PDB Short entry for 2EDB HEADER APOPTOSIS 14-FEB-07 2EDB TITLE SOLUTION STRUCTURE OF THE FOURTH FIBRONECTIN TYPE III DOMAIN OF HUMAN TITLE 2 NETRIN RECEPTOR DCC COMPND MOL_ID: 1; COMPND 2 MOLECULE: NETRIN RECEPTOR DCC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FOURTH FN3 DOMAIN; COMPND 5 SYNONYM: TUMOR SUPPRESSOR PROTEIN DCC, COLORECTAL CANCER SUPPRESSOR; COMPND 6 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: DCC; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050905-22; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS TUMOR SUPPRESSOR PROTEIN DCC, COLORECTAL CANCER SUPPRESSOR, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.TOCHIO,S.KOSHIBA,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2EDB 1 REMARK SEQADV REVDAT 2 24-FEB-09 2EDB 1 VERSN REVDAT 1 04-MAR-08 2EDB 0 JRNL AUTH N.TOCHIO,S.KOSHIBA,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE FOURTH FIBRONECTIN TYPE III DOMAIN JRNL TITL 2 OF HUMAN NETRIN RECEPTOR DCC 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 2EDB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000026523. 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 SAMPLE U-15N,13C; 20MM D REMARK 210 -TRIS-HCL; 100MM NACL; 1MM D-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 REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMNMRVIEW REMARK 210 5.0.4, 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 : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,TARGET REMARK 210 FUNCTION 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 GLU A 9 107.40 -58.01 REMARK 500 1 ASN A 10 -65.14 -102.05 REMARK 500 1 SER A 22 -37.07 -31.60 REMARK 500 1 THR A 30 -70.75 -53.67 REMARK 500 1 PRO A 59 14.44 -69.82 REMARK 500 1 VAL A 98 102.98 -32.81 REMARK 500 1 ALA A 104 107.85 -163.91 REMARK 500 1 THR A 106 171.32 -45.21 REMARK 500 1 SER A 111 151.17 -46.88 REMARK 500 2 SER A 2 42.11 -101.67 REMARK 500 2 SER A 3 42.15 -81.26 REMARK 500 2 PRO A 8 -173.53 -69.73 REMARK 500 2 GLU A 9 87.68 -68.92 REMARK 500 2 ASP A 19 173.76 -49.71 REMARK 500 2 SER A 22 -34.68 -32.92 REMARK 500 2 THR A 30 -71.04 -47.60 REMARK 500 2 LEU A 41 -19.92 -47.57 REMARK 500 2 PRO A 59 14.61 -69.74 REMARK 500 2 VAL A 98 103.37 -33.90 REMARK 500 2 ALA A 104 114.71 -164.36 REMARK 500 2 THR A 106 168.05 -44.20 REMARK 500 2 SER A 114 71.89 -68.97 REMARK 500 3 SER A 2 119.09 -160.89 REMARK 500 3 SER A 6 40.21 -92.44 REMARK 500 3 PRO A 8 -171.92 -69.78 REMARK 500 3 ASP A 11 46.51 73.34 REMARK 500 3 SER A 22 -38.58 -31.53 REMARK 500 3 PRO A 59 13.49 -69.83 REMARK 500 3 VAL A 98 103.38 -34.21 REMARK 500 3 ALA A 104 112.39 -163.53 REMARK 500 3 THR A 106 172.47 -45.77 REMARK 500 4 SER A 5 41.71 -83.18 REMARK 500 4 PRO A 8 -168.44 -69.80 REMARK 500 4 ASP A 11 38.60 74.95 REMARK 500 4 SER A 22 -38.00 -34.17 REMARK 500 4 PRO A 28 92.85 -69.77 REMARK 500 4 PRO A 59 15.63 -69.74 REMARK 500 4 SER A 81 52.29 73.98 REMARK 500 4 VAL A 98 102.79 -35.51 REMARK 500 4 SER A 115 131.88 -34.72 REMARK 500 5 GLU A 9 84.52 -54.79 REMARK 500 5 ASN A 10 -58.67 -127.52 REMARK 500 5 SER A 22 -36.49 -31.81 REMARK 500 5 THR A 30 -70.71 -48.64 REMARK 500 5 PRO A 59 15.80 -69.82 REMARK 500 5 VAL A 98 101.92 -35.13 REMARK 500 5 THR A 106 158.83 -43.34 REMARK 500 6 SER A 5 42.23 -81.60 REMARK 500 6 PRO A 8 -165.28 -69.77 REMARK 500 6 ASP A 19 172.93 -56.19 REMARK 500 REMARK 500 THIS ENTRY HAS 183 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002001052.4 RELATED DB: TARGETDB DBREF 2EDB A 8 110 UNP P43146 DCC_HUMAN 716 818 SEQADV 2EDB GLY A 1 UNP P43146 EXPRESSION TAG SEQADV 2EDB SER A 2 UNP P43146 EXPRESSION TAG SEQADV 2EDB SER A 3 UNP P43146 EXPRESSION TAG SEQADV 2EDB GLY A 4 UNP P43146 EXPRESSION TAG SEQADV 2EDB SER A 5 UNP P43146 EXPRESSION TAG SEQADV 2EDB SER A 6 UNP P43146 EXPRESSION TAG SEQADV 2EDB GLY A 7 UNP P43146 EXPRESSION TAG SEQADV 2EDB SER A 111 UNP P43146 EXPRESSION TAG SEQADV 2EDB GLY A 112 UNP P43146 EXPRESSION TAG SEQADV 2EDB PRO A 113 UNP P43146 EXPRESSION TAG SEQADV 2EDB SER A 114 UNP P43146 EXPRESSION TAG SEQADV 2EDB SER A 115 UNP P43146 EXPRESSION TAG SEQADV 2EDB GLY A 116 UNP P43146 EXPRESSION TAG SEQRES 1 A 116 GLY SER SER GLY SER SER GLY PRO GLU ASN ASP LEU ASP SEQRES 2 A 116 GLU SER GLN VAL PRO ASP GLN PRO SER SER LEU HIS VAL SEQRES 3 A 116 ARG PRO GLN THR ASN CYS ILE ILE MET SER TRP THR PRO SEQRES 4 A 116 PRO LEU ASN PRO ASN ILE VAL VAL ARG GLY TYR ILE ILE SEQRES 5 A 116 GLY TYR GLY VAL GLY SER PRO TYR ALA GLU THR VAL ARG SEQRES 6 A 116 VAL ASP SER LYS GLN ARG TYR TYR SER ILE GLU ARG LEU SEQRES 7 A 116 GLU SER SER SER HIS TYR VAL ILE SER LEU LYS ALA PHE SEQRES 8 A 116 ASN ASN ALA GLY GLU GLY VAL PRO LEU TYR GLU SER ALA SEQRES 9 A 116 THR THR ARG SER ILE THR SER GLY PRO SER SER GLY SHEET 1 A 3 LEU A 24 PRO A 28 0 SHEET 2 A 3 ILE A 33 TRP A 37 -1 O ILE A 34 N ARG A 27 SHEET 3 A 3 TYR A 72 ILE A 75 -1 O ILE A 75 N ILE A 33 SHEET 1 B 4 GLU A 62 ASP A 67 0 SHEET 2 B 4 GLY A 49 VAL A 56 -1 N ILE A 52 O VAL A 64 SHEET 3 B 4 TYR A 84 ASN A 92 -1 O LYS A 89 N ILE A 51 SHEET 4 B 4 GLY A 95 GLU A 96 -1 O GLY A 95 N ASN A 92 SHEET 1 C 4 GLU A 62 ASP A 67 0 SHEET 2 C 4 GLY A 49 VAL A 56 -1 N ILE A 52 O VAL A 64 SHEET 3 C 4 TYR A 84 ASN A 92 -1 O LYS A 89 N ILE A 51 SHEET 4 C 4 LEU A 100 GLU A 102 -1 O LEU A 100 N LEU A 88 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