PDB Short entry for 2EDD HEADER APOPTOSIS 14-FEB-07 2EDD TITLE SOLUTION STRUCTURE OF THE FIFTH 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: FIFTH 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: P050905-23; 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.TOMIZAWA,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2EDD 1 REMARK SEQADV REVDAT 2 24-FEB-09 2EDD 1 VERSN REVDAT 1 04-MAR-08 2EDD 0 JRNL AUTH N.TOCHIO,S.KOSHIBA,T.TOMIZAWA,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE FIFTH 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 2EDD 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_1000026524. 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 : 800 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 SER A 3 47.43 -84.27 REMARK 500 1 THR A 10 -62.93 -97.37 REMARK 500 1 SER A 16 61.27 -102.93 REMARK 500 1 PRO A 18 4.45 -69.71 REMARK 500 1 PRO A 22 -179.06 -69.80 REMARK 500 1 PRO A 45 -173.66 -69.75 REMARK 500 1 GLN A 48 137.73 -172.51 REMARK 500 1 ARG A 54 143.49 -173.94 REMARK 500 1 PHE A 64 49.66 72.03 REMARK 500 1 ASN A 100 32.29 71.30 REMARK 500 1 ALA A 112 109.42 -168.64 REMARK 500 1 ALA A 117 172.74 -56.58 REMARK 500 2 SER A 2 -53.73 -122.30 REMARK 500 2 PRO A 18 -176.30 -69.76 REMARK 500 2 MET A 19 139.59 -35.67 REMARK 500 2 VAL A 25 105.13 -59.30 REMARK 500 2 ASP A 33 43.86 -108.17 REMARK 500 2 PRO A 45 -174.83 -69.72 REMARK 500 2 SER A 51 77.39 -100.82 REMARK 500 2 THR A 76 36.17 -89.00 REMARK 500 2 LEU A 78 32.18 -87.51 REMARK 500 2 ASN A 100 47.21 70.76 REMARK 500 2 MET A 108 129.52 -35.79 REMARK 500 2 ALA A 112 112.87 -174.60 REMARK 500 2 ALA A 117 49.43 -76.46 REMARK 500 2 SER A 121 92.44 -67.17 REMARK 500 2 SER A 122 100.89 -47.09 REMARK 500 3 SER A 5 124.79 -173.80 REMARK 500 3 PHE A 8 139.53 -171.36 REMARK 500 3 PRO A 13 88.33 -69.72 REMARK 500 3 PRO A 18 4.95 -69.80 REMARK 500 3 PRO A 45 -162.90 -69.79 REMARK 500 3 LYS A 46 92.25 -30.89 REMARK 500 3 ASN A 47 46.17 28.05 REMARK 500 3 SER A 67 50.58 34.23 REMARK 500 3 THR A 76 31.15 -89.74 REMARK 500 3 ASN A 100 47.36 74.96 REMARK 500 3 ALA A 112 108.31 -163.86 REMARK 500 3 ALA A 117 175.02 -48.06 REMARK 500 3 PRO A 120 87.10 -69.78 REMARK 500 4 PHE A 8 145.78 -34.52 REMARK 500 4 PRO A 18 -171.40 -69.79 REMARK 500 4 MET A 19 169.97 -48.37 REMARK 500 4 SER A 51 75.17 -108.11 REMARK 500 4 THR A 62 127.72 -33.85 REMARK 500 4 ALA A 66 -72.11 -40.65 REMARK 500 4 THR A 76 31.10 -92.81 REMARK 500 4 ASN A 100 47.20 74.29 REMARK 500 4 MET A 108 151.62 -34.74 REMARK 500 5 SER A 6 101.60 -40.31 REMARK 500 REMARK 500 THIS ENTRY HAS 220 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002001052.5 RELATED DB: TARGETDB DBREF 2EDD A 8 117 UNP P43146 DCC_HUMAN 833 942 SEQADV 2EDD GLY A 1 UNP P43146 EXPRESSION TAG SEQADV 2EDD SER A 2 UNP P43146 EXPRESSION TAG SEQADV 2EDD SER A 3 UNP P43146 EXPRESSION TAG SEQADV 2EDD GLY A 4 UNP P43146 EXPRESSION TAG SEQADV 2EDD SER A 5 UNP P43146 EXPRESSION TAG SEQADV 2EDD SER A 6 UNP P43146 EXPRESSION TAG SEQADV 2EDD GLY A 7 UNP P43146 EXPRESSION TAG SEQADV 2EDD SER A 118 UNP P43146 EXPRESSION TAG SEQADV 2EDD GLY A 119 UNP P43146 EXPRESSION TAG SEQADV 2EDD PRO A 120 UNP P43146 EXPRESSION TAG SEQADV 2EDD SER A 121 UNP P43146 EXPRESSION TAG SEQADV 2EDD SER A 122 UNP P43146 EXPRESSION TAG SEQADV 2EDD GLY A 123 UNP P43146 EXPRESSION TAG SEQRES 1 A 123 GLY SER SER GLY SER SER GLY PHE PRO THR SER VAL PRO SEQRES 2 A 123 ASP LEU SER THR PRO MET LEU PRO PRO VAL GLY VAL GLN SEQRES 3 A 123 ALA VAL ALA LEU THR HIS ASP ALA VAL ARG VAL SER TRP SEQRES 4 A 123 ALA ASP ASN SER VAL PRO LYS ASN GLN LYS THR SER GLU SEQRES 5 A 123 VAL ARG LEU TYR THR VAL ARG TRP ARG THR SER PHE SER SEQRES 6 A 123 ALA SER ALA LYS TYR LYS SER GLU ASP THR THR SER LEU SEQRES 7 A 123 SER TYR THR ALA THR GLY LEU LYS PRO ASN THR MET TYR SEQRES 8 A 123 GLU PHE SER VAL MET VAL THR LYS ASN ARG ARG SER SER SEQRES 9 A 123 THR TRP SER MET THR ALA HIS ALA THR THR TYR GLU ALA SEQRES 10 A 123 SER GLY PRO SER SER GLY SHEET 1 A 3 VAL A 23 THR A 31 0 SHEET 2 A 3 ALA A 34 ALA A 40 -1 O ARG A 36 N VAL A 28 SHEET 3 A 3 SER A 79 THR A 83 -1 O TYR A 80 N VAL A 37 SHEET 1 B 4 GLU A 73 THR A 75 0 SHEET 2 B 4 TYR A 56 THR A 62 -1 N TYR A 56 O THR A 75 SHEET 3 B 4 MET A 90 VAL A 97 -1 O GLU A 92 N ARG A 61 SHEET 4 B 4 ALA A 110 THR A 113 -1 O ALA A 110 N PHE A 93 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