HEADER IMMUNE SYSTEM/HYDROLASE 27-JUL-17 5Y32 TITLE CRYSTAL STRUCTURE OF PTP DELTA IG1-IG2 IN COMPLEX WITH IL1RAPL1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 RECEPTOR ACCESSORY PROTEIN-LIKE 1; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 19-352; COMPND 5 SYNONYM: IL1RAPL-1,X-LINKED INTERLEUKIN-1 RECEPTOR ACCESSORY PROTEIN- COMPND 6 LIKE 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE DELTA; COMPND 10 CHAIN: A; COMPND 11 FRAGMENT: UNP RESIDUES 21-318; COMPND 12 SYNONYM: R-PTP-DELTA; COMPND 13 EC: 3.1.3.48; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: IL1RAPL1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 GENE: PTPRD; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS TRANS-SYNAPTIC, ADHESION COMPLEX, IMMUNE SYSTEM-HYDROLASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.YAMAGATA,S.FUKAI REVDAT 4 22-NOV-23 5Y32 1 HETSYN LINK REVDAT 3 29-JUL-20 5Y32 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 27-FEB-19 5Y32 1 JRNL REVDAT 1 16-AUG-17 5Y32 0 SPRSDE 16-AUG-17 5Y32 4YFC JRNL AUTH A.YAMAGATA,T.YOSHIDA,Y.SATO,S.GOTO-ITO,T.UEMURA,A.MAEDA, JRNL AUTH 2 T.SHIROSHIMA,S.IWASAWA-OKAMOTO,H.MORI,M.MISHINA,S.FUKAI JRNL TITL MECHANISMS OF SPLICING-DEPENDENT TRANS-SYNAPTIC ADHESION BY JRNL TITL 2 PTP DELTA-IL1RAPL1/IL-1RACP FOR SYNAPTIC DIFFERENTIATION. JRNL REF NAT COMMUN V. 6 6926 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 25908590 JRNL DOI 10.1038/NCOMMS7926 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 32242 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1638 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.7353 - 6.1801 0.99 2654 166 0.1983 0.2522 REMARK 3 2 6.1801 - 4.9072 1.00 2613 151 0.1694 0.2087 REMARK 3 3 4.9072 - 4.2874 1.00 2599 135 0.1361 0.1954 REMARK 3 4 4.2874 - 3.8956 1.00 2600 140 0.1618 0.2065 REMARK 3 5 3.8956 - 3.6165 1.00 2608 125 0.2015 0.2207 REMARK 3 6 3.6165 - 3.4034 0.99 2574 128 0.2145 0.2795 REMARK 3 7 3.4034 - 3.2330 0.99 2568 142 0.2369 0.2641 REMARK 3 8 3.2330 - 3.0923 0.99 2585 141 0.2626 0.3171 REMARK 3 9 3.0923 - 2.9733 0.98 2514 132 0.2809 0.3222 REMARK 3 10 2.9733 - 2.8707 0.98 2551 118 0.3071 0.3224 REMARK 3 11 2.8707 - 2.7809 0.97 2484 125 0.3334 0.3510 REMARK 3 12 2.7809 - 2.7014 0.87 2254 135 0.3693 0.4147 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 4454 REMARK 3 ANGLE : 1.262 6036 REMARK 3 CHIRALITY : 0.069 693 REMARK 3 PLANARITY : 0.005 766 REMARK 3 DIHEDRAL : 15.842 1688 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -51.2714 -10.8237 19.7707 REMARK 3 T TENSOR REMARK 3 T11: 0.2403 T22: 0.2472 REMARK 3 T33: 0.2366 T12: -0.0088 REMARK 3 T13: 0.0103 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.7296 L22: 1.5015 REMARK 3 L33: 1.3732 L12: -0.2952 REMARK 3 L13: 0.5241 L23: -0.1288 REMARK 3 S TENSOR REMARK 3 S11: 0.0258 S12: 0.0519 S13: 0.0008 REMARK 3 S21: 0.3013 S22: -0.0474 S23: -0.2209 REMARK 3 S31: -0.0225 S32: 0.1303 S33: -0.0048 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5Y32 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300004591. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32256 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2YD6, 4DEP, 3O4O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG4 000, 0.1 M MES, PH 6.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 81.48750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.58750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 81.48750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.58750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, C, D, E 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO B 14 REMARK 465 ALA B 15 REMARK 465 ALA B 16 REMARK 465 ARG B 17 REMARK 465 ASP B 18 REMARK 465 LEU B 19 REMARK 465 LYS B 20 REMARK 465 VAL B 21 REMARK 465 VAL B 22 REMARK 465 THR B 23 REMARK 465 LYS B 24 REMARK 465 ARG B 25 REMARK 465 GLY B 26 REMARK 465 SER B 27 REMARK 465 ALA B 28 REMARK 465 ASP B 29 REMARK 465 GLY B 30 REMARK 465 LYS B 353 REMARK 465 HIS B 354 REMARK 465 HIS B 355 REMARK 465 HIS B 356 REMARK 465 HIS B 357 REMARK 465 HIS B 358 REMARK 465 HIS B 359 REMARK 465 GLU A 237 REMARK 465 VAL A 238 REMARK 465 ARG A 239 REMARK 465 ARG A 240 REMARK 465 VAL A 241 REMARK 465 PRO A 242 REMARK 465 PRO A 243 REMARK 465 ARG A 244 REMARK 465 PHE A 245 REMARK 465 SER A 246 REMARK 465 ILE A 247 REMARK 465 PRO A 248 REMARK 465 PRO A 249 REMARK 465 THR A 250 REMARK 465 ASN A 251 REMARK 465 HIS A 252 REMARK 465 GLU A 253 REMARK 465 ILE A 254 REMARK 465 MET A 255 REMARK 465 PRO A 256 REMARK 465 GLY A 257 REMARK 465 GLY A 258 REMARK 465 SER A 259 REMARK 465 VAL A 260 REMARK 465 ASN A 261 REMARK 465 ILE A 262 REMARK 465 THR A 263 REMARK 465 CYS A 264 REMARK 465 VAL A 265 REMARK 465 ALA A 266 REMARK 465 VAL A 267 REMARK 465 GLY A 268 REMARK 465 SER A 269 REMARK 465 PRO A 270 REMARK 465 MET A 271 REMARK 465 PRO A 272 REMARK 465 TYR A 273 REMARK 465 VAL A 274 REMARK 465 LYS A 275 REMARK 465 TRP A 276 REMARK 465 MET A 277 REMARK 465 LEU A 278 REMARK 465 GLY A 279 REMARK 465 ALA A 280 REMARK 465 GLU A 281 REMARK 465 ASP A 282 REMARK 465 LEU A 283 REMARK 465 THR A 284 REMARK 465 PRO A 285 REMARK 465 GLU A 286 REMARK 465 ASP A 287 REMARK 465 ASP A 288 REMARK 465 MET A 289 REMARK 465 PRO A 290 REMARK 465 ILE A 291 REMARK 465 GLY A 292 REMARK 465 ARG A 293 REMARK 465 ASN A 294 REMARK 465 VAL A 295 REMARK 465 LEU A 296 REMARK 465 GLU A 297 REMARK 465 LEU A 298 REMARK 465 ASN A 299 REMARK 465 ASP A 300 REMARK 465 VAL A 301 REMARK 465 ARG A 302 REMARK 465 GLN A 303 REMARK 465 SER A 304 REMARK 465 ALA A 305 REMARK 465 ASN A 306 REMARK 465 TYR A 307 REMARK 465 THR A 308 REMARK 465 CYS A 309 REMARK 465 VAL A 310 REMARK 465 ALA A 311 REMARK 465 MET A 312 REMARK 465 SER A 313 REMARK 465 THR A 314 REMARK 465 LEU A 315 REMARK 465 GLY A 316 REMARK 465 VAL A 317 REMARK 465 ILE A 318 REMARK 465 GLU A 319 REMARK 465 ALA A 320 REMARK 465 ILE A 321 REMARK 465 ALA A 322 REMARK 465 GLN A 323 REMARK 465 ILE A 324 REMARK 465 THR A 325 REMARK 465 LYS A 326 REMARK 465 HIS A 327 REMARK 465 HIS A 328 REMARK 465 HIS A 329 REMARK 465 HIS A 330 REMARK 465 HIS A 331 REMARK 465 HIS A 332 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O THR B 174 O HOH B 501 2.14 REMARK 500 O LEU B 172 NH2 ARG B 198 2.15 REMARK 500 OD2 ASP B 139 OG SER B 146 2.18 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 SER B 35 -151.63 57.72 REMARK 500 VAL B 45 108.99 -56.21 REMARK 500 TYR B 57 36.48 -98.67 REMARK 500 ASP B 92 -151.89 -92.44 REMARK 500 SER B 94 -79.41 -97.60 REMARK 500 ARG B 95 -71.00 -69.04 REMARK 500 LYS B 98 78.35 -112.39 REMARK 500 ASN B 122 -154.72 -99.29 REMARK 500 LYS B 197 -164.73 -118.27 REMARK 500 TYR B 220 128.65 -176.66 REMARK 500 PRO B 241 170.78 -54.34 REMARK 500 LEU B 245 -76.51 -118.59 REMARK 500 TRP B 299 143.85 -175.01 REMARK 500 HIS B 309 83.37 -152.89 REMARK 500 LEU B 310 76.15 51.14 REMARK 500 ASN A 73 137.55 -172.55 REMARK 500 THR A 147 -4.09 75.67 REMARK 500 PHE A 170 -5.57 76.84 REMARK 500 SER A 189 92.45 75.48 REMARK 500 REMARK 500 REMARK: NULL 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 PHE B 85 GLU B 86 -145.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 539 DISTANCE = 6.42 ANGSTROMS DBREF 5Y32 B 19 352 UNP P59823 IRPL1_MOUSE 19 352 DBREF 5Y32 A 28 325 UNP Q64487 PTPRD_MOUSE 21 318 SEQADV 5Y32 PRO B 14 UNP P59823 EXPRESSION TAG SEQADV 5Y32 ALA B 15 UNP P59823 EXPRESSION TAG SEQADV 5Y32 ALA B 16 UNP P59823 EXPRESSION TAG SEQADV 5Y32 ARG B 17 UNP P59823 EXPRESSION TAG SEQADV 5Y32 ASP B 18 UNP P59823 EXPRESSION TAG SEQADV 5Y32 LYS B 353 UNP P59823 EXPRESSION TAG SEQADV 5Y32 HIS B 354 UNP P59823 EXPRESSION TAG SEQADV 5Y32 HIS B 355 UNP P59823 EXPRESSION TAG SEQADV 5Y32 HIS B 356 UNP P59823 EXPRESSION TAG SEQADV 5Y32 HIS B 357 UNP P59823 EXPRESSION TAG SEQADV 5Y32 HIS B 358 UNP P59823 EXPRESSION TAG SEQADV 5Y32 HIS B 359 UNP P59823 EXPRESSION TAG SEQADV 5Y32 LYS A 326 UNP Q64487 EXPRESSION TAG SEQADV 5Y32 HIS A 327 UNP Q64487 EXPRESSION TAG SEQADV 5Y32 HIS A 328 UNP Q64487 EXPRESSION TAG SEQADV 5Y32 HIS A 329 UNP Q64487 EXPRESSION TAG SEQADV 5Y32 HIS A 330 UNP Q64487 EXPRESSION TAG SEQADV 5Y32 HIS A 331 UNP Q64487 EXPRESSION TAG SEQADV 5Y32 HIS A 332 UNP Q64487 EXPRESSION TAG SEQRES 1 B 346 PRO ALA ALA ARG ASP LEU LYS VAL VAL THR LYS ARG GLY SEQRES 2 B 346 SER ALA ASP GLY CYS THR ASP TRP SER VAL ASP ILE LYS SEQRES 3 B 346 LYS TYR GLN VAL LEU VAL GLY GLU PRO VAL ARG ILE LYS SEQRES 4 B 346 CYS ALA LEU PHE TYR GLY TYR ILE ARG THR ASN TYR SER SEQRES 5 B 346 LEU ALA GLN SER ALA GLY LEU SER LEU MET TRP TYR LYS SEQRES 6 B 346 SER SER GLY PRO GLY ASP PHE GLU GLU PRO ILE ALA PHE SEQRES 7 B 346 ASP GLY SER ARG MET SER LYS GLU GLU ASP SER ILE TRP SEQRES 8 B 346 PHE ARG PRO THR LEU LEU GLN ASP SER GLY LEU TYR ALA SEQRES 9 B 346 CYS VAL ILE ARG ASN SER THR TYR CYS MET LYS VAL SER SEQRES 10 B 346 ILE SER LEU THR VAL GLY GLU ASN ASP THR GLY LEU CYS SEQRES 11 B 346 TYR ASN SER LYS MET LYS TYR PHE GLU LYS ALA GLU LEU SEQRES 12 B 346 SER LYS SER LYS GLU ILE SER CYS ARG ASP ILE GLU ASP SEQRES 13 B 346 PHE LEU LEU PRO THR ARG GLU PRO GLU ILE LEU TRP TYR SEQRES 14 B 346 LYS GLU CYS ARG THR LYS ALA TRP ARG PRO SER ILE VAL SEQRES 15 B 346 PHE LYS ARG ASP THR LEU LEU ILE LYS GLU VAL LYS GLU SEQRES 16 B 346 ASP ASP ILE GLY ASN TYR THR CYS GLU LEU LYS TYR GLY SEQRES 17 B 346 GLY PHE VAL VAL ARG ARG THR THR GLU LEU THR VAL THR SEQRES 18 B 346 ALA PRO LEU THR ASP LYS PRO PRO LYS LEU LEU TYR PRO SEQRES 19 B 346 MET GLU SER LYS LEU THR VAL GLN GLU THR GLN LEU GLY SEQRES 20 B 346 GLY SER ALA ASN LEU THR CYS ARG ALA PHE PHE GLY TYR SEQRES 21 B 346 SER GLY ASP VAL SER PRO LEU ILE TYR TRP MET LYS GLY SEQRES 22 B 346 GLU LYS PHE ILE GLU ASP LEU ASP GLU ASN ARG VAL TRP SEQRES 23 B 346 GLU SER ASP ILE ARG ILE LEU LYS GLU HIS LEU GLY GLU SEQRES 24 B 346 GLN GLU VAL SER ILE SER LEU ILE VAL ASP SER VAL GLU SEQRES 25 B 346 GLU GLY ASP LEU GLY ASN TYR SER CYS TYR VAL GLU ASN SEQRES 26 B 346 GLY ASN GLY ARG ARG HIS ALA SER VAL LEU LEU HIS LYS SEQRES 27 B 346 ARG LYS HIS HIS HIS HIS HIS HIS SEQRES 1 A 305 GLU THR PRO PRO ARG PHE THR ARG THR PRO VAL ASP GLN SEQRES 2 A 305 THR GLY VAL SER GLY GLY VAL ALA SER PHE ILE CYS GLN SEQRES 3 A 305 ALA THR GLY ASP PRO ARG PRO LYS ILE VAL TRP ASN LYS SEQRES 4 A 305 LYS GLY LYS LYS VAL SER ASN GLN ARG PHE GLU VAL ILE SEQRES 5 A 305 GLU PHE ASP ASP GLY SER GLY SER VAL LEU ARG ILE GLN SEQRES 6 A 305 PRO LEU ARG THR PRO ARG ASP GLU ALA ILE TYR GLU CYS SEQRES 7 A 305 VAL ALA SER ASN ASN VAL GLY GLU ILE SER VAL SER THR SEQRES 8 A 305 ARG LEU THR VAL LEU ARG GLU ASP GLN ILE PRO ARG GLY SEQRES 9 A 305 PHE PRO THR ILE ASP MET GLY PRO GLN LEU LYS VAL VAL SEQRES 10 A 305 GLU ARG THR ARG THR ALA THR MET LEU CYS ALA ALA SER SEQRES 11 A 305 GLY ASN PRO ASP PRO GLU ILE THR TRP PHE LYS ASP PHE SEQRES 12 A 305 LEU PRO VAL ASP THR SER ASN ASN ASN GLY ARG ILE LYS SEQRES 13 A 305 GLN LEU ARG SER GLU SER ILE GLY GLY THR PRO ILE ARG SEQRES 14 A 305 GLY ALA LEU GLN ILE GLU GLN SER GLU GLU SER ASP GLN SEQRES 15 A 305 GLY LYS TYR GLU CYS VAL ALA THR ASN SER ALA GLY THR SEQRES 16 A 305 ARG TYR SER ALA PRO ALA ASN LEU TYR VAL ARG GLU LEU SEQRES 17 A 305 ARG GLU VAL ARG ARG VAL PRO PRO ARG PHE SER ILE PRO SEQRES 18 A 305 PRO THR ASN HIS GLU ILE MET PRO GLY GLY SER VAL ASN SEQRES 19 A 305 ILE THR CYS VAL ALA VAL GLY SER PRO MET PRO TYR VAL SEQRES 20 A 305 LYS TRP MET LEU GLY ALA GLU ASP LEU THR PRO GLU ASP SEQRES 21 A 305 ASP MET PRO ILE GLY ARG ASN VAL LEU GLU LEU ASN ASP SEQRES 22 A 305 VAL ARG GLN SER ALA ASN TYR THR CYS VAL ALA MET SER SEQRES 23 A 305 THR LEU GLY VAL ILE GLU ALA ILE ALA GLN ILE THR LYS SEQRES 24 A 305 HIS HIS HIS HIS HIS HIS HET NAG C 1 14 HET NAG C 2 14 HET FUC C 3 10 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET FUC E 4 10 HET NAG B 409 14 HET NAG B 410 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 3 NAG 8(C8 H15 N O6) FORMUL 3 FUC 2(C6 H12 O5) FORMUL 5 BMA C6 H12 O6 FORMUL 8 HOH *77(H2 O) HELIX 1 AA1 ALA B 54 GLY B 58 5 5 HELIX 2 AA2 ASN B 63 ALA B 70 1 8 HELIX 3 AA3 LEU B 109 SER B 113 5 5 HELIX 4 AA4 LYS B 207 ILE B 211 5 5 HELIX 5 AA5 GLU A 205 GLN A 209 5 5 SHEET 1 AA1 3 THR B 32 VAL B 36 0 SHEET 2 AA1 3 CYS B 126 GLY B 136 1 O LYS B 128 N TRP B 34 SHEET 3 AA1 3 TYR B 41 LEU B 44 1 N TYR B 41 O THR B 134 SHEET 1 AA2 5 THR B 32 VAL B 36 0 SHEET 2 AA2 5 CYS B 126 GLY B 136 1 O LYS B 128 N TRP B 34 SHEET 3 AA2 5 GLY B 114 ARG B 121 -1 N CYS B 118 O VAL B 129 SHEET 4 AA2 5 SER B 73 SER B 79 -1 N SER B 79 O LEU B 115 SHEET 5 AA2 5 GLU B 87 PRO B 88 -1 O GLU B 87 N LYS B 78 SHEET 1 AA3 2 VAL B 49 LYS B 52 0 SHEET 2 AA3 2 SER B 102 PHE B 105 -1 O ILE B 103 N ILE B 51 SHEET 1 AA4 4 TYR B 150 GLU B 155 0 SHEET 2 AA4 4 PHE B 223 THR B 234 1 O GLU B 230 N TYR B 150 SHEET 3 AA4 4 GLY B 212 TYR B 220 -1 N TYR B 220 O PHE B 223 SHEET 4 AA4 4 LEU B 180 LYS B 183 -1 N TYR B 182 O THR B 215 SHEET 1 AA5 3 LYS B 160 SER B 163 0 SHEET 2 AA5 3 THR B 200 ILE B 203 -1 O LEU B 201 N ILE B 162 SHEET 3 AA5 3 ILE B 194 PHE B 196 -1 N VAL B 195 O LEU B 202 SHEET 1 AA6 4 LYS B 243 TYR B 246 0 SHEET 2 AA6 4 ALA B 263 PHE B 271 -1 O ARG B 268 N TYR B 246 SHEET 3 AA6 4 GLN B 313 VAL B 321 -1 O ILE B 317 N CYS B 267 SHEET 4 AA6 4 VAL B 298 GLU B 300 -1 N TRP B 299 O ILE B 320 SHEET 1 AA7 4 LYS B 243 TYR B 246 0 SHEET 2 AA7 4 ALA B 263 PHE B 271 -1 O ARG B 268 N TYR B 246 SHEET 3 AA7 4 GLN B 313 VAL B 321 -1 O ILE B 317 N CYS B 267 SHEET 4 AA7 4 ARG B 304 GLU B 308 -1 N ARG B 304 O SER B 316 SHEET 1 AA8 5 THR B 253 THR B 257 0 SHEET 2 AA8 5 GLY B 341 LYS B 351 1 O LEU B 348 N GLN B 255 SHEET 3 AA8 5 GLY B 330 ASN B 338 -1 N TYR B 332 O VAL B 347 SHEET 4 AA8 5 LEU B 280 LYS B 285 -1 N TYR B 282 O TYR B 335 SHEET 5 AA8 5 LYS B 288 PHE B 289 -1 O LYS B 288 N LYS B 285 SHEET 1 AA9 4 THR A 29 ARG A 35 0 SHEET 2 AA9 4 ALA A 48 ASP A 57 -1 O GLN A 53 N THR A 34 SHEET 3 AA9 4 GLY A 86 ILE A 91 -1 O ILE A 91 N ALA A 48 SHEET 4 AA9 4 PHE A 76 GLU A 80 -1 N GLU A 77 O ARG A 90 SHEET 1 AB1 5 GLN A 40 VAL A 43 0 SHEET 2 AB1 5 GLU A 113 LEU A 123 1 O THR A 121 N GLY A 42 SHEET 3 AB1 5 ALA A 101 SER A 108 -1 N ALA A 107 O ILE A 114 SHEET 4 AB1 5 LYS A 61 LYS A 66 -1 N ASN A 65 O GLU A 104 SHEET 5 AB1 5 LYS A 69 LYS A 70 -1 O LYS A 69 N LYS A 66 SHEET 1 AB2 4 THR A 134 MET A 137 0 SHEET 2 AB2 4 ALA A 150 SER A 157 -1 O ALA A 155 N MET A 137 SHEET 3 AB2 4 ILE A 195 ILE A 201 -1 O ILE A 201 N ALA A 150 SHEET 4 AB2 4 ILE A 182 ARG A 186 -1 N LYS A 183 O GLN A 200 SHEET 1 AB3 5 LYS A 142 GLU A 145 0 SHEET 2 AB3 5 ALA A 228 ARG A 233 1 O TYR A 231 N LYS A 142 SHEET 3 AB3 5 GLY A 210 ASN A 218 -1 N TYR A 212 O ALA A 228 SHEET 4 AB3 5 GLU A 163 LYS A 168 -1 N GLU A 163 O THR A 217 SHEET 5 AB3 5 LEU A 171 PRO A 172 -1 O LEU A 171 N LYS A 168 SHEET 1 AB4 4 LYS A 142 GLU A 145 0 SHEET 2 AB4 4 ALA A 228 ARG A 233 1 O TYR A 231 N LYS A 142 SHEET 3 AB4 4 GLY A 210 ASN A 218 -1 N TYR A 212 O ALA A 228 SHEET 4 AB4 4 GLY A 221 TYR A 224 -1 O ARG A 223 N ALA A 216 SSBOND 1 CYS B 31 CYS B 126 1555 1555 2.03 SSBOND 2 CYS B 53 CYS B 118 1555 1555 2.04 SSBOND 3 CYS B 143 CYS B 185 1555 1555 2.03 SSBOND 4 CYS B 164 CYS B 216 1555 1555 2.03 SSBOND 5 CYS B 267 CYS B 334 1555 1555 2.04 SSBOND 6 CYS A 52 CYS A 105 1555 1555 2.02 SSBOND 7 CYS A 154 CYS A 214 1555 1555 2.04 LINK ND2 ASN B 63 C1 NAG B 410 1555 1555 1.46 LINK ND2 ASN B 122 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN B 138 C1 NAG B 409 1555 1555 1.45 LINK ND2 ASN B 213 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN B 264 C1 NAG E 1 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O6 NAG C 1 C1 FUC C 3 1555 1555 1.46 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.46 LINK O6 NAG E 1 C1 FUC E 4 1555 1555 1.46 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.48 CISPEP 1 PRO B 82 GLY B 83 0 0.80 CISPEP 2 ARG B 106 PRO B 107 0 -1.80 CISPEP 3 ARG B 165 ASP B 166 0 -7.59 CISPEP 4 GLU B 176 PRO B 177 0 -0.56 CISPEP 5 GLY B 221 GLY B 222 0 1.29 CISPEP 6 TYR B 246 PRO B 247 0 -10.51 CISPEP 7 LEU B 310 GLY B 311 0 -16.00 CISPEP 8 ASP A 57 PRO A 58 0 2.63 CISPEP 9 GLN A 92 PRO A 93 0 -1.98 CISPEP 10 THR A 96 PRO A 97 0 3.77 CISPEP 11 ASN A 159 PRO A 160 0 1.49 CRYST1 162.975 81.175 91.480 90.00 91.27 90.00 C 1 2 1 4 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 0.006136 0.000000 0.000136 0.00000 SCALE2 0.000000 0.012319 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010934 0.00000