[Scop | Full Entry | Seq (local cached copy) | More Options ]
HEADER OXIDOREDUCTASE 03-AUG-01 1GJX TITLE SOLUTION STRUCTURE OF THE LIPOYL DOMAIN OF THE CHIMERIC TITLE 2 DIHYDROLIPOYL DEHYDROGENASE P64K FROM NEISSERIA TITLE 3 MENINGITIDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIPOYL DOMAIN RESIDUES 2-82; COMPND 5 SYNONYM: LIPOAMIDE DEHYDROGENASE, E3 COMPONENT; COMPND 6 EC: 1.8.1.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 4 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE; SOURCE 5 EXPRESSION_SYSTEM_PLASMID: PM-143 KEYWDS LIPOYL DOMAIN, DIHYDROLIPOYL DEHYDROGENASE, MULTIENZYME KEYWDS 2 COMPLEX, NEISSERIA MENINGITIDIS, POST-TRANSLATIONAL KEYWDS 3 MODIFICATION EXPDTA NMR, 18 STRUCTURES AUTHOR K.TOZAWA,R.W.BROADHURST,A.R.C.RAINE,C.FULLER,A.ALVAREZ, AUTHOR 2 G.GUILLEN,G.PADRON,R.N.PERHAM REVDAT 1 28-NOV-01 1GJX 0 JRNL AUTH K.TOZAWA,R.W.BROADHURST,A.R.RAINE,C.FULLER, JRNL AUTH 2 A.ALVAREZ,G.GUILLEN,G.PADRON,R.N.PERHAM JRNL TITL SOLUTION STRUCTURE OF THE LIPOYL DOMAIN OF THE JRNL TITL 2 CHIMERIC DIHYDROLIPOYL DEHYDROGENASE P64K FROM JRNL TITL 3 NEISSERIA MENINGITIDIS. JRNL REF EUR.J.BIOCHEM. V. 268 4908 2001 JRNL REFN ASTM EJBCAI IX ISSN 0014-2956 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER NUMBER OF NON-HYDROGEN ATOMS USED IN REMARK 3 REFINEMENT. PROTEIN ATOMS : 583 NUCLEIC ACID REMARK 3 ATOMS : 0 HETEROGEN ATOMS : 0 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE REMARK 4 REMARK 4 1GJX COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.101 (2007-05-31) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI. REMARK 100 THE EBI ID CODE IS EBI-8427. 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 : 20 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY, TOCSY, HNCA, HN REMARK 210 (CO)CA, 15N NOESY-HSQC, 15N- REMARK 210 TOCSY-HSQC, HCCH-TOCSY, 13C- REMARK 210 NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AZARA, ANSIG3.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO VIOLATIONS, LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELED LIPOYL DOMAIN 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 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 ILE A 19 CA ILE A 19 CB 0.039 REMARK 500 2 ILE A 19 CA ILE A 19 CB 0.037 REMARK 500 3 ILE A 19 CA ILE A 19 CB 0.036 REMARK 500 4 ILE A 19 CA ILE A 19 CB 0.038 REMARK 500 5 ILE A 19 CA ILE A 19 CB 0.038 REMARK 500 6 ILE A 19 CA ILE A 19 CB 0.038 REMARK 500 7 ILE A 19 CA ILE A 19 CB 0.036 REMARK 500 8 ILE A 19 CA ILE A 19 CB 0.034 REMARK 500 9 ILE A 19 CA ILE A 19 CB 0.042 REMARK 500 10 ILE A 19 CA ILE A 19 CB 0.030 REMARK 500 11 ILE A 19 CA ILE A 19 CB 0.035 REMARK 500 12 ILE A 19 CA ILE A 19 CB 0.033 REMARK 500 13 ILE A 19 CA ILE A 19 CB 0.039 REMARK 500 14 ILE A 19 CA ILE A 19 CB 0.039 REMARK 500 14 ILE A 66 CA ILE A 66 CB 0.025 REMARK 500 15 ILE A 19 CA ILE A 19 CB 0.028 REMARK 500 16 ILE A 19 CA ILE A 19 CB 0.028 REMARK 500 17 ILE A 19 CA ILE A 19 CB 0.029 REMARK 500 18 ILE A 19 CA ILE A 19 CB 0.037 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 THR A 40 CA - CB - CG2 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 ILE A 19 CA - CB - CG1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ILE A 19 CA - CB - CG1 ANGL. DEV. = 3.7 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 1 ALA A 49 150.05 59.67 REMARK 500 1 ALA A 77 138.04 57.12 REMARK 500 2 ALA A 77 147.05 56.73 REMARK 500 3 ALA A 49 163.93 56.57 REMARK 500 3 ALA A 77 124.18 56.39 REMARK 500 4 ALA A 77 122.66 57.57 REMARK 500 5 ALA A 49 -51.25 81.64 REMARK 500 7 VAL A 7 147.04 58.75 REMARK 500 7 VAL A 25 131.58 63.40 REMARK 500 7 ALA A 77 131.06 59.40 REMARK 500 8 VAL A 25 -86.88 66.73 REMARK 500 8 ALA A 49 168.34 54.23 REMARK 500 8 ALA A 77 159.84 53.62 REMARK 500 8 GLU A 78 -65.41 72.46 REMARK 500 10 ALA A 49 151.44 59.28 REMARK 500 10 ALA A 77 133.44 57.21 REMARK 500 11 ALA A 49 160.91 57.88 REMARK 500 12 VAL A 25 -82.20 65.92 REMARK 500 12 ALA A 77 149.03 56.94 REMARK 500 14 ALA A 49 164.44 56.17 REMARK 500 14 ALA A 77 139.88 58.35 REMARK 500 15 VAL A 7 145.62 60.83 REMARK 500 15 VAL A 25 120.55 60.63 REMARK 500 15 ALA A 77 132.70 59.60 REMARK 500 16 VAL A 7 139.46 59.83 REMARK 500 16 VAL A 25 -86.48 66.07 REMARK 500 16 ALA A 77 125.64 57.71 REMARK 500 17 VAL A 25 124.70 62.72 REMARK 500 18 VAL A 7 149.27 58.55 REMARK 500 18 VAL A 25 127.98 62.33 REMARK 500 18 ALA A 77 162.86 54.06 REMARK 500 18 GLU A 78 -67.95 69.63 DBREF 1GJX A 1 81 UNP Q9JZ09 Q9JZ09_NEIMB 2 82 SEQRES 1 A 81 ALA LEU VAL GLU LEU LYS VAL PRO ASP ILE GLY GLY HIS SEQRES 2 A 81 GLU ASN VAL ASP ILE ILE ALA VAL GLU VAL ASN VAL GLY SEQRES 3 A 81 ASP THR ILE ALA VAL ASP ASP THR LEU ILE THR LEU GLU SEQRES 4 A 81 THR ASP LYS ALA THR MET ASP VAL PRO ALA GLU VAL ALA SEQRES 5 A 81 GLY VAL VAL LYS GLU VAL LYS VAL LYS VAL GLY ASP LYS SEQRES 6 A 81 ILE SER GLU GLY GLY LEU ILE VAL VAL VAL GLU ALA GLU SEQRES 7 A 81 GLY THR ALA SHEET 1 AA 4 LEU A 2 LYS A 6 0 SHEET 2 AA 4 ILE A 72 ALA A 77 -1 O VAL A 75 N VAL A 3 SHEET 3 AA 4 LYS A 56 LYS A 61 -1 O GLU A 76 N LYS A 56 SHEET 4 AA 4 ASP A 27 ALA A 30 -1 O LYS A 56 N ASP A 27 SHEET 1 AB 4 ALA A 43 VAL A 47 0 SHEET 2 AB 4 LEU A 35 THR A 40 -1 O ILE A 36 N VAL A 47 SHEET 3 AB 4 ILE A 18 VAL A 21 -1 O ASP A 17 N GLU A 39 SHEET 4 AB 4 ASP A 64 SER A 67 -1 O ILE A 66 N VAL A 16 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