PDB Short entry for 1X5Z HEADER HYDROLASE 17-MAY-05 1X5Z TITLE SOLUTION STRUCTURE OF THE FIBRONECTIN TYPE-III DOMAIN OF HUMAN PROTEIN TITLE 2 TYROSINE PHOSPHATASE, RECEPTOR TYPE, D ISOFORM 4 VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE DELTA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FIBRONECTIN TYPE-III DOMAIN; COMPND 5 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE DELTA, R-PTP-DELTA, PROTEIN COMPND 6 TYROSINE PHOSPHATASE, RECEPTOR TYPE, D ISOFORM 4; COMPND 7 EC: 3.1.3.48; COMPND 8 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: PTPRD; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050131-05; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS FIBRONECTIN TYPE III DOMAIN CONTAINING PROTEIN, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 3 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.YONEYAMA,K.SAITO,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 02-MAR-22 1X5Z 1 REMARK SEQADV REVDAT 3 24-FEB-09 1X5Z 1 VERSN REVDAT 2 17-JAN-06 1X5Z 1 JRNL TITLE REVDAT 1 17-NOV-05 1X5Z 0 JRNL AUTH M.YONEYAMA,K.SAITO,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE FIBRONECTIN TYPE-III DOMAIN OF JRNL TITL 2 HUMAN PROTEIN TYROSINE PHOSPHATASE, RECEPTOR TYPE, D ISOFORM JRNL TITL 3 4 VARIANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1X5Z COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024421. 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 : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.37MM FN3 DOMAIN U-15N, 13C; REMARK 210 20MM D-TRIS-HCL (PH7.0); 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 : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20020425, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9295, 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,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 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 SER A 2 -54.78 -129.77 REMARK 500 1 GLN A 20 144.46 -37.51 REMARK 500 1 PRO A 28 92.19 -69.76 REMARK 500 1 PRO A 41 -177.46 -69.82 REMARK 500 1 SER A 43 108.13 -46.49 REMARK 500 1 ASP A 55 103.08 -56.11 REMARK 500 1 HIS A 58 31.62 -91.88 REMARK 500 1 PRO A 68 82.03 -69.73 REMARK 500 1 ASN A 80 51.80 37.25 REMARK 500 1 ALA A 88 108.22 -162.83 REMARK 500 1 PRO A 112 86.48 -69.79 REMARK 500 2 GLN A 10 94.68 -67.65 REMARK 500 2 GLN A 20 145.80 -38.96 REMARK 500 2 PRO A 28 93.13 -69.77 REMARK 500 2 SER A 43 104.79 -49.37 REMARK 500 2 HIS A 58 34.00 -89.65 REMARK 500 2 PRO A 68 83.16 -69.75 REMARK 500 2 ALA A 100 154.53 -42.50 REMARK 500 3 VAL A 17 146.68 -39.23 REMARK 500 3 PRO A 28 96.96 -69.77 REMARK 500 3 PRO A 41 -176.71 -69.85 REMARK 500 3 ASN A 48 -175.75 -176.24 REMARK 500 3 PRO A 68 79.89 -69.74 REMARK 500 3 THR A 70 -34.30 -131.93 REMARK 500 3 PRO A 92 2.02 -69.78 REMARK 500 4 ASP A 8 79.24 -69.93 REMARK 500 4 GLN A 10 41.08 -104.07 REMARK 500 4 THR A 13 31.25 -83.97 REMARK 500 4 GLN A 20 148.29 -34.56 REMARK 500 4 PRO A 41 -165.16 -69.73 REMARK 500 4 SER A 43 102.01 -45.76 REMARK 500 4 ASN A 48 -175.03 -176.60 REMARK 500 4 ASP A 55 100.38 -55.47 REMARK 500 4 PRO A 68 80.48 -69.79 REMARK 500 4 ALA A 88 105.54 -164.68 REMARK 500 4 THR A 106 176.25 -59.60 REMARK 500 4 GLN A 108 86.00 -52.19 REMARK 500 5 THR A 15 126.43 -39.10 REMARK 500 5 GLN A 20 144.05 -35.32 REMARK 500 5 PRO A 28 93.08 -69.69 REMARK 500 5 SER A 43 103.23 -48.77 REMARK 500 5 HIS A 58 30.82 -86.54 REMARK 500 5 PRO A 68 82.29 -69.71 REMARK 500 5 ALA A 88 105.36 -165.85 REMARK 500 5 PRO A 92 2.17 -69.81 REMARK 500 6 SER A 6 113.82 -174.87 REMARK 500 6 GLN A 20 146.13 -34.51 REMARK 500 6 PRO A 21 -176.79 -69.80 REMARK 500 6 SER A 43 103.40 -43.76 REMARK 500 6 PRO A 68 80.27 -69.70 REMARK 500 REMARK 500 THIS ENTRY HAS 167 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002001101.1 RELATED DB: TARGETDB DBREF 1X5Z A 8 109 UNP P23468 PTPRD_HUMAN 506 607 SEQADV 1X5Z GLY A 1 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z SER A 2 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z SER A 3 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z GLY A 4 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z SER A 5 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z SER A 6 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z GLY A 7 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z SER A 110 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z GLY A 111 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z PRO A 112 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z SER A 113 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z SER A 114 UNP P23468 CLONING ARTIFACT SEQADV 1X5Z GLY A 115 UNP P23468 CLONING ARTIFACT SEQRES 1 A 115 GLY SER SER GLY SER SER GLY ASP ILE GLN VAL ILE THR SEQRES 2 A 115 GLN THR GLY VAL PRO GLY GLN PRO LEU ASN PHE LYS ALA SEQRES 3 A 115 GLU PRO GLU SER GLU THR SER ILE LEU LEU SER TRP THR SEQRES 4 A 115 PRO PRO ARG SER ASP THR ILE ALA ASN TYR GLU LEU VAL SEQRES 5 A 115 TYR LYS ASP GLY GLU HIS GLY GLU GLU GLN ARG ILE THR SEQRES 6 A 115 ILE GLU PRO GLY THR SER TYR ARG LEU GLN GLY LEU LYS SEQRES 7 A 115 PRO ASN SER LEU TYR TYR PHE ARG LEU ALA ALA ARG SER SEQRES 8 A 115 PRO GLN GLY LEU GLY ALA SER THR ALA GLU ILE SER ALA SEQRES 9 A 115 ARG THR MET GLN SER SER GLY PRO SER SER GLY SHEET 1 A 3 LEU A 22 GLU A 27 0 SHEET 2 A 3 SER A 33 THR A 39 -1 O SER A 37 N LYS A 25 SHEET 3 A 3 SER A 71 GLN A 75 -1 O LEU A 74 N ILE A 34 SHEET 1 B 4 THR A 65 ILE A 66 0 SHEET 2 B 4 ASN A 48 LEU A 51 -1 N TYR A 49 O ILE A 66 SHEET 3 B 4 LEU A 87 ARG A 90 -1 O ARG A 90 N ASN A 48 SHEET 4 B 4 LEU A 95 SER A 98 -1 O GLY A 96 N ALA A 89 SHEET 1 C 3 LYS A 54 ASP A 55 0 SHEET 2 C 3 LEU A 82 PHE A 85 -1 O TYR A 84 N LYS A 54 SHEET 3 C 3 ILE A 102 ARG A 105 -1 O ILE A 102 N PHE A 85 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