PDB Short entry for 1XHR HEADER HYDROLASE 20-SEP-04 1XHR TITLE HUMAN PARAOXONASE 1 BY HOMOLOGY TO DFPASE CAVEAT 1XHR CHIRALITY ERRORS AT THE CA CENTER OF GLU 148 AND LEU 305 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERUM PARAOXONASE/ARYLESTERASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 40-355; COMPND 5 SYNONYM: SERUM PARAOXONASE 1, PON 1, SERUM COMPND 6 ARYLDIALKYLPHOSPHATASE 1, A-ESTERASE 1, AROMATIC ESTERASE COMPND 7 1, K-45; COMPND 8 EC: 3.1.1.2, 3.1.8.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN KEYWDS PARAOXONASE, HUMAN PARAOXONASE, HUMAN SERUM PARAOXONASE, KEYWDS 2 PON CALCIUM-BINDING SITE, BETA-PROPELLER EXPDTA THEORETICAL MODEL AUTHOR J.D.NICHOLSON,D.JOSSE REVDAT 1 12-OCT-04 1XHR 0 JRNL AUTH D.T.YEUNG,D.JOSSE,J.D.NICHOLSON,A.KHANAL, JRNL AUTH 2 C.W.MCANDREW,B.J.BAHNSON,D.E.LENZ,D.M.CERASOLI JRNL TITL STRUCTURE/FUNCTION ANALYSES OF HUMAN SERUM JRNL TITL 2 PARAOXONASE (HUPON1) MUTANTS DESIGNED FROM A JRNL TITL 3 DFPASE-LIKE HOMOLOGY MODEL JRNL REF BIOCHIM.BIOPHYS.ACTA V.1702 67 2004 JRNL REFN ASTM BBACAQ NE ISSN 0006-3002 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XHR COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-SEP-2004. REMARK 100 THE RCSB ID CODE IS RCSB030376. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THE STRUCTURE PRESENTED IN THIS ENTRY IS A MODEL OF REMARK 220 HUMAN PARAOXONASE 1 (PON1) BASED ON HOMOLOGY TO 1E1A REMARK 220 (DFPASE FROM LOLLIGO VULGARIS). THE STRUCTURE WAS REMARK 220 DERIVED FROM AN INITIAL HOMOLOGY MODEL TO DFPASE AFTER REMARK 220 ADDITION OF RESIDUES 40-51, CREATION OF THE SINGLE REMARK 220 DISULFIDE BOND, AND AN UNCONSTRAINED DYNAMICS SIMULATION REMARK 220 IN A PRESSURIZED WATER BOX FOR 30 PS (30,000 TIMESTEPS) REMARK 220 FOLLOWED BY CONSTRAINED MINIMIZATION FOR 10 TIMESTEPS TO REMARK 220 RESTORE PLANARITY TO AROMATIC RINGS. THE HOMOLOGY MODEL REMARK 220 WAS BUILT USING INSIGHT/DISCOVER'S HOMOLOGY MODULE. THE REMARK 220 DYNAMICS RUN WAS PERFORMED, AFTER MANY LOCAL REMARK 220 MINIMIZATIONS, USING INSIGHT/DISCOVER'S DISCOVER3 MODULE REMARK 220 ON SILICON GRAPHICS HARDWARE PROVIDED BY THE INSTITUTE REMARK 220 OF CHEMICAL DEFENSE, APG, MD, USA AS WELL AS HARDWARE REMARK 220 PROVIDED BY THE NATIONAL CANCER INSTITUTE'S ADVANCED REMARK 220 BIOMEDICAL COMPUTING CENTER, FREDERICK, MD, USA. THE REMARK 220 DISCOVER DYNAMICS WAS RUN UNDER NPT WITH 1 FS TIMESTEP, REMARK 220 .1 MPA UNIFORM PRESSURE IN A WATER BOX WITH 76 ANG REMARK 220 SIDES. ALL CALCULATIONS WERE PERFORMED USING THE CVFF REMARK 220 FORCEFIELD. REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. 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 M RES CSSEQI PSI PHI REMARK 500 VAL A 45 -103.91 86.67 REMARK 500 LYS A 46 -84.37 66.85 REMARK 500 GLU A 53 -100.72 42.23 REMARK 500 LYS A 75 -83.21 60.62 REMARK 500 PHE A 77 -100.63 60.29 REMARK 500 ASN A 80 -94.33 106.13 REMARK 500 LYS A 84 121.83 78.06 REMARK 500 VAL A 109 -50.72 76.46 REMARK 500 SER A 111 -67.55 71.88 REMARK 500 PHE A 144 -43.58 88.52 REMARK 500 TYR A 185 -78.70 63.44 REMARK 500 TYR A 207 120.80 66.84 REMARK 500 TRP A 254 -55.21 91.27 REMARK 500 LEU A 267 142.02 67.19 REMARK 500 ASN A 298 -56.65 107.79 REMARK 500 ILE A 307 -47.80 72.68 REMARK 500 GLN A 308 -41.43 77.76 REMARK 500 LEU A 311 -30.14 86.03 REMARK 500 LEU A 342 -68.13 85.94 REMARK 500 THR A 345 -87.57 76.50 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 80 SER A 81 -133.46 REMARK 500 LEU A 100 GLY A 101 -147.58 REMARK 500 MET A 127 TYR A 128 -148.39 REMARK 500 ASN A 133 HIS A 134 149.74 REMARK 500 ASN A 182 ASP A 183 -148.06 REMARK 500 ASP A 183 HIS A 184 147.82 REMARK 500 THR A 318 GLN A 319 141.97 REMARK 500 LEU A 341 LEU A 342 140.12 DBREF 1XHR A 40 355 UNP P27169 PON1_HUMAN 39 354 SEQRES 1 A 316 PRO ASN CYS ASN LEU VAL LYS GLY ILE GLU THR GLY SER SEQRES 2 A 316 GLU ASP MET GLU ILE LEU PRO ASN GLY LEU ALA PHE ILE SEQRES 3 A 316 SER SER GLY LEU LYS TYR PRO GLY ILE LYS SER PHE ASN SEQRES 4 A 316 PRO ASN SER PRO GLY LYS ILE LEU LEU MET ASP LEU ASN SEQRES 5 A 316 GLU GLU ASP PRO THR VAL LEU GLU LEU GLY ILE THR GLY SEQRES 6 A 316 SER LYS PHE ASP VAL SER SER PHE ASN PRO HIS GLY ILE SEQRES 7 A 316 SER THR PHE THR ASP GLU ASP ASN ALA MET TYR LEU LEU SEQRES 8 A 316 VAL VAL ASN HIS PRO ASP ALA LYS SER THR VAL GLU LEU SEQRES 9 A 316 PHE LYS PHE GLN GLU GLU GLU LYS SER LEU LEU HIS LEU SEQRES 10 A 316 LYS THR ILE ARG HIS LYS LEU LEU PRO ASN LEU ASN ASP SEQRES 11 A 316 ILE VAL ALA VAL GLY PRO GLU HIS PHE TYR GLY THR ASN SEQRES 12 A 316 ASP HIS TYR PHE LEU ASP PRO TYR LEU GLN SER TRP GLU SEQRES 13 A 316 MET TYR LEU GLY LEU ALA TRP SER TYR VAL VAL TYR TYR SEQRES 14 A 316 SER PRO SER GLU VAL ARG VAL VAL ALA GLU GLY PHE ASP SEQRES 15 A 316 PHE ALA ASN GLY ILE ASN ILE SER PRO ASP GLY LYS TYR SEQRES 16 A 316 VAL TYR ILE ALA GLU LEU LEU ALA HIS LYS ILE HIS VAL SEQRES 17 A 316 TYR GLU LYS HIS ALA ASN TRP THR LEU THR PRO LEU LYS SEQRES 18 A 316 SER LEU ASP PHE ASN THR LEU VAL ASP ASN ILE SER VAL SEQRES 19 A 316 ASP PRO GLU THR GLY ASP LEU TRP VAL GLY CYS HIS PRO SEQRES 20 A 316 ASN GLY MET LYS ILE PHE PHE TYR ASP SER GLU ASN PRO SEQRES 21 A 316 PRO ALA SER GLU VAL LEU ARG ILE GLN ASN ILE LEU THR SEQRES 22 A 316 GLU GLU PRO LYS VAL THR GLN VAL TYR ALA GLU ASN GLY SEQRES 23 A 316 THR VAL LEU GLN GLY SER THR VAL ALA SER VAL TYR LYS SEQRES 24 A 316 GLY LYS LEU LEU ILE GLY THR VAL PHE HIS LYS ALA LEU SEQRES 25 A 316 TYR CYS GLU LEU HET CA 402 1 HET CA 401 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) SHEET 1 A 4 ASP A 54 ILE A 57 0 SHEET 2 A 4 ALA A 63 SER A 66 -1 O SER A 66 N ASP A 54 SHEET 3 A 4 ILE A 85 ASP A 89 -1 O MET A 88 N ALA A 63 SHEET 4 A 4 ASP A 94 VAL A 97 -1 O THR A 96 N LEU A 87 SHEET 1 B 3 GLY A 116 THR A 119 0 SHEET 2 B 3 MET A 127 VAL A 132 -1 O VAL A 131 N SER A 118 SHEET 3 B 3 ALA A 137 VAL A 141 -1 O THR A 140 N TYR A 128 SHEET 1 C 4 ILE A 170 ALA A 172 0 SHEET 2 C 4 PHE A 178 ASN A 182 -1 O TYR A 179 N VAL A 171 SHEET 3 C 4 ALA A 201 VAL A 205 -1 O TRP A 202 N ASN A 182 SHEET 4 C 4 ALA A 217 PHE A 220 -1 O PHE A 220 N ALA A 201 SHEET 1 D 3 ILE A 226 ASN A 227 0 SHEET 2 D 3 TYR A 234 GLU A 239 -1 O TYR A 236 N ASN A 227 SHEET 3 D 3 LYS A 244 GLU A 249 -1 O HIS A 246 N ILE A 237 SHEET 1 E 3 ASN A 270 ILE A 271 0 SHEET 2 E 3 TRP A 281 GLY A 283 -1 O GLY A 283 N ASN A 270 SHEET 3 E 3 PHE A 292 PHE A 293 -1 O PHE A 292 N VAL A 282 SHEET 1 F 3 LYS A 316 VAL A 320 0 SHEET 2 F 3 LEU A 328 THR A 332 -1 O GLN A 329 N VAL A 320 SHEET 3 F 3 LYS A 338 LEU A 341 -1 O GLY A 339 N GLY A 330 SSBOND 1 CYS A 42 CYS A 353 CISPEP 1 ASN A 78 PRO A 79 0 1.88 CISPEP 2 ASP A 188 PRO A 189 0 19.46 CISPEP 3 ASP A 231 GLY A 232 0 7.06 CISPEP 4 THR A 277 GLY A 278 0 -20.67 CRYST1 76.000 76.000 76.000 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 0.013158 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013158 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013158 0.00000