PDB Short entry for 2DN7 HEADER SIGNALING PROTEIN, HYDROLASE 25-APR-06 2DN7 TITLE SOLUTION STRUCTURES OF THE 6TH FN3 DOMAIN OF HUMAN RECEPTOR-TYPE TITLE 2 TYROSINE-PROTEIN PHOSPHATASE F COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FIBRONECTIN TYPE III DOMAIN; COMPND 5 SYNONYM: LAR PROTEIN, LEUKOCYTE ANTIGEN RELATED; COMPND 6 EC: 3.1.3.48; COMPND 7 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: PTPRF, LAR; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P050719-01; SOURCE 9 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS LAR PROTEIN, LEUKOCYTE ANTIGEN RELATED, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 2 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 3 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, SIGNALING KEYWDS 4 PROTEIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.SATO,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DN7 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DN7 1 VERSN REVDAT 1 25-OCT-06 2DN7 0 JRNL AUTH M.SATO,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURES OF THE 6TH FN3 DOMAIN OF HUMAN JRNL TITL 2 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F 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 2DN7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025613. 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 : 1MM FN3 DOMAIN U-15N,13C; 20MM D REMARK 210 -TRIS HCL; 100MM NACL; 1MM D-DTT; REMARK 210 0.02% NAN3; 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, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.932, 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 THR A 18 -73.54 -112.71 REMARK 500 1 PRO A 34 95.95 -69.77 REMARK 500 1 LYS A 59 -26.13 -39.96 REMARK 500 1 ASP A 61 94.19 -62.95 REMARK 500 1 SER A 105 40.98 -99.62 REMARK 500 2 SER A 6 46.90 -80.71 REMARK 500 2 THR A 18 -73.41 -122.71 REMARK 500 2 PRO A 34 96.04 -69.83 REMARK 500 2 ASP A 61 92.53 -64.45 REMARK 500 2 GLU A 89 175.86 -58.94 REMARK 500 2 SER A 102 108.85 -51.69 REMARK 500 2 PRO A 104 90.05 -69.70 REMARK 500 3 SER A 6 73.08 -100.50 REMARK 500 3 THR A 18 -75.11 -106.91 REMARK 500 3 PRO A 34 96.18 -69.77 REMARK 500 3 ASP A 61 94.85 -64.50 REMARK 500 3 LEU A 101 179.65 -56.67 REMARK 500 4 PRO A 34 96.52 -69.75 REMARK 500 4 ASP A 61 91.23 -66.16 REMARK 500 4 GLU A 89 172.53 -57.42 REMARK 500 5 THR A 18 -61.15 -126.94 REMARK 500 5 PRO A 34 97.25 -69.76 REMARK 500 5 ASP A 61 97.71 -68.60 REMARK 500 5 GLU A 99 -32.96 -34.33 REMARK 500 5 ASP A 100 130.58 -175.63 REMARK 500 6 THR A 18 -66.51 -106.44 REMARK 500 6 PRO A 34 95.91 -69.73 REMARK 500 6 ASP A 61 96.01 -64.16 REMARK 500 6 GLU A 99 177.10 -52.47 REMARK 500 7 SER A 6 101.22 -58.53 REMARK 500 7 THR A 18 -66.66 -120.03 REMARK 500 7 PRO A 34 96.91 -69.75 REMARK 500 7 ASP A 61 97.87 -68.02 REMARK 500 7 GLU A 89 174.80 -54.29 REMARK 500 7 SER A 102 42.59 -102.44 REMARK 500 7 PRO A 104 2.45 -69.77 REMARK 500 8 SER A 2 114.62 -39.50 REMARK 500 8 GLU A 32 32.42 -86.89 REMARK 500 8 ASP A 61 91.32 -69.20 REMARK 500 8 GLU A 89 174.10 -49.46 REMARK 500 8 PRO A 104 94.66 -69.77 REMARK 500 8 SER A 105 161.45 -45.85 REMARK 500 9 SER A 6 40.83 38.38 REMARK 500 9 GLU A 32 33.04 -86.30 REMARK 500 9 PRO A 34 96.03 -69.78 REMARK 500 9 ASP A 61 90.49 -66.20 REMARK 500 9 GLU A 99 163.84 -41.83 REMARK 500 9 PRO A 104 88.50 -69.76 REMARK 500 10 THR A 18 -69.46 -105.48 REMARK 500 10 GLU A 32 37.46 -83.19 REMARK 500 REMARK 500 THIS ENTRY HAS 93 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK003001516.1 RELATED DB: TARGETDB DBREF 2DN7 A 8 101 UNP P10586 PTPRF_HUMAN 811 904 SEQADV 2DN7 GLY A 1 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 SER A 2 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 SER A 3 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 GLY A 4 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 SER A 5 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 SER A 6 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 GLY A 7 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 SER A 102 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 GLY A 103 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 PRO A 104 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 SER A 105 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 SER A 106 UNP P10586 CLONING ARTIFACT SEQADV 2DN7 GLY A 107 UNP P10586 CLONING ARTIFACT SEQRES 1 A 107 GLY SER SER GLY SER SER GLY PRO GLY ARG PRO THR MET SEQRES 2 A 107 MET ILE SER THR THR ALA MET ASN THR ALA LEU LEU GLN SEQRES 3 A 107 TRP HIS PRO PRO LYS GLU LEU PRO GLY GLU LEU LEU GLY SEQRES 4 A 107 TYR ARG LEU GLN TYR CYS ARG ALA ASP GLU ALA ARG PRO SEQRES 5 A 107 ASN THR ILE ASP PHE GLY LYS ASP ASP GLN HIS PHE THR SEQRES 6 A 107 VAL THR GLY LEU HIS LYS GLY THR THR TYR ILE PHE ARG SEQRES 7 A 107 LEU ALA ALA LYS ASN ARG ALA GLY LEU GLY GLU GLU PHE SEQRES 8 A 107 GLU LYS GLU ILE ARG THR PRO GLU ASP LEU SER GLY PRO SEQRES 9 A 107 SER SER GLY SHEET 1 A 3 THR A 12 THR A 17 0 SHEET 2 A 3 THR A 22 HIS A 28 -1 O LEU A 24 N SER A 16 SHEET 3 A 3 HIS A 63 THR A 67 -1 O PHE A 64 N LEU A 25 SHEET 1 B 4 ASN A 53 GLY A 58 0 SHEET 2 B 4 GLY A 39 ARG A 46 -1 N LEU A 42 O ILE A 55 SHEET 3 B 4 THR A 74 ASN A 83 -1 O ARG A 78 N GLN A 43 SHEET 4 B 4 GLY A 86 ARG A 96 -1 O GLY A 86 N ASN A 83 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