HEADER TRANSFERASE 26-APR-06 2DNE TITLE SOLUTION STRUCTURE OF RSGI RUH-058, A LIPOYL DOMAIN OF HUMAN 2-OXOACID TITLE 2 DEHYDROGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF COMPND 3 PYRUVATE DEHYDROGENASE COMPLEX; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: N-TERMINAL DOMAIN OF 2-OXOACID DEHYDROGENASE, LIPOYL- COMPND 6 BINDING DOMAIN; COMPND 7 SYNONYM: PYRUVATE DEHYDROGENASE COMPLEX E2 SUBUNIT, PDCE2, E2, COMPND 8 DIHYDROLIPOAMIDE S-ACETYLTRANSFERASE COMPONENT OF PYRUVATE COMPND 9 DEHYDROGENASE COMPLEX, PDC-E2, 70 KDA MITOCHONDRIAL AUTOANTIGEN OF COMPND 10 PRIMARY BILIARY CIRRHOSIS, PBC, M2 ANTIGEN COMPLEX 70 KDA SUBUNIT; COMPND 11 EC: 2.3.1.12; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050829-14; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS LIPOYL DOMAIN, LIPOIC ACID, 2-OXOACID DEHYDROGENASE, OXOACID KEYWDS 2 DEHYDROGENASE, SYNTHESIS OF ACYL COA, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 3 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 4 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.Z.M.RUHUL MOMEN,H.HIROTA,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DNE 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DNE 1 VERSN REVDAT 1 26-OCT-06 2DNE 0 JRNL AUTH A.Z.M.RUHUL MOMEN,H.HIROTA,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF RSGI RUH-058, A LIPOYL DOMAIN OF HUMAN JRNL TITL 2 2-OXOACID DEHYDROGENASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 1.0.7 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DNE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025618. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.09MM DOMAIN U-15N, 13C; 20MM D REMARK 210 -TRIS-HCL(PH 7.0); 100MM NACL; REMARK 210 1MM D-DTT; 0.02% NAN3; 10% D2O, REMARK 210 90% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.04, REMARK 210 KUJIRA 0.955, CYANA 1.0.7 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH REMARK 210 THE LOWEST ENERGY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H ILE A 35 O CYS A 59 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 SER A 2 106.16 -170.67 REMARK 500 1 LEU A 12 100.06 -39.99 REMARK 500 1 THR A 18 35.47 -93.30 REMARK 500 1 ILE A 24 92.56 -66.38 REMARK 500 1 GLU A 28 -31.95 -38.81 REMARK 500 1 ALA A 49 -174.90 167.32 REMARK 500 1 GLU A 57 -176.83 -176.34 REMARK 500 1 CYS A 59 -174.41 169.99 REMARK 500 1 ILE A 64 75.98 -110.95 REMARK 500 1 THR A 70 102.71 -54.29 REMARK 500 1 ASP A 72 35.43 86.52 REMARK 500 1 ILE A 78 123.68 -39.90 REMARK 500 1 ASN A 94 70.89 -119.18 REMARK 500 1 ASP A 98 96.19 50.13 REMARK 500 1 SER A 99 94.32 -61.05 REMARK 500 1 SER A 100 109.09 -177.35 REMARK 500 1 SER A 103 93.21 -162.36 REMARK 500 1 SER A 107 93.18 49.59 REMARK 500 2 SER A 2 81.66 39.83 REMARK 500 2 SER A 6 -172.63 67.53 REMARK 500 2 LEU A 12 104.28 -46.26 REMARK 500 2 THR A 18 32.69 -92.19 REMARK 500 2 GLU A 28 -36.80 -37.60 REMARK 500 2 GLU A 37 120.89 -38.62 REMARK 500 2 ALA A 49 -174.92 173.95 REMARK 500 2 CYS A 59 -171.90 -170.15 REMARK 500 2 ILE A 64 76.47 -113.11 REMARK 500 2 THR A 70 102.66 -54.05 REMARK 500 2 ASP A 72 40.69 83.71 REMARK 500 2 SER A 103 -58.24 -165.89 REMARK 500 3 SER A 6 68.99 -167.55 REMARK 500 3 LEU A 12 102.34 -43.03 REMARK 500 3 THR A 18 36.16 -97.15 REMARK 500 3 GLU A 28 -29.99 -39.88 REMARK 500 3 ALA A 49 -174.93 166.46 REMARK 500 3 CYS A 59 -173.94 168.50 REMARK 500 3 ILE A 64 79.66 -117.29 REMARK 500 3 ALA A 67 -162.43 -77.66 REMARK 500 3 THR A 70 104.23 -36.37 REMARK 500 3 ASP A 72 50.42 78.24 REMARK 500 3 ASP A 98 114.92 -174.75 REMARK 500 3 SER A 106 92.30 55.95 REMARK 500 4 SER A 2 92.28 -62.51 REMARK 500 4 SER A 6 123.01 65.40 REMARK 500 4 LEU A 12 103.72 -45.28 REMARK 500 4 THR A 18 32.89 -94.47 REMARK 500 4 ILE A 24 92.11 -66.13 REMARK 500 4 ALA A 49 -175.01 166.88 REMARK 500 4 CYS A 59 -171.89 177.18 REMARK 500 4 ILE A 64 77.32 -113.20 REMARK 500 REMARK 500 THIS ENTRY HAS 290 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002000527.1 RELATED DB: TARGETDB DBREF 2DNE A 8 102 UNP P10515 ODP2_HUMAN 59 153 SEQADV 2DNE GLY A 1 UNP P10515 CLONING ARTIFACT SEQADV 2DNE SER A 2 UNP P10515 CLONING ARTIFACT SEQADV 2DNE SER A 3 UNP P10515 CLONING ARTIFACT SEQADV 2DNE GLY A 4 UNP P10515 CLONING ARTIFACT SEQADV 2DNE SER A 5 UNP P10515 CLONING ARTIFACT SEQADV 2DNE SER A 6 UNP P10515 CLONING ARTIFACT SEQADV 2DNE GLY A 7 UNP P10515 CLONING ARTIFACT SEQADV 2DNE SER A 103 UNP P10515 CLONING ARTIFACT SEQADV 2DNE GLY A 104 UNP P10515 CLONING ARTIFACT SEQADV 2DNE PRO A 105 UNP P10515 CLONING ARTIFACT SEQADV 2DNE SER A 106 UNP P10515 CLONING ARTIFACT SEQADV 2DNE SER A 107 UNP P10515 CLONING ARTIFACT SEQADV 2DNE GLY A 108 UNP P10515 CLONING ARTIFACT SEQRES 1 A 108 GLY SER SER GLY SER SER GLY GLN LYS VAL PRO LEU PRO SEQRES 2 A 108 SER LEU SER PRO THR MET GLN ALA GLY THR ILE ALA ARG SEQRES 3 A 108 TRP GLU LYS LYS GLU GLY ASP LYS ILE ASN GLU GLY ASP SEQRES 4 A 108 LEU ILE ALA GLU VAL GLU THR ASP LYS ALA THR VAL GLY SEQRES 5 A 108 PHE GLU SER LEU GLU GLU CYS TYR MET ALA LYS ILE LEU SEQRES 6 A 108 VAL ALA GLU GLY THR ARG ASP VAL PRO ILE GLY ALA ILE SEQRES 7 A 108 ILE CYS ILE THR VAL GLY LYS PRO GLU ASP ILE GLU ALA SEQRES 8 A 108 PHE LYS ASN TYR THR LEU ASP SER SER ALA ALA SER GLY SEQRES 9 A 108 PRO SER SER GLY HELIX 1 1 LYS A 85 ASN A 94 1 10 SHEET 1 A 4 GLN A 8 PRO A 11 0 SHEET 2 A 4 ILE A 78 VAL A 83 -1 O ILE A 79 N VAL A 10 SHEET 3 A 4 CYS A 59 LYS A 63 -1 N LYS A 63 O ILE A 81 SHEET 4 A 4 LYS A 34 ILE A 35 -1 N ILE A 35 O CYS A 59 SHEET 1 B 4 THR A 50 GLU A 54 0 SHEET 2 B 4 LEU A 40 GLU A 45 -1 N ILE A 41 O PHE A 53 SHEET 3 B 4 ALA A 21 ARG A 26 -1 N ALA A 25 O GLU A 43 SHEET 4 B 4 VAL A 73 PRO A 74 -1 O VAL A 73 N GLY A 22 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1