HEADER ISOMERASE 30-MAR-06 2DJ1 TITLE THE SOLUTION STRUCTURE OF THE FIRST THIOREDOXIN DOMAIN OF MOUSE TITLE 2 PROTEIN DISULFIDE-ISOMERASE A4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DISULFIDE-ISOMERASE A4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 1ST THIOREDOXIN DOMAIN; COMPND 5 SYNONYM: PROTEIN ERP-72, ERP72; COMPND 6 EC: 5.3.4.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PDIA4, CAI, ERP72; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P050509-10; SOURCE 9 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS PROTEIN ERP-72, ERP72, CAI, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, ISOMERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 29-MAY-24 2DJ1 1 REMARK REVDAT 3 09-MAR-22 2DJ1 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DJ1 1 VERSN REVDAT 1 30-SEP-06 2DJ1 0 JRNL AUTH N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL THE SOLUTION STRUCTURE OF THE FIRST THIOREDOXIN DOMAIN OF JRNL TITL 2 MOUSE PROTEIN DISULFIDE-ISOMERASE A4 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DJ1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025470. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2MM THIOREDOXIN DOMAIN U REMARK 210 -15N,13C; 20MM D-TRIS HCL; 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.955, CYANA 2.0.17 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 LEAST RESTRAINT 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: 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 LEU A 11 89.82 -59.67 REMARK 500 1 ASP A 24 -19.69 -47.35 REMARK 500 1 PHE A 27 -70.76 -58.56 REMARK 500 1 ASP A 33 51.89 -112.98 REMARK 500 1 ASP A 88 44.99 38.08 REMARK 500 1 VAL A 89 87.54 -69.38 REMARK 500 1 LYS A 100 26.89 43.80 REMARK 500 1 ARG A 110 80.96 -68.33 REMARK 500 1 PRO A 131 -168.65 -69.76 REMARK 500 1 PRO A 137 93.14 -69.73 REMARK 500 1 SER A 138 42.37 36.62 REMARK 500 1 SER A 139 99.88 -50.46 REMARK 500 2 ASP A 8 43.38 37.86 REMARK 500 2 ASN A 66 156.44 -41.99 REMARK 500 2 PRO A 69 96.68 -69.82 REMARK 500 2 ASP A 88 46.16 39.13 REMARK 500 2 ARG A 110 82.88 -67.45 REMARK 500 2 SER A 123 -38.21 -39.56 REMARK 500 2 PRO A 131 95.38 -69.76 REMARK 500 3 ASP A 8 111.89 -172.88 REMARK 500 3 LEU A 11 99.17 -69.29 REMARK 500 3 PHE A 27 -72.84 -72.27 REMARK 500 3 TYR A 106 -60.46 -95.43 REMARK 500 3 ASP A 107 50.81 35.41 REMARK 500 3 PRO A 131 -171.58 -69.80 REMARK 500 3 PRO A 137 2.83 -69.70 REMARK 500 4 ASP A 9 47.90 39.43 REMARK 500 4 ASP A 10 -68.53 -103.98 REMARK 500 4 LYS A 14 -175.09 -68.30 REMARK 500 4 ASP A 88 44.48 37.33 REMARK 500 4 VAL A 89 97.63 -69.41 REMARK 500 4 LYS A 100 27.84 47.27 REMARK 500 4 PRO A 131 -178.58 -69.74 REMARK 500 5 ASN A 17 41.64 74.21 REMARK 500 5 CYS A 49 -27.02 -38.96 REMARK 500 5 ASP A 65 31.37 -88.19 REMARK 500 5 PRO A 69 96.95 -69.72 REMARK 500 5 ASP A 88 48.09 39.11 REMARK 500 5 LYS A 100 26.91 48.93 REMARK 500 5 ASP A 107 48.43 -97.55 REMARK 500 5 PRO A 131 0.89 -69.72 REMARK 500 6 ASP A 88 42.53 39.69 REMARK 500 6 VAL A 89 98.48 -65.24 REMARK 500 6 ARG A 110 95.22 -49.03 REMARK 500 6 PRO A 131 81.74 -69.70 REMARK 500 6 SER A 138 148.90 -35.21 REMARK 500 6 SER A 139 97.28 -60.70 REMARK 500 7 SER A 5 145.23 -171.51 REMARK 500 7 ASP A 10 -52.16 -124.69 REMARK 500 7 ASP A 24 -19.66 -47.89 REMARK 500 REMARK 500 THIS ENTRY HAS 177 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MMT008000334.2 RELATED DB: TARGETDB DBREF 2DJ1 A 8 134 UNP P08003 PDIA4_MOUSE 46 172 SEQADV 2DJ1 GLY A 1 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 SER A 2 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 SER A 3 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 GLY A 4 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 SER A 5 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 SER A 6 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 GLY A 7 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 SER A 135 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 GLY A 136 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 PRO A 137 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 SER A 138 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 SER A 139 UNP P08003 CLONING ARTIFACT SEQADV 2DJ1 GLY A 140 UNP P08003 CLONING ARTIFACT SEQRES 1 A 140 GLY SER SER GLY SER SER GLY ASP ASP ASP LEU GLU VAL SEQRES 2 A 140 LYS GLU GLU ASN GLY VAL TRP VAL LEU ASN ASP GLY ASN SEQRES 3 A 140 PHE ASP ASN PHE VAL ALA ASP LYS ASP THR VAL LEU LEU SEQRES 4 A 140 GLU PHE TYR ALA PRO TRP CYS GLY HIS CYS LYS GLN PHE SEQRES 5 A 140 ALA PRO GLU TYR GLU LYS ILE ALA SER THR LEU LYS ASP SEQRES 6 A 140 ASN ASP PRO PRO ILE ALA VAL ALA LYS ILE ASP ALA THR SEQRES 7 A 140 SER ALA SER MET LEU ALA SER LYS PHE ASP VAL SER GLY SEQRES 8 A 140 TYR PRO THR ILE LYS ILE LEU LYS LYS GLY GLN ALA VAL SEQRES 9 A 140 ASP TYR ASP GLY SER ARG THR GLN GLU GLU ILE VAL ALA SEQRES 10 A 140 LYS VAL ARG GLU VAL SER GLN PRO ASP TRP THR PRO PRO SEQRES 11 A 140 PRO GLU VAL THR SER GLY PRO SER SER GLY HELIX 1 1 ASN A 26 ALA A 32 1 7 HELIX 2 2 CYS A 46 GLN A 51 1 6 HELIX 3 3 PHE A 52 ASP A 65 1 14 HELIX 4 4 ALA A 80 PHE A 87 1 8 HELIX 5 5 THR A 111 GLN A 124 1 14 SHEET 1 A 6 LYS A 14 GLU A 16 0 SHEET 2 A 6 VAL A 19 VAL A 21 -1 O VAL A 21 N LYS A 14 SHEET 3 A 6 ALA A 71 ILE A 75 1 O LYS A 74 N TRP A 20 SHEET 4 A 6 THR A 36 PHE A 41 1 N GLU A 40 O ILE A 75 SHEET 5 A 6 THR A 94 LYS A 99 -1 O THR A 94 N PHE A 41 SHEET 6 A 6 GLN A 102 ASP A 105 -1 O VAL A 104 N ILE A 97 CISPEP 1 ASP A 67 PRO A 68 1 -0.04 CISPEP 2 TYR A 92 PRO A 93 1 -0.09 CISPEP 3 ASP A 67 PRO A 68 2 0.05 CISPEP 4 TYR A 92 PRO A 93 2 -0.09 CISPEP 5 ASP A 67 PRO A 68 3 0.07 CISPEP 6 TYR A 92 PRO A 93 3 -0.13 CISPEP 7 ASP A 67 PRO A 68 4 0.07 CISPEP 8 TYR A 92 PRO A 93 4 0.00 CISPEP 9 ASP A 67 PRO A 68 5 0.03 CISPEP 10 TYR A 92 PRO A 93 5 -0.09 CISPEP 11 ASP A 67 PRO A 68 6 0.01 CISPEP 12 TYR A 92 PRO A 93 6 -0.03 CISPEP 13 ASP A 67 PRO A 68 7 -0.01 CISPEP 14 TYR A 92 PRO A 93 7 -0.05 CISPEP 15 ASP A 67 PRO A 68 8 0.00 CISPEP 16 TYR A 92 PRO A 93 8 -0.11 CISPEP 17 ASP A 67 PRO A 68 9 -0.02 CISPEP 18 TYR A 92 PRO A 93 9 0.03 CISPEP 19 ASP A 67 PRO A 68 10 0.05 CISPEP 20 TYR A 92 PRO A 93 10 -0.02 CISPEP 21 ASP A 67 PRO A 68 11 0.03 CISPEP 22 TYR A 92 PRO A 93 11 -0.16 CISPEP 23 ASP A 67 PRO A 68 12 0.10 CISPEP 24 TYR A 92 PRO A 93 12 -0.02 CISPEP 25 ASP A 67 PRO A 68 13 -0.04 CISPEP 26 TYR A 92 PRO A 93 13 -0.07 CISPEP 27 ASP A 67 PRO A 68 14 -0.03 CISPEP 28 TYR A 92 PRO A 93 14 0.00 CISPEP 29 ASP A 67 PRO A 68 15 -0.04 CISPEP 30 TYR A 92 PRO A 93 15 -0.06 CISPEP 31 ASP A 67 PRO A 68 16 0.02 CISPEP 32 TYR A 92 PRO A 93 16 -0.07 CISPEP 33 ASP A 67 PRO A 68 17 0.02 CISPEP 34 TYR A 92 PRO A 93 17 -0.04 CISPEP 35 ASP A 67 PRO A 68 18 -0.01 CISPEP 36 TYR A 92 PRO A 93 18 -0.02 CISPEP 37 ASP A 67 PRO A 68 19 0.04 CISPEP 38 TYR A 92 PRO A 93 19 -0.08 CISPEP 39 ASP A 67 PRO A 68 20 0.00 CISPEP 40 TYR A 92 PRO A 93 20 -0.04 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