PDB Short entry for 1QJO HEADER DIHYDROLIPOAMIDE ACETYLTRANSFERASE 29-JUN-99 1QJO TITLE INNERMOST LIPOYL DOMAIN OF THE PYRUVATE DEHYDROGENASE FROM ESCHERICHIA TITLE 2 COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROLIPOAMIDE ACETYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIPOAMIDE BINDING DOMAIN OF E2P; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI BL21(DE3); SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 CELLULAR_LOCATION: CYTOPLASM; SOURCE 5 GENE: E2P_ECOLI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: T7; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11C KEYWDS DIHYDROLIPOAMIDE ACETYLTRANSFERASE, LIPOYL DOMAIN, PYRUVATE KEYWDS 2 DEHYDROGENASE EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR D.D.JONES,M.J.HOWARD,R.N.PERHAM REVDAT 5 31-JAN-18 1QJO 1 SOURCE JRNL REMARK REVDAT 4 24-FEB-09 1QJO 1 VERSN REVDAT 3 21-JUL-00 1QJO 1 JRNL REVDAT 2 04-JUL-00 1QJO 1 JRNL REVDAT 1 30-JUN-99 1QJO 0 JRNL AUTH D.D.JONES,K.M.STOTT,M.J.HOWARD,R.N.PERHAM JRNL TITL RESTRICTED MOTION OF THE LIPOYL-LYSINE SWINGING ARM IN THE JRNL TITL 2 PYRUVATE DEHYDROGENASE COMPLEX OF ESCHERICHIA COLI. JRNL REF BIOCHEMISTRY V. 39 8448 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10913250 JRNL DOI 10.1021/BI992978I REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.J.HOWARD,H.J.CHAUHAN,G.J.DOMINGO,C.FULLER,R.N.PERHAM REMARK 1 TITL PROTEIN-PROTEIN INTERACTION REVEALED BY NMR T(2) RELAXATION REMARK 1 TITL 2 EXPERIMENTS: THE LIPOYL DOMAIN AND E1 COMPONENT OF THE REMARK 1 TITL 3 PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX OF BACILLUS REMARK 1 TITL 4 STEAROTHERMOPHILUS REMARK 1 REF J.MOL.BIOL. V. 295 1023 2000 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 10656808 REMARK 1 DOI 10.1006/JMBI.1999.3391 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE N-TERMINAL MET IS AN ARTIFACT OF REMARK 3 THE EXPRESSION SYSTEM USED AND NO RESTRAINTS WERE USED TO REMARK 3 CALCULATE ITS PART IN THE STRUCTURE. REMARK 4 REMARK 4 1QJO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1290001228. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 20MM NAPI REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 90% H2O/ 10%D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQFCOSY; HMQC REMARK 210 -NOESY; HMQC-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AM REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANSIG REMARK 210 METHOD USED : XPLOR REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 GLU A 75 CB GLU A 75 CG 0.118 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ASP A 9 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 ASP A 63 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 1 PHE A 74 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 ASP A 13 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 3 ASP A 26 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 3 ASP A 63 CB - CG - OD2 ANGL. DEV. = -9.0 DEGREES REMARK 500 6 ASP A 9 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 7 ASP A 13 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 8 ASP A 26 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 9 ASP A 13 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 9 ASP A 13 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 9 ASP A 40 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 10 ASP A 13 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 10 PHE A 74 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 10 PHE A 74 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 11 ASP A 13 N - CA - CB ANGL. DEV. = -13.3 DEGREES REMARK 500 11 ASP A 13 N - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 11 ASP A 26 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 11 ASP A 40 N - CA - CB ANGL. DEV. = -11.3 DEGREES REMARK 500 11 ASP A 40 CB - CG - OD2 ANGL. DEV. = -7.9 DEGREES REMARK 500 11 ASP A 63 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 12 ASP A 13 N - CA - CB ANGL. DEV. = -13.2 DEGREES REMARK 500 12 ASP A 26 CB - CG - OD1 ANGL. DEV. = -6.9 DEGREES REMARK 500 12 ASP A 40 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 13 ASP A 13 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 13 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 13 ASP A 63 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 14 ASP A 9 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 15 ASP A 40 CB - CG - OD2 ANGL. DEV. = -9.6 DEGREES REMARK 500 19 ASP A 63 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 20 ASP A 13 N - CA - CB ANGL. DEV. = -11.3 DEGREES REMARK 500 21 ASP A 63 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 22 GLU A 38 OE1 - CD - OE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 22 GLU A 56 N - CA - CB ANGL. DEV. = -12.2 DEGREES REMARK 500 23 ASP A 40 CB - CG - OD2 ANGL. DEV. = -9.8 DEGREES REMARK 500 23 ASP A 63 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 23 ASP A 63 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 24 ASP A 63 CB - CG - OD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 26 ASP A 40 CB - CG - OD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 27 ASP A 13 N - CA - CB ANGL. DEV. = -12.4 DEGREES REMARK 500 28 ASP A 63 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 29 ASP A 9 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 29 ASP A 13 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 29 ASP A 63 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 30 ASP A 9 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 30 ASP A 13 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 30 ASP A 63 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES 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 PRO A 8 -90.72 -66.58 REMARK 500 1 ASP A 13 -106.33 -9.95 REMARK 500 1 GLU A 31 -16.54 60.49 REMARK 500 1 SER A 33 138.44 -36.57 REMARK 500 1 ASP A 40 -106.25 -111.02 REMARK 500 1 LYS A 58 52.54 -90.65 REMARK 500 1 SER A 69 132.92 -38.31 REMARK 500 1 ILE A 71 -63.99 -23.12 REMARK 500 1 VAL A 76 73.60 -60.30 REMARK 500 1 GLU A 77 -155.30 83.22 REMARK 500 1 ALA A 79 50.91 4.31 REMARK 500 2 VAL A 2 161.24 -48.91 REMARK 500 2 ALA A 30 173.83 -57.45 REMARK 500 2 GLU A 31 -18.67 62.79 REMARK 500 2 LEU A 34 -64.52 -92.77 REMARK 500 2 GLU A 38 -142.96 -131.49 REMARK 500 2 ASP A 40 58.06 28.61 REMARK 500 2 LYS A 41 -6.39 159.02 REMARK 500 2 ALA A 42 140.73 -179.27 REMARK 500 2 GLU A 77 82.25 -58.19 REMARK 500 2 ALA A 79 153.12 114.16 REMARK 500 3 VAL A 2 103.34 10.67 REMARK 500 3 ILE A 10 64.14 -53.49 REMARK 500 3 GLU A 14 149.17 41.40 REMARK 500 3 VAL A 24 91.95 -59.37 REMARK 500 3 ALA A 30 157.58 -44.05 REMARK 500 3 GLU A 31 -20.05 61.49 REMARK 500 3 LYS A 41 -6.83 -24.31 REMARK 500 3 LYS A 66 154.59 149.94 REMARK 500 3 THR A 67 103.59 -25.09 REMARK 500 3 ILE A 71 -58.25 -22.75 REMARK 500 3 VAL A 76 33.92 -54.39 REMARK 500 3 ALA A 79 -90.41 97.43 REMARK 500 4 VAL A 2 119.58 85.48 REMARK 500 4 VAL A 7 122.71 -20.75 REMARK 500 4 PRO A 8 -172.10 -65.36 REMARK 500 4 ASP A 9 45.08 -65.66 REMARK 500 4 ILE A 10 48.61 -80.25 REMARK 500 4 MET A 21 -51.69 -20.30 REMARK 500 4 VAL A 24 94.99 -54.24 REMARK 500 4 GLU A 31 -21.55 118.89 REMARK 500 4 LEU A 34 -57.25 -29.99 REMARK 500 4 ASP A 40 59.78 -3.94 REMARK 500 4 VAL A 76 56.27 -91.15 REMARK 500 4 GLU A 77 -173.27 66.26 REMARK 500 4 ALA A 79 -102.02 -156.73 REMARK 500 5 VAL A 2 123.88 -11.73 REMARK 500 5 ASP A 9 53.77 -69.20 REMARK 500 5 ILE A 10 21.14 -70.87 REMARK 500 5 ASP A 13 -74.02 -77.89 REMARK 500 REMARK 500 THIS ENTRY HAS 459 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DPC RELATED DB: PDB DBREF 1QJO A 2 80 UNP P06959 ODP2_ECOLI 207 284 SEQRES 1 A 80 MET VAL LYS GLU VAL ASN VAL PRO ASP ILE GLY GLY ASP SEQRES 2 A 80 GLU VAL GLU VAL THR GLU VAL MET VAL LYS VAL GLY ASP SEQRES 3 A 80 LYS VAL ALA ALA GLU GLN SER LEU ILE THR VAL GLU GLY SEQRES 4 A 80 ASP LYS ALA SER MET GLU VAL PRO ALA PRO PHE ALA GLY SEQRES 5 A 80 VAL VAL LYS GLU LEU LYS VAL ASN VAL GLY ASP LYS VAL SEQRES 6 A 80 LYS THR GLY SER LEU ILE MET ILE PHE GLU VAL GLU GLY SEQRES 7 A 80 ALA ALA SHEET 1 A 4 VAL A 2 ASN A 6 0 SHEET 2 A 4 LEU A 70 VAL A 76 -1 O MET A 72 N VAL A 5 SHEET 3 A 4 GLY A 52 LYS A 58 -1 O VAL A 53 N GLU A 75 SHEET 4 A 4 ASP A 26 VAL A 28 -1 O VAL A 28 N GLY A 52 SHEET 1 B 4 ALA A 42 PRO A 47 0 SHEET 2 B 4 LEU A 34 GLY A 39 -1 N LEU A 34 O VAL A 46 SHEET 3 B 4 VAL A 15 VAL A 20 -1 O GLU A 16 N GLU A 38 SHEET 4 B 4 ASP A 63 VAL A 65 -1 O VAL A 65 N VAL A 15 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