HEADER SIGNALING PROTEIN 28-MAR-07 2ENS TITLE SOLUTION STRUCTURE OF THE THIRD IG-LIKE DOMAIN FROM HUMAN ADVANCED TITLE 2 GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IG-LIKE DOMAIN, UNP RESIDUES 235-323; COMPND 5 SYNONYM: RECEPTOR FOR ADVANCED GLYCOSYLATION END PRODUCTS; 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: AGER; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P060515-22; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS BETA-SANDWICH, C2-SET, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT KEYWDS 2 ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.WAKABAYASHI,C.KUROSAKI,M.YOSHIDA,F.HAYASHI,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2ENS 1 REMARK SEQADV REVDAT 2 24-FEB-09 2ENS 1 VERSN REVDAT 1 01-APR-08 2ENS 0 JRNL AUTH M.WAKABAYASHI,C.KUROSAKI,M.YOSHIDA,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE THIRD IG-LIKE DOMAIN FROM HUMAN JRNL TITL 2 ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DELTA NMR 4.3.2, CYANA 2.0.17 REMARK 3 AUTHORS : JEOL (DELTA NMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ENS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000026886. 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 : 1.17MM 13C,15N-LAVELED PROTEIN; REMARK 210 20MM D-TRIS-HCL(PH7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 90% REMARK 210 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 : ECA REMARK 210 SPECTROMETER MANUFACTURER : JEOL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1C, NMRPIPE 20031121, REMARK 210 NMRVIEW 5.0.4, KUJIRA 0.9815, REMARK 210 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 PRO A 24 83.32 -69.78 REMARK 500 1 PRO A 40 -176.59 -69.72 REMARK 500 1 ASP A 47 33.31 74.50 REMARK 500 1 PRO A 52 79.89 -69.77 REMARK 500 1 PRO A 57 1.68 -69.76 REMARK 500 1 SER A 79 153.21 -36.83 REMARK 500 1 PRO A 83 80.88 -69.78 REMARK 500 2 PRO A 24 87.32 -69.76 REMARK 500 2 PRO A 38 -163.78 -69.67 REMARK 500 2 SER A 39 75.23 -107.52 REMARK 500 2 PRO A 40 -163.94 -69.79 REMARK 500 2 PRO A 52 80.84 -69.80 REMARK 500 2 PRO A 57 1.96 -69.81 REMARK 500 2 LEU A 61 76.12 -108.04 REMARK 500 2 SER A 79 -39.06 -39.26 REMARK 500 2 PRO A 83 80.04 -69.79 REMARK 500 2 ARG A 87 170.24 -50.53 REMARK 500 3 PRO A 24 90.09 -69.76 REMARK 500 3 PRO A 40 -173.63 -69.73 REMARK 500 3 PRO A 52 84.19 -69.73 REMARK 500 3 PRO A 57 0.36 -69.72 REMARK 500 3 PRO A 83 90.24 -69.76 REMARK 500 4 GLU A 10 -63.59 -99.26 REMARK 500 4 VAL A 11 137.03 -37.49 REMARK 500 4 PRO A 24 86.42 -69.75 REMARK 500 4 PRO A 40 -177.62 -69.78 REMARK 500 4 PRO A 52 83.72 -69.71 REMARK 500 4 LEU A 61 71.48 -110.30 REMARK 500 5 PRO A 24 88.48 -69.79 REMARK 500 5 PRO A 40 -179.05 -69.78 REMARK 500 5 PRO A 52 85.78 -69.85 REMARK 500 5 PRO A 57 1.45 -69.74 REMARK 500 5 LEU A 61 73.69 -109.95 REMARK 500 5 SER A 73 135.75 -170.21 REMARK 500 5 PRO A 83 95.35 -69.74 REMARK 500 6 LEU A 13 94.63 -68.07 REMARK 500 6 PRO A 24 87.81 -69.79 REMARK 500 6 PRO A 38 -163.76 -69.78 REMARK 500 6 PRO A 40 -163.67 -69.76 REMARK 500 6 PRO A 52 81.32 -69.76 REMARK 500 6 PRO A 57 2.86 -69.78 REMARK 500 6 LEU A 61 78.14 -107.25 REMARK 500 6 THR A 77 118.00 -174.44 REMARK 500 6 PRO A 83 95.10 -69.76 REMARK 500 6 ARG A 87 178.19 -56.76 REMARK 500 7 PRO A 24 83.47 -69.78 REMARK 500 7 PRO A 52 80.01 -69.71 REMARK 500 7 LEU A 61 75.41 -108.99 REMARK 500 7 PRO A 83 97.83 -69.77 REMARK 500 7 ARG A 87 174.96 -53.92 REMARK 500 REMARK 500 THIS ENTRY HAS 174 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSS001003863.1 RELATED DB: TARGETDB DBREF 2ENS A 8 96 UNP Q15109 RAGE_HUMAN 235 323 SEQADV 2ENS GLY A 1 UNP Q15109 EXPRESSION TAG SEQADV 2ENS SER A 2 UNP Q15109 EXPRESSION TAG SEQADV 2ENS SER A 3 UNP Q15109 EXPRESSION TAG SEQADV 2ENS GLY A 4 UNP Q15109 EXPRESSION TAG SEQADV 2ENS SER A 5 UNP Q15109 EXPRESSION TAG SEQADV 2ENS SER A 6 UNP Q15109 EXPRESSION TAG SEQADV 2ENS GLY A 7 UNP Q15109 EXPRESSION TAG SEQRES 1 A 96 GLY SER SER GLY SER SER GLY LEU GLU GLU VAL GLN LEU SEQRES 2 A 96 VAL VAL GLU PRO GLU GLY GLY ALA VAL ALA PRO GLY GLY SEQRES 3 A 96 THR VAL THR LEU THR CYS GLU VAL PRO ALA GLN PRO SER SEQRES 4 A 96 PRO GLN ILE HIS TRP MET LYS ASP GLY VAL PRO LEU PRO SEQRES 5 A 96 LEU PRO PRO SER PRO VAL LEU ILE LEU PRO GLU ILE GLY SEQRES 6 A 96 PRO GLN ASP GLN GLY THR TYR SER CYS VAL ALA THR HIS SEQRES 7 A 96 SER SER HIS GLY PRO GLN GLU SER ARG ALA VAL SER ILE SEQRES 8 A 96 SER ILE ILE GLU PRO SHEET 1 A 3 VAL A 14 GLU A 16 0 SHEET 2 A 3 THR A 27 THR A 31 -1 O THR A 31 N VAL A 14 SHEET 3 A 3 VAL A 58 PRO A 62 -1 O LEU A 61 N VAL A 28 SHEET 1 B 4 ALA A 21 VAL A 22 0 SHEET 2 B 4 VAL A 89 ILE A 93 1 O SER A 92 N VAL A 22 SHEET 3 B 4 GLY A 70 SER A 73 -1 N TYR A 72 O VAL A 89 SHEET 4 B 4 MET A 45 LYS A 46 -1 N MET A 45 O SER A 73 SHEET 1 C 2 VAL A 75 ALA A 76 0 SHEET 2 C 2 GLN A 84 GLU A 85 -1 O GLN A 84 N ALA A 76 SSBOND 1 CYS A 32 CYS A 74 1555 1555 2.00 CISPEP 1 GLU A 16 PRO A 17 1 -0.04 CISPEP 2 GLU A 16 PRO A 17 2 -0.01 CISPEP 3 GLU A 16 PRO A 17 3 -0.07 CISPEP 4 GLU A 16 PRO A 17 4 -0.03 CISPEP 5 GLU A 16 PRO A 17 5 -0.05 CISPEP 6 GLU A 16 PRO A 17 6 -0.02 CISPEP 7 GLU A 16 PRO A 17 7 0.03 CISPEP 8 GLU A 16 PRO A 17 8 -0.05 CISPEP 9 GLU A 16 PRO A 17 9 -0.01 CISPEP 10 GLU A 16 PRO A 17 10 0.00 CISPEP 11 GLU A 16 PRO A 17 11 0.01 CISPEP 12 GLU A 16 PRO A 17 12 -0.02 CISPEP 13 GLU A 16 PRO A 17 13 -0.04 CISPEP 14 GLU A 16 PRO A 17 14 -0.01 CISPEP 15 GLU A 16 PRO A 17 15 0.00 CISPEP 16 GLU A 16 PRO A 17 16 0.00 CISPEP 17 GLU A 16 PRO A 17 17 0.04 CISPEP 18 GLU A 16 PRO A 17 18 0.02 CISPEP 19 GLU A 16 PRO A 17 19 0.00 CISPEP 20 GLU A 16 PRO A 17 20 -0.02 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