.55
X-RAY DIFFRACTIONr_mcbond_it1.487225241
X-RAY DIFFRACTIONr_mcangle_it2.633340427
X-RAY DIFFRACTIONr_scbond_it1.705214067
X-RAY DIFFRACTIONr_scangle_it2.814312744
LS refinement shellHighest resolution: 2.59 Å / Num. reflection Rwork: 12897 / Total num. of bins used: 10

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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