HEADER HYDROLASE 03-APR-07 2YS0 TITLE SOLUTION STRUCTURE OF THE SOMATOMEDIN B DOMAIN OF HUMAN ECTONUCLEOTIDE TITLE 2 PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY COMPND 3 MEMBER 1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: SOMATOMEDIN_B; COMPND 6 SYNONYM: 'ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE 1, E-NPP COMPND 7 1, PHOSPHODIESTERASE I/NUCLEOTIDE PYROPHOSPHATASE 1, PLASMA-CELL COMPND 8 MEMBRANE GLYCOPROTEIN PC-1; COMPND 9 EC: 3.1.4.1, 3.6.1.9; COMPND 10 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: ENPP1; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050118-03; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS E-NPP 1, PHOSPHODIESTERASE I/NUCLEOTIDE PYROPHOSPHATASE 1, PLASMA- KEYWDS 2 CELL MEMBRANE GLYCOPROTEIN PC-1, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 3 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 4 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.ABE,A.SASAGAWA,N.TOCHIO,T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 16-MAR-22 2YS0 1 REMARK SEQADV REVDAT 2 24-FEB-09 2YS0 1 VERSN REVDAT 1 09-OCT-07 2YS0 0 JRNL AUTH H.ABE,A.SASAGAWA,N.TOCHIO,T.TOMIZAWA,S.KOSHIBA,M.INOUE, JRNL AUTH 2 T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE SOMATOMEDIN B DOMAIN OF HUMAN JRNL TITL 2 ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY JRNL TITL 3 MEMBER 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 2YS0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027060. 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 : 0.80MM 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 : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9820, 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 10 SG CYS A 38 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 TRP A 8 41.84 -82.94 REMARK 500 1 CYS A 27 40.39 -101.19 REMARK 500 1 CYS A 38 155.45 -43.71 REMARK 500 1 ASN A 40 41.83 -107.43 REMARK 500 1 GLN A 46 48.38 -78.95 REMARK 500 1 SER A 50 119.02 -164.55 REMARK 500 1 SER A 55 48.66 -81.74 REMARK 500 2 THR A 9 164.21 -47.70 REMARK 500 2 CYS A 15 99.35 -44.25 REMARK 500 2 CYS A 27 42.74 -96.84 REMARK 500 3 TRP A 8 40.95 -96.08 REMARK 500 3 CYS A 15 107.93 -42.09 REMARK 500 3 CYS A 38 159.61 -41.54 REMARK 500 3 GLN A 46 43.73 -79.87 REMARK 500 3 SER A 54 153.65 -36.88 REMARK 500 4 TRP A 8 42.12 -82.42 REMARK 500 4 CYS A 15 108.26 -40.37 REMARK 500 4 SER A 23 159.57 -39.55 REMARK 500 4 ASP A 29 44.32 -80.30 REMARK 500 4 ASP A 30 -38.37 -131.48 REMARK 500 4 GLN A 46 43.92 -79.96 REMARK 500 4 SER A 50 105.70 -174.95 REMARK 500 5 CYS A 15 101.65 -36.13 REMARK 500 5 ARG A 19 46.28 35.77 REMARK 500 5 LEU A 20 66.06 -102.84 REMARK 500 5 SER A 23 119.87 -165.45 REMARK 500 5 CYS A 27 39.68 -92.68 REMARK 500 5 CYS A 38 170.52 -45.40 REMARK 500 5 SER A 50 41.30 -98.63 REMARK 500 5 PRO A 53 2.01 -69.73 REMARK 500 6 SER A 3 124.43 -172.70 REMARK 500 6 SER A 5 79.47 -111.31 REMARK 500 6 SER A 6 41.78 -86.00 REMARK 500 6 CYS A 15 89.88 -48.66 REMARK 500 6 LYS A 18 41.91 -105.68 REMARK 500 6 CYS A 27 40.76 -106.54 REMARK 500 6 ASP A 30 35.93 -84.54 REMARK 500 6 ASN A 40 42.10 -106.98 REMARK 500 6 SER A 51 141.14 -39.94 REMARK 500 6 PRO A 53 85.99 -69.72 REMARK 500 7 CYS A 15 105.49 -45.76 REMARK 500 7 ARG A 19 125.18 -37.64 REMARK 500 7 CYS A 27 42.72 -91.36 REMARK 500 7 ASP A 29 42.87 -80.76 REMARK 500 7 ASP A 30 -33.68 -133.11 REMARK 500 7 CYS A 38 157.34 -39.95 REMARK 500 7 PRO A 53 89.95 -69.78 REMARK 500 8 CYS A 15 100.70 -33.47 REMARK 500 8 LYS A 18 154.99 -41.22 REMARK 500 8 ARG A 22 98.78 -38.86 REMARK 500 REMARK 500 THIS ENTRY HAS 151 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002000477.1 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SWISSPROT SHOWS THAT THERE IS VARIANT AT THIS POSITION DBREF 2YS0 A 8 50 UNP P22413 ENPP1_HUMAN 147 189 SEQADV 2YS0 GLY A 1 UNP P22413 EXPRESSION TAG SEQADV 2YS0 SER A 2 UNP P22413 EXPRESSION TAG SEQADV 2YS0 SER A 3 UNP P22413 EXPRESSION TAG SEQADV 2YS0 GLY A 4 UNP P22413 EXPRESSION TAG SEQADV 2YS0 SER A 5 UNP P22413 EXPRESSION TAG SEQADV 2YS0 SER A 6 UNP P22413 EXPRESSION TAG SEQADV 2YS0 GLY A 7 UNP P22413 EXPRESSION TAG SEQADV 2YS0 GLN A 34 UNP P22413 LYS 173 SEE REMARK 999 SEQADV 2YS0 SER A 51 UNP P22413 EXPRESSION TAG SEQADV 2YS0 GLY A 52 UNP P22413 EXPRESSION TAG SEQADV 2YS0 PRO A 53 UNP P22413 EXPRESSION TAG SEQADV 2YS0 SER A 54 UNP P22413 EXPRESSION TAG SEQADV 2YS0 SER A 55 UNP P22413 EXPRESSION TAG SEQADV 2YS0 GLY A 56 UNP P22413 EXPRESSION TAG SEQRES 1 A 56 GLY SER SER GLY SER SER GLY TRP THR CYS ASN LYS PHE SEQRES 2 A 56 ARG CYS GLY GLU LYS ARG LEU THR ARG SER LEU CYS ALA SEQRES 3 A 56 CYS SER ASP ASP CYS LYS ASP GLN GLY ASP CYS CYS ILE SEQRES 4 A 56 ASN TYR SER SER VAL CYS GLN GLY GLU LYS SER SER GLY SEQRES 5 A 56 PRO SER SER GLY HELIX 1 1 SER A 28 GLY A 35 1 8 HELIX 2 2 ASN A 40 CYS A 45 1 6 SSBOND 1 CYS A 10 CYS A 27 1555 1555 2.01 SSBOND 2 CYS A 15 CYS A 45 1555 1555 2.07 SSBOND 3 CYS A 25 CYS A 38 1555 1555 2.02 SSBOND 4 CYS A 31 CYS A 37 1555 1555 2.07 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 MODEL 1