PDB Short entry for 2D8K HEADER ENDOCYTOSIS/EXOCYTOSIS 06-DEC-05 2D8K TITLE SOLUTION STRUCTURE OF THE FIRST C2 DOMAIN OF SYNAPTOTAGMIN VII COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN VII; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2 DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SYT7; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050620-09; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS EXOCYTOSIS, CALCIUM BINDING, LYSOSOME, C2 DOMAIN, SYNAPTOTAGMIN, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2D8K 1 REMARK SEQADV REVDAT 2 24-FEB-09 2D8K 1 VERSN REVDAT 1 06-JUN-06 2D8K 0 JRNL AUTH T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE FIRST C2 DOMAIN OF SYNAPTOTAGMIN JRNL TITL 2 VII 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 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D8K COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000025121. 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 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.20MM C2 DOMAIN U-15N,13C; 20MM REMARK 210 TRISHCL, 100MM NACL, 1MM DTT, REMARK 210 0.02% NAN3; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20020425, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.901, 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 LOWEST ENERGY 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 MET A 33 -75.30 -40.78 REMARK 500 1 LYS A 34 -178.77 -174.89 REMARK 500 1 LYS A 41 -39.45 -131.61 REMARK 500 1 ASP A 48 79.43 -108.32 REMARK 500 1 ASP A 58 126.63 -33.28 REMARK 500 1 LYS A 66 178.97 -56.95 REMARK 500 1 ASN A 77 35.01 34.47 REMARK 500 1 LYS A 89 -60.17 -99.55 REMARK 500 1 VAL A 90 -30.50 -38.48 REMARK 500 1 TYR A 102 105.64 -57.76 REMARK 500 1 ASN A 108 119.65 -163.91 REMARK 500 1 ASP A 122 78.07 -62.63 REMARK 500 1 LEU A 133 99.36 -34.54 REMARK 500 1 PRO A 135 95.57 -69.70 REMARK 500 1 PRO A 138 -173.38 -69.72 REMARK 500 2 ASN A 11 52.72 -97.24 REMARK 500 2 MET A 33 -75.90 -47.07 REMARK 500 2 SER A 44 -70.81 -35.52 REMARK 500 2 ASP A 58 96.55 -33.73 REMARK 500 2 LYS A 60 -62.41 -95.14 REMARK 500 2 ASN A 77 33.63 34.78 REMARK 500 2 ARG A 107 104.30 -38.88 REMARK 500 2 ASP A 122 81.84 -68.85 REMARK 500 2 LEU A 133 102.24 -42.47 REMARK 500 3 ASN A 11 74.54 -68.23 REMARK 500 3 MET A 33 -74.63 -44.03 REMARK 500 3 LYS A 34 -176.05 -174.70 REMARK 500 3 ASP A 48 69.96 -108.42 REMARK 500 3 ASP A 58 128.89 -33.48 REMARK 500 3 ASN A 77 33.18 35.14 REMARK 500 3 ASP A 122 91.01 -67.53 REMARK 500 3 LEU A 133 108.61 -37.20 REMARK 500 3 PRO A 135 96.86 -69.73 REMARK 500 4 ASN A 11 45.54 -83.39 REMARK 500 4 PHE A 23 -70.70 -83.70 REMARK 500 4 MET A 33 -75.92 -36.32 REMARK 500 4 ASP A 48 78.56 -110.86 REMARK 500 4 ASP A 58 126.69 -33.77 REMARK 500 4 LYS A 66 170.51 -46.32 REMARK 500 4 ASN A 73 50.75 -117.72 REMARK 500 4 VAL A 90 -37.10 -34.96 REMARK 500 4 THR A 124 -29.61 -36.88 REMARK 500 4 LEU A 133 99.63 -34.17 REMARK 500 5 SER A 5 152.12 -49.96 REMARK 500 5 ASN A 11 77.94 -67.32 REMARK 500 5 MET A 33 -75.84 -46.27 REMARK 500 5 LYS A 34 -179.48 -171.18 REMARK 500 5 LYS A 41 47.59 -86.41 REMARK 500 5 ASP A 42 116.07 -172.63 REMARK 500 5 ASP A 58 125.06 -32.49 REMARK 500 REMARK 500 THIS ENTRY HAS 241 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002002479.1 RELATED DB: TARGETDB DBREF 2D8K A 8 135 GB 38570146 NP_004191 132 259 SEQADV 2D8K GLY A 1 GB 38570146 CLONING ARTIFACT SEQADV 2D8K SER A 2 GB 38570146 CLONING ARTIFACT SEQADV 2D8K SER A 3 GB 38570146 CLONING ARTIFACT SEQADV 2D8K GLY A 4 GB 38570146 CLONING ARTIFACT SEQADV 2D8K SER A 5 GB 38570146 CLONING ARTIFACT SEQADV 2D8K SER A 6 GB 38570146 CLONING ARTIFACT SEQADV 2D8K GLY A 7 GB 38570146 CLONING ARTIFACT SEQADV 2D8K SER A 136 GB 38570146 CLONING ARTIFACT SEQADV 2D8K GLY A 137 GB 38570146 CLONING ARTIFACT SEQADV 2D8K PRO A 138 GB 38570146 CLONING ARTIFACT SEQADV 2D8K SER A 139 GB 38570146 CLONING ARTIFACT SEQADV 2D8K SER A 140 GB 38570146 CLONING ARTIFACT SEQADV 2D8K GLY A 141 GB 38570146 CLONING ARTIFACT SEQRES 1 A 141 GLY SER SER GLY SER SER GLY SER ARG GLU ASN LEU GLY SEQRES 2 A 141 ARG ILE GLN PHE SER VAL GLY TYR ASN PHE GLN GLU SER SEQRES 3 A 141 THR LEU THR VAL LYS ILE MET LYS ALA GLN GLU LEU PRO SEQRES 4 A 141 ALA LYS ASP PHE SER GLY THR SER ASP PRO PHE VAL LYS SEQRES 5 A 141 ILE TYR LEU LEU PRO ASP LYS LYS HIS LYS LEU GLU THR SEQRES 6 A 141 LYS VAL LYS ARG LYS ASN LEU ASN PRO HIS TRP ASN GLU SEQRES 7 A 141 THR PHE LEU PHE GLU GLY PHE PRO TYR GLU LYS VAL VAL SEQRES 8 A 141 GLN ARG ILE LEU TYR LEU GLN VAL LEU ASP TYR ASP ARG SEQRES 9 A 141 PHE SER ARG ASN ASP PRO ILE GLY GLU VAL SER ILE PRO SEQRES 10 A 141 LEU ASN LYS VAL ASP LEU THR GLN MET GLN THR PHE TRP SEQRES 11 A 141 LYS ASP LEU LYS PRO SER GLY PRO SER SER GLY HELIX 1 1 PRO A 86 VAL A 91 1 6 SHEET 1 A 4 GLU A 78 PHE A 82 0 SHEET 2 A 4 LEU A 28 GLN A 36 -1 N ILE A 32 O GLU A 78 SHEET 3 A 4 ARG A 14 TYR A 21 -1 N SER A 18 O LYS A 31 SHEET 4 A 4 GLN A 127 LYS A 131 -1 O GLN A 127 N VAL A 19 SHEET 1 B 5 LYS A 62 GLU A 64 0 SHEET 2 B 5 PRO A 49 LEU A 56 -1 N ILE A 53 O LEU A 63 SHEET 3 B 5 ILE A 94 ASP A 101 -1 O LEU A 100 N PHE A 50 SHEET 4 B 5 ASP A 109 PRO A 117 -1 O ILE A 116 N LEU A 95 SHEET 5 B 5 LYS A 134 PRO A 135 -1 O LYS A 134 N GLU A 113 CISPEP 1 LEU A 56 PRO A 57 1 -0.10 CISPEP 2 LEU A 56 PRO A 57 2 -0.12 CISPEP 3 LEU A 56 PRO A 57 3 -0.15 CISPEP 4 LEU A 56 PRO A 57 4 -0.12 CISPEP 5 LEU A 56 PRO A 57 5 -0.07 CISPEP 6 LEU A 56 PRO A 57 6 -0.14 CISPEP 7 LEU A 56 PRO A 57 7 -0.11 CISPEP 8 LEU A 56 PRO A 57 8 -0.12 CISPEP 9 LEU A 56 PRO A 57 9 -0.19 CISPEP 10 LEU A 56 PRO A 57 10 -0.09 CISPEP 11 LEU A 56 PRO A 57 11 -0.16 CISPEP 12 LEU A 56 PRO A 57 12 -0.18 CISPEP 13 LEU A 56 PRO A 57 13 -0.05 CISPEP 14 LEU A 56 PRO A 57 14 -0.06 CISPEP 15 LEU A 56 PRO A 57 15 -0.12 CISPEP 16 LEU A 56 PRO A 57 16 -0.17 CISPEP 17 LEU A 56 PRO A 57 17 -0.15 CISPEP 18 LEU A 56 PRO A 57 18 -0.14 CISPEP 19 LEU A 56 PRO A 57 19 -0.20 CISPEP 20 LEU A 56 PRO A 57 20 -0.19 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