PDB Short entry for 2E5E HEADER SIGNALING PROTEIN 20-DEC-06 2E5E TITLE SOLUTION STRUCTURE OF VARIABLE-TYPE DOMAIN OF HUMAN RECEPTOR FOR TITLE 2 ADVANCED GLYCATION ENDPRODUCTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VARIABLE-TYPE DOMAIN; COMPND 5 SYNONYM: RECEPTOR FOR ADVANCED GLYCATION ENDPRODUCTS, RECEPTOR FOR COMPND 6 ADVANCED GLYCOSYLATION END PRODUCTS; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ORIGAMI B (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32B KEYWDS VARIABLE-TYPE IMMUNOGLOBULIN-LIKE FOLD, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR S.MATSUMOTO,T.YOSHIDA,I.YASUMATSU,H.YAMAMOTO,Y.KOBAYASHI,T.OHKUBO REVDAT 4 09-MAR-22 2E5E 1 REMARK SEQADV REVDAT 3 24-FEB-09 2E5E 1 VERSN REVDAT 2 08-JUL-08 2E5E 1 ATOM REVDAT 1 25-DEC-07 2E5E 0 JRNL AUTH S.MATSUMOTO,T.YOSHIDA,I.YASUMATSU,H.YAMAMOTO,Y.KOBAYASHI, JRNL AUTH 2 T.OHKUBO JRNL TITL SOLUTION STRUCTURE OF VARIABLE-TYPE DOMAIN OF HUMAN RECEPTOR JRNL TITL 2 FOR ADVANCED GLYCATION ENDPRODUCTS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2E5E COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000026246. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.2MM VARIABLE-TYPE DOMAIN OF REMARK 210 RECEPTOR FOR ADVANCED GLYCATION REMARK 210 ENDPRODUCTS U-15N, 13C; 20MM REMARK 210 PHOSPHATE BUFFER NA, 100MM REMARK 210 NA2SO4; 90% H2O, 10% D2O; 0.2MM REMARK 210 VARIABLE-TYPE DOMAIN OF RECEPTOR REMARK 210 FOR ADVANCED GLYCATION REMARK 210 ENDPRODUCTS; 20MM PHOSPHATE REMARK 210 BUFFER NA, 100MM NA2SO4; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY; 2D REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 ALA A 23 142.09 -175.96 REMARK 500 1 LYS A 39 -176.15 -65.31 REMARK 500 1 PRO A 42 -166.72 -56.21 REMARK 500 1 PRO A 45 167.69 -49.82 REMARK 500 1 PRO A 46 105.54 -55.29 REMARK 500 1 THR A 58 104.86 62.13 REMARK 500 1 GLU A 59 16.67 -140.92 REMARK 500 1 ALA A 88 105.48 -167.53 REMARK 500 1 GLU A 94 178.16 -50.92 REMARK 500 1 SER A 111 124.88 -171.15 REMARK 500 1 TYR A 118 -77.99 -52.99 REMARK 500 2 LYS A 39 -174.11 -69.73 REMARK 500 2 ALA A 41 105.31 -52.26 REMARK 500 2 PRO A 42 -160.65 -61.96 REMARK 500 2 PRO A 45 108.27 -55.59 REMARK 500 2 THR A 58 76.91 64.58 REMARK 500 2 GLU A 94 177.31 -50.62 REMARK 500 2 SER A 111 112.26 -166.60 REMARK 500 3 ALA A 23 129.35 63.56 REMARK 500 3 LYS A 39 170.87 -55.55 REMARK 500 3 PRO A 42 -158.32 -57.68 REMARK 500 3 ARG A 57 -77.57 -107.11 REMARK 500 3 THR A 58 -173.37 -176.32 REMARK 500 3 GLU A 59 96.92 60.99 REMARK 500 3 ALA A 60 -68.97 -178.82 REMARK 500 3 PRO A 66 84.56 -69.13 REMARK 500 3 GLN A 67 79.84 66.07 REMARK 500 3 SER A 83 -169.53 -119.31 REMARK 500 3 ALA A 88 108.10 -165.89 REMARK 500 3 GLU A 94 177.39 -50.35 REMARK 500 4 MET A 22 175.08 60.01 REMARK 500 4 ALA A 23 -172.33 -62.31 REMARK 500 4 LYS A 39 179.55 -58.81 REMARK 500 4 PRO A 42 178.67 -51.94 REMARK 500 4 ARG A 57 -68.12 69.81 REMARK 500 4 THR A 58 140.75 173.97 REMARK 500 4 GLU A 59 38.89 -179.53 REMARK 500 4 ALA A 60 -29.76 171.37 REMARK 500 4 PRO A 66 63.93 -69.58 REMARK 500 4 GLN A 67 -60.01 -145.50 REMARK 500 4 GLU A 94 178.81 -53.63 REMARK 500 5 PRO A 42 -178.08 -52.77 REMARK 500 5 THR A 58 67.69 62.39 REMARK 500 5 GLN A 67 97.44 -176.17 REMARK 500 5 GLU A 94 178.43 -51.96 REMARK 500 5 GLN A 100 117.35 -160.32 REMARK 500 5 SER A 111 119.56 -166.26 REMARK 500 5 TYR A 118 -78.68 -54.31 REMARK 500 6 PRO A 42 176.97 -53.22 REMARK 500 6 PRO A 46 88.73 -53.93 REMARK 500 REMARK 500 THIS ENTRY HAS 133 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2E5E A 23 121 UNP Q15109 RAGE_HUMAN 23 121 SEQADV 2E5E ALA A 21 UNP Q15109 EXPRESSION TAG SEQADV 2E5E MET A 22 UNP Q15109 EXPRESSION TAG SEQRES 1 A 101 ALA MET ALA GLN ASN ILE THR ALA ARG ILE GLY GLU PRO SEQRES 2 A 101 LEU VAL LEU LYS CYS LYS GLY ALA PRO LYS LYS PRO PRO SEQRES 3 A 101 GLN ARG LEU GLU TRP LYS LEU ASN THR GLY ARG THR GLU SEQRES 4 A 101 ALA TRP LYS VAL LEU SER PRO GLN GLY GLY GLY PRO TRP SEQRES 5 A 101 ASP SER VAL ALA ARG VAL LEU PRO ASN GLY SER LEU PHE SEQRES 6 A 101 LEU PRO ALA VAL GLY ILE GLN ASP GLU GLY ILE PHE ARG SEQRES 7 A 101 CYS GLN ALA MET ASN ARG ASN GLY LYS GLU THR LYS SER SEQRES 8 A 101 ASN TYR ARG VAL ARG VAL TYR GLN ILE PRO HELIX 1 1 PRO A 71 ALA A 76 1 6 SHEET 1 A 4 GLN A 24 THR A 27 0 SHEET 2 A 4 ASN A 112 ARG A 116 1 O ARG A 114 N GLN A 24 SHEET 3 A 4 GLY A 95 MET A 102 -1 N GLY A 95 O VAL A 115 SHEET 4 A 4 ARG A 48 ASN A 54 -1 N GLU A 50 O GLN A 100 SHEET 1 B 2 GLU A 32 LYS A 37 0 SHEET 2 B 2 SER A 83 VAL A 89 -1 O LEU A 84 N LEU A 36 SSBOND 1 CYS A 38 CYS A 99 1555 1555 2.03 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