HEADER HYDROLASE/CELL ADHESION 23-JUN-20 7CEG TITLE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN MOUSE PTP DELTA AND TITLE 2 NEUROLIGIN-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM C OF RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE COMPND 3 DELTA; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: R-PTP-DELTA; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NEUROLIGIN-3; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: GLIOTACTIN HOMOLOG; COMPND 12 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: PTPRD; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 CELL_LINE: HEK293F; SOURCE 14 GENE: NLGN3; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM_CELL_LINE: HEK293F KEYWDS SYNAPSE ORGANIZATION, TRANS-SYNAPTIC COMPLEX, ESTERASE DOMAIN, KEYWDS 2 HYDROLASE-CELL ADHESION COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.YAMAGATA,T.YOSHIDA,T.SHIROSHIMA,A.MAEDA,S.FUKAI REVDAT 3 29-NOV-23 7CEG 1 REMARK REVDAT 2 07-APR-21 7CEG 1 JRNL REVDAT 1 24-FEB-21 7CEG 0 JRNL AUTH T.YOSHIDA,A.YAMAGATA,A.IMAI,J.KIM,H.IZUMI,S.NAKASHIMA, JRNL AUTH 2 T.SHIROSHIMA,A.MAEDA,S.IWASAWA-OKAMOTO,K.AZECHI,F.OSAKA, JRNL AUTH 3 T.SAITOH,K.MAENAKA,T.SHIMADA,Y.FUKATA,M.FUKATA,J.MATSUMOTO, JRNL AUTH 4 H.NISHIJO,K.TAKAO,S.TANAKA,S.OKABE,K.TABUCHI,T.UEMURA, JRNL AUTH 5 M.MISHINA,H.MORI,S.FUKAI JRNL TITL CANONICAL VERSUS NON-CANONICAL TRANSSYNAPTIC SIGNALING OF JRNL TITL 2 NEUROLIGIN 3 TUNES DEVELOPMENT OF SOCIALITY IN MICE. JRNL REF NAT COMMUN V. 12 1848 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33758193 JRNL DOI 10.1038/S41467-021-22059-6 REMARK 2 REMARK 2 RESOLUTION. 3.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.17.1_3660: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 19070 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.255 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 928 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 49.6900 - 7.3500 1.00 2716 123 0.2289 0.2560 REMARK 3 2 7.3500 - 5.8400 1.00 2635 140 0.2960 0.3159 REMARK 3 3 5.8400 - 5.1000 1.00 2595 120 0.2526 0.2817 REMARK 3 4 5.1000 - 4.6300 1.00 2593 119 0.2425 0.2887 REMARK 3 5 4.6300 - 4.3000 1.00 2576 139 0.2488 0.3053 REMARK 3 6 4.3000 - 4.0500 1.00 2542 155 0.2753 0.3049 REMARK 3 7 4.0500 - 3.8500 0.98 2485 132 0.3186 0.3789 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.630 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 142.0 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 : 0.002 7470 REMARK 3 ANGLE : 0.499 10200 REMARK 3 CHIRALITY : 0.046 1135 REMARK 3 PLANARITY : 0.004 1334 REMARK 3 DIHEDRAL : 14.420 2740 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN B AND RESID 37:363 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.182 -26.448 -20.500 REMARK 3 T TENSOR REMARK 3 T11: 1.7922 T22: 1.3063 REMARK 3 T33: 1.1924 T12: 0.2656 REMARK 3 T13: 0.2022 T23: 0.0305 REMARK 3 L TENSOR REMARK 3 L11: 2.7112 L22: 5.1392 REMARK 3 L33: 1.2705 L12: -0.1218 REMARK 3 L13: -1.0778 L23: 0.3516 REMARK 3 S TENSOR REMARK 3 S11: -0.1654 S12: -0.8097 S13: 0.0972 REMARK 3 S21: 0.8198 S22: 0.1281 S23: -0.0122 REMARK 3 S31: 0.5338 S32: -0.4108 S33: 0.0677 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN B AND RESID 364:615 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.206 -32.453 -44.551 REMARK 3 T TENSOR REMARK 3 T11: 2.5505 T22: 1.2173 REMARK 3 T33: 1.8362 T12: 0.0553 REMARK 3 T13: 0.2948 T23: 0.2908 REMARK 3 L TENSOR REMARK 3 L11: 2.2876 L22: 1.3620 REMARK 3 L33: 6.4564 L12: 0.3371 REMARK 3 L13: -0.3538 L23: 1.0268 REMARK 3 S TENSOR REMARK 3 S11: -0.5941 S12: -0.5359 S13: -0.5150 REMARK 3 S21: -0.2083 S22: 0.5669 S23: 0.1165 REMARK 3 S31: 1.2575 S32: -0.8978 S33: 0.0520 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 28:137 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.584 18.028 -26.087 REMARK 3 T TENSOR REMARK 3 T11: 1.8461 T22: 1.5177 REMARK 3 T33: 1.5094 T12: 0.8020 REMARK 3 T13: 0.0689 T23: -0.2126 REMARK 3 L TENSOR REMARK 3 L11: 6.2179 L22: 9.2998 REMARK 3 L33: 6.4971 L12: 1.2352 REMARK 3 L13: 4.6120 L23: -3.9398 REMARK 3 S TENSOR REMARK 3 S11: -0.3444 S12: 0.5542 S13: 0.5045 REMARK 3 S21: -0.0335 S22: 0.1818 S23: -0.3767 REMARK 3 S31: 0.3243 S32: -0.2123 S33: 0.1236 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 138:302 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.409 -13.514 -36.215 REMARK 3 T TENSOR REMARK 3 T11: 2.0405 T22: 1.2235 REMARK 3 T33: 1.4893 T12: 0.4364 REMARK 3 T13: 0.0036 T23: -0.0807 REMARK 3 L TENSOR REMARK 3 L11: 4.4620 L22: 5.8760 REMARK 3 L33: 2.6242 L12: -3.9444 REMARK 3 L13: 0.7990 L23: -1.2981 REMARK 3 S TENSOR REMARK 3 S11: 0.4721 S12: 0.5006 S13: -0.1286 REMARK 3 S21: -0.8657 S22: -0.4673 S23: 0.3437 REMARK 3 S31: -0.0025 S32: 0.6643 S33: -0.0846 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 303:413 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.420 -61.586 -2.804 REMARK 3 T TENSOR REMARK 3 T11: 2.3267 T22: 1.6662 REMARK 3 T33: 1.7023 T12: 0.9961 REMARK 3 T13: -0.1808 T23: -0.1544 REMARK 3 L TENSOR REMARK 3 L11: -0.7280 L22: 5.1268 REMARK 3 L33: 3.4283 L12: -0.8863 REMARK 3 L13: 1.3028 L23: -5.0841 REMARK 3 S TENSOR REMARK 3 S11: 0.1792 S12: -0.1317 S13: 0.9581 REMARK 3 S21: 0.2820 S22: -0.3916 S23: -0.1349 REMARK 3 S31: -0.1407 S32: 0.0903 S33: 0.2147 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 7CEG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1300017474. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-14 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19070 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.850 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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, 4YFD, 4YFE, 3BIX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 0.1 M AMMONIUM IODIDE, REMARK 280 0.1 M MES-NA, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -Y,-X,-Z+1/3 REMARK 290 5555 -X+Y,Y,-Z+2/3 REMARK 290 6555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 247.74200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 123.87100 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 123.87100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 247.74200 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLU B 148 REMARK 465 ASP B 149 REMARK 465 GLY B 150 REMARK 465 SER B 151 REMARK 465 GLY B 152 REMARK 465 ALA B 153 REMARK 465 LYS B 154 REMARK 465 LYS B 155 REMARK 465 GLN B 156 REMARK 465 GLY B 157 REMARK 465 GLU B 158 REMARK 465 ASP B 159 REMARK 465 LEU B 160 REMARK 465 ALA B 161 REMARK 465 ASP B 162 REMARK 465 ASN B 163 REMARK 465 ASP B 164 REMARK 465 GLY B 165 REMARK 465 ASP B 166 REMARK 465 GLU B 167 REMARK 465 ASP B 168 REMARK 465 GLU B 169 REMARK 465 ASP B 170 REMARK 465 ILE B 171 REMARK 465 ARG B 172 REMARK 465 ASP B 173 REMARK 465 THR B 555 REMARK 465 LYS B 556 REMARK 465 PHE B 557 REMARK 465 ILE B 558 REMARK 465 HIS B 559 REMARK 465 THR B 560 REMARK 465 LYS B 561 REMARK 465 ALA B 562 REMARK 465 ASN B 563 REMARK 465 ARG B 564 REMARK 465 PHE B 565 REMARK 465 GLU B 566 REMARK 465 GLU B 567 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 ARG A 35 88.85 -158.67 REMARK 500 LYS A 67 58.38 -100.03 REMARK 500 SER A 189 -72.07 -68.72 REMARK 500 ALA A 192 -158.81 -142.33 REMARK 500 ASN A 212 -155.61 -131.68 REMARK 500 ARG A 230 70.60 -159.76 REMARK 500 ALA A 270 -48.12 -139.37 REMARK 500 GLU A 276 -44.25 66.99 REMARK 500 ARG A 292 -66.26 -128.32 REMARK 500 PRO A 357 170.06 -58.28 REMARK 500 TYR A 383 57.26 37.35 REMARK 500 ASN A 394 -162.61 -119.53 REMARK 500 GLU B 133 72.04 54.47 REMARK 500 PHE B 221 12.87 -141.89 REMARK 500 ARG B 258 55.16 -113.30 REMARK 500 GLN B 303 54.25 -150.59 REMARK 500 ASP B 358 -70.19 -130.67 REMARK 500 TYR B 420 70.13 51.75 REMARK 500 TYR B 435 51.46 -97.49 REMARK 500 ASP B 440 76.18 -159.51 REMARK 500 TRP B 460 -50.06 -120.46 REMARK 500 ASP B 497 -159.16 -100.25 REMARK 500 LYS B 586 79.63 -116.21 REMARK 500 ARG B 590 -169.51 -121.31 REMARK 500 ASN B 610 59.89 -97.46 REMARK 500 LEU B 611 38.91 -81.94 REMARK 500 REMARK 500 REMARK: NULL DBREF 7CEG A 28 408 UNP Q64487 PTPRD_MOUSE 21 401 DBREF 7CEG B 37 615 UNP Q8BYM5 NLGN3_MOUSE 37 615 SEQADV 7CEG LYS A 409 UNP Q64487 EXPRESSION TAG SEQADV 7CEG HIS A 410 UNP Q64487 EXPRESSION TAG SEQADV 7CEG HIS A 411 UNP Q64487 EXPRESSION TAG SEQADV 7CEG HIS A 412 UNP Q64487 EXPRESSION TAG SEQADV 7CEG HIS A 413 UNP Q64487 EXPRESSION TAG SEQRES 1 A 386 GLU THR PRO PRO ARG PHE THR ARG THR PRO VAL ASP GLN SEQRES 2 A 386 THR GLY VAL SER GLY GLY VAL ALA SER PHE ILE CYS GLN SEQRES 3 A 386 ALA THR GLY ASP PRO ARG PRO LYS ILE VAL TRP ASN LYS SEQRES 4 A 386 LYS GLY LYS LYS VAL SER ASN GLN ARG PHE GLU VAL ILE SEQRES 5 A 386 GLU PHE ASP ASP GLY SER GLY SER VAL LEU ARG ILE GLN SEQRES 6 A 386 PRO LEU ARG THR PRO ARG ASP GLU ALA ILE TYR GLU CYS SEQRES 7 A 386 VAL ALA SER ASN ASN VAL GLY GLU ILE SER VAL SER THR SEQRES 8 A 386 ARG LEU THR VAL LEU ARG GLU ASP GLN ILE PRO ARG GLY SEQRES 9 A 386 PHE PRO THR ILE ASP MET GLY PRO GLN LEU LYS VAL VAL SEQRES 10 A 386 GLU ARG THR ARG THR ALA THR MET LEU CYS ALA ALA SER SEQRES 11 A 386 GLY ASN PRO ASP PRO GLU ILE THR TRP PHE LYS ASP PHE SEQRES 12 A 386 LEU PRO VAL ASP THR SER ASN ASN ASN GLY ARG ILE LYS SEQRES 13 A 386 GLN LEU ARG SER GLU SER ILE GLY ALA LEU GLN ILE GLU SEQRES 14 A 386 GLN SER GLU GLU SER ASP GLN GLY LYS TYR GLU CYS VAL SEQRES 15 A 386 ALA THR ASN SER ALA GLY THR ARG TYR SER ALA PRO ALA SEQRES 16 A 386 ASN LEU TYR VAL ARG VAL ARG ARG VAL PRO PRO ARG PHE SEQRES 17 A 386 SER ILE PRO PRO THR ASN HIS GLU ILE MET PRO GLY GLY SEQRES 18 A 386 SER VAL ASN ILE THR CYS VAL ALA VAL GLY SER PRO MET SEQRES 19 A 386 PRO TYR VAL LYS TRP MET LEU GLY ALA GLU ASP LEU THR SEQRES 20 A 386 PRO GLU ASP ASP MET PRO ILE GLY ARG ASN VAL LEU GLU SEQRES 21 A 386 LEU ASN ASP VAL ARG GLN SER ALA ASN TYR THR CYS VAL SEQRES 22 A 386 ALA MET SER THR LEU GLY VAL ILE GLU ALA ILE ALA GLN SEQRES 23 A 386 ILE THR VAL LYS ALA LEU PRO LYS PRO PRO GLY THR PRO SEQRES 24 A 386 VAL VAL THR GLU SER THR ALA THR SER ILE THR LEU THR SEQRES 25 A 386 TRP ASP SER GLY ASN PRO GLU PRO VAL SER TYR TYR ILE SEQRES 26 A 386 ILE GLN HIS LYS PRO LYS ASN SER GLU GLU PRO TYR LYS SEQRES 27 A 386 GLU ILE ASP GLY ILE ALA THR THR ARG TYR SER VAL ALA SEQRES 28 A 386 GLY LEU SER PRO TYR SER ASP TYR GLU PHE ARG VAL VAL SEQRES 29 A 386 ALA VAL ASN ASN ILE GLY ARG GLY PRO ALA SER GLU PRO SEQRES 30 A 386 VAL LEU THR GLN LYS HIS HIS HIS HIS SEQRES 1 B 579 PRO ALA PRO THR VAL ASN THR HIS PHE GLY LYS LEU ARG SEQRES 2 B 579 GLY ALA ARG VAL PRO LEU PRO SER GLU ILE LEU GLY PRO SEQRES 3 B 579 VAL ASP GLN TYR LEU GLY VAL PRO TYR ALA ALA PRO PRO SEQRES 4 B 579 ILE GLY GLU LYS ARG PHE LEU PRO PRO GLU PRO PRO PRO SEQRES 5 B 579 SER TRP SER GLY ILE ARG ASN ALA THR HIS PHE PRO PRO SEQRES 6 B 579 VAL CYS PRO GLN ASN ILE HIS THR ALA VAL PRO GLU VAL SEQRES 7 B 579 MET LEU PRO VAL TRP PHE THR ALA ASN LEU ASP ILE VAL SEQRES 8 B 579 ALA THR TYR ILE GLN GLU PRO ASN GLU ASP CYS LEU TYR SEQRES 9 B 579 LEU ASN VAL TYR VAL PRO THR GLU ASP GLY SER GLY ALA SEQRES 10 B 579 LYS LYS GLN GLY GLU ASP LEU ALA ASP ASN ASP GLY ASP SEQRES 11 B 579 GLU ASP GLU ASP ILE ARG ASP SER GLY ALA LYS PRO VAL SEQRES 12 B 579 MET VAL TYR ILE HIS GLY GLY SER TYR MET GLU GLY THR SEQRES 13 B 579 GLY ASN MET ILE ASP GLY SER VAL LEU ALA SER TYR GLY SEQRES 14 B 579 ASN VAL ILE VAL ILE THR LEU ASN TYR ARG VAL GLY VAL SEQRES 15 B 579 LEU GLY PHE LEU SER THR GLY ASP GLN ALA ALA LYS GLY SEQRES 16 B 579 ASN TYR GLY LEU LEU ASP GLN ILE GLN ALA LEU ARG TRP SEQRES 17 B 579 VAL SER GLU ASN ILE ALA PHE PHE GLY GLY ASP PRO ARG SEQRES 18 B 579 ARG ILE THR VAL PHE GLY SER GLY ILE GLY ALA SER CYS SEQRES 19 B 579 VAL SER LEU LEU THR LEU SER HIS HIS SER GLU GLY LEU SEQRES 20 B 579 PHE GLN ARG ALA ILE ILE GLN SER GLY SER ALA LEU SER SEQRES 21 B 579 SER TRP ALA VAL ASN TYR GLN PRO VAL LYS TYR THR SER SEQRES 22 B 579 LEU LEU ALA ASP LYS VAL GLY CYS ASN VAL LEU ASP THR SEQRES 23 B 579 VAL ASP MET VAL ASP CYS LEU ARG GLN LYS SER ALA LYS SEQRES 24 B 579 GLU LEU VAL GLU GLN ASP ILE GLN PRO ALA ARG TYR HIS SEQRES 25 B 579 VAL ALA PHE GLY PRO VAL ILE ASP GLY ASP VAL ILE PRO SEQRES 26 B 579 ASP ASP PRO GLU ILE LEU MET GLU GLN GLY GLU PHE LEU SEQRES 27 B 579 ASN TYR ASP ILE MET LEU GLY VAL ASN GLN GLY GLU GLY SEQRES 28 B 579 LEU LYS PHE VAL GLU GLY VAL VAL ASP PRO GLU ASP GLY SEQRES 29 B 579 VAL SER GLY THR ASP PHE ASP TYR SER VAL SER ASN PHE SEQRES 30 B 579 VAL ASP ASN LEU TYR GLY TYR PRO GLU GLY LYS ASP THR SEQRES 31 B 579 LEU ARG GLU THR ILE LYS PHE MET TYR THR ASP TRP ALA SEQRES 32 B 579 ASP ARG ASP ASN PRO GLU THR ARG ARG LYS THR LEU VAL SEQRES 33 B 579 ALA LEU PHE THR ASP HIS GLN TRP VAL GLU PRO SER VAL SEQRES 34 B 579 VAL THR ALA ASP LEU HIS ALA ARG TYR GLY SER PRO THR SEQRES 35 B 579 TYR PHE TYR ALA PHE TYR HIS HIS CYS GLN SER LEU MET SEQRES 36 B 579 LYS PRO ALA TRP SER ASP ALA ALA HIS GLY ASP GLU VAL SEQRES 37 B 579 PRO TYR VAL PHE GLY VAL PRO MET VAL GLY PRO THR ASP SEQRES 38 B 579 LEU PHE PRO CYS ASN PHE SER LYS ASN ASP VAL MET LEU SEQRES 39 B 579 SER ALA VAL VAL MET THR TYR TRP THR ASN PHE ALA LYS SEQRES 40 B 579 THR GLY ASP PRO ASN LYS PRO VAL PRO GLN ASP THR LYS SEQRES 41 B 579 PHE ILE HIS THR LYS ALA ASN ARG PHE GLU GLU VAL ALA SEQRES 42 B 579 TRP SER LYS TYR ASN PRO ARG ASP GLN LEU TYR LEU HIS SEQRES 43 B 579 ILE GLY LEU LYS PRO ARG VAL ARG ASP HIS TYR ARG ALA SEQRES 44 B 579 THR LYS VAL ALA PHE TRP LYS HIS LEU VAL PRO HIS LEU SEQRES 45 B 579 TYR ASN LEU HIS ASP MET PHE HET NAG A 501 14 HET NAG A 502 14 HET NAG B 701 14 HET NAG B 702 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 3 NAG 4(C8 H15 N O6) HELIX 1 AA1 GLU A 199 GLN A 203 5 5 HELIX 2 AA2 PRO B 117 ASN B 123 1 7 HELIX 3 AA3 ASN B 123 GLN B 132 1 10 HELIX 4 AA4 THR B 192 ILE B 196 5 5 HELIX 5 AA5 GLY B 198 ASN B 206 1 9 HELIX 6 AA6 GLY B 217 LEU B 222 1 6 HELIX 7 AA7 ASN B 232 ILE B 249 1 18 HELIX 8 AA8 ALA B 250 PHE B 252 5 3 HELIX 9 AA9 ILE B 266 SER B 277 1 12 HELIX 10 AB1 GLN B 303 GLY B 316 1 14 HELIX 11 AB2 ASP B 321 LYS B 332 1 12 HELIX 12 AB3 SER B 333 GLN B 340 1 8 HELIX 13 AB4 ASP B 363 GLN B 370 1 8 HELIX 14 AB5 GLY B 387 GLY B 393 1 7 HELIX 15 AB6 SER B 402 GLY B 419 1 18 HELIX 16 AB7 LYS B 424 TYR B 435 1 12 HELIX 17 AB8 ASN B 443 TRP B 460 1 18 HELIX 18 AB9 TRP B 460 ARG B 473 1 14 HELIX 19 AC1 GLU B 503 GLY B 509 1 7 HELIX 20 AC2 VAL B 510 VAL B 513 5 4 HELIX 21 AC3 SER B 524 GLY B 545 1 22 HELIX 22 AC4 ARG B 594 HIS B 603 1 10 HELIX 23 AC5 HIS B 603 ASN B 610 1 8 HELIX 24 AC6 LEU B 611 PHE B 615 5 5 SHEET 1 AA1 4 THR A 29 ARG A 35 0 SHEET 2 AA1 4 ALA A 48 ASP A 57 -1 O THR A 55 N ARG A 32 SHEET 3 AA1 4 GLY A 86 ILE A 91 -1 O LEU A 89 N PHE A 50 SHEET 4 AA1 4 GLU A 77 GLU A 80 -1 N ILE A 79 O VAL A 88 SHEET 1 AA2 4 GLN A 40 VAL A 43 0 SHEET 2 AA2 4 GLU A 113 LEU A 123 1 O ARG A 119 N GLN A 40 SHEET 3 AA2 4 ILE A 102 SER A 108 -1 N TYR A 103 O THR A 118 SHEET 4 AA2 4 LYS A 61 LYS A 66 -1 N VAL A 63 O VAL A 106 SHEET 1 AA3 2 THR A 134 MET A 137 0 SHEET 2 AA3 2 ALA A 155 SER A 157 -1 O ALA A 155 N MET A 137 SHEET 1 AA4 5 LYS A 142 VAL A 143 0 SHEET 2 AA4 5 ALA A 222 TYR A 225 1 O TYR A 225 N LYS A 142 SHEET 3 AA4 5 GLY A 204 THR A 211 -1 N TYR A 206 O ALA A 222 SHEET 4 AA4 5 GLU A 163 LYS A 168 -1 N PHE A 167 O GLU A 207 SHEET 5 AA4 5 LEU A 171 PRO A 172 -1 O LEU A 171 N LYS A 168 SHEET 1 AA5 4 LYS A 142 VAL A 143 0 SHEET 2 AA5 4 ALA A 222 TYR A 225 1 O TYR A 225 N LYS A 142 SHEET 3 AA5 4 GLY A 204 THR A 211 -1 N TYR A 206 O ALA A 222 SHEET 4 AA5 4 THR A 216 TYR A 218 -1 O ARG A 217 N ALA A 210 SHEET 1 AA6 3 ALA A 150 MET A 152 0 SHEET 2 AA6 3 GLY A 191 ILE A 195 -1 O ILE A 195 N ALA A 150 SHEET 3 AA6 3 ILE A 182 ARG A 186 -1 N LYS A 183 O GLN A 194 SHEET 1 AA7 2 VAL A 231 ILE A 237 0 SHEET 2 AA7 2 VAL A 255 SER A 259 -1 O VAL A 257 N ARG A 234 SHEET 1 AA8 2 VAL A 250 ILE A 252 0 SHEET 2 AA8 2 LEU A 286 LEU A 288 -1 O LEU A 286 N ILE A 252 SHEET 1 AA9 3 TYR A 263 MET A 267 0 SHEET 2 AA9 3 ALA A 295 MET A 302 -1 O VAL A 300 N LYS A 265 SHEET 3 AA9 3 VAL A 307 ILE A 314 -1 O ALA A 312 N TYR A 297 SHEET 1 AB1 3 VAL A 327 SER A 331 0 SHEET 2 AB1 3 SER A 335 THR A 339 -1 O THR A 337 N THR A 329 SHEET 3 AB1 3 ARG A 374 ALA A 378 -1 O VAL A 377 N ILE A 336 SHEET 1 AB2 4 LYS A 365 ILE A 370 0 SHEET 2 AB2 4 TYR A 350 PRO A 357 -1 N ILE A 353 O ILE A 367 SHEET 3 AB2 4 TYR A 386 VAL A 393 -1 O ARG A 389 N GLN A 354 SHEET 4 AB2 4 ARG A 398 ALA A 401 -1 O GLY A 399 N ALA A 392 SHEET 1 AB3 4 LYS A 365 ILE A 370 0 SHEET 2 AB3 4 TYR A 350 PRO A 357 -1 N ILE A 353 O ILE A 367 SHEET 3 AB3 4 TYR A 386 VAL A 393 -1 O ARG A 389 N GLN A 354 SHEET 4 AB3 4 VAL A 405 LEU A 406 -1 O VAL A 405 N PHE A 388 SHEET 1 AB4 3 THR B 40 THR B 43 0 SHEET 2 AB4 3 GLY B 46 ARG B 49 -1 O LEU B 48 N VAL B 41 SHEET 3 AB4 3 ILE B 93 ASN B 95 1 O ARG B 94 N LYS B 47 SHEET 1 AB511 ALA B 51 VAL B 53 0 SHEET 2 AB511 VAL B 63 PRO B 70 -1 O VAL B 63 N VAL B 53 SHEET 3 AB511 TYR B 140 PRO B 146 -1 O VAL B 145 N ASP B 64 SHEET 4 AB511 ILE B 208 LEU B 212 -1 O THR B 211 N ASN B 142 SHEET 5 AB511 LYS B 177 GLY B 185 1 N MET B 180 O ILE B 208 SHEET 6 AB511 GLY B 254 GLY B 265 1 O PHE B 262 N VAL B 181 SHEET 7 AB511 ARG B 286 GLN B 290 1 O GLN B 290 N GLY B 265 SHEET 8 AB511 ASP B 377 ASN B 383 1 O MET B 379 N ILE B 289 SHEET 9 AB511 THR B 478 PHE B 483 1 O PHE B 483 N VAL B 382 SHEET 10 AB511 LEU B 579 ILE B 583 1 O ILE B 583 N ALA B 482 SHEET 11 AB511 ARG B 588 ASP B 591 -1 O ARG B 588 N HIS B 582 SSBOND 1 CYS A 52 CYS A 105 1555 1555 2.03 SSBOND 2 CYS A 154 CYS A 208 1555 1555 2.03 SSBOND 3 CYS A 254 CYS A 299 1555 1555 2.04 SSBOND 4 CYS B 103 CYS B 138 1555 1555 2.03 SSBOND 5 CYS B 317 CYS B 328 1555 1555 2.04 SSBOND 6 CYS B 487 CYS B 521 1555 1555 2.03 LINK ND2 ASN A 251 C1 NAG A 502 1555 1555 1.45 LINK ND2 ASN A 296 C1 NAG A 501 1555 1555 1.44 LINK ND2 ASN B 95 C1 NAG B 701 1555 1555 1.44 LINK ND2 ASN B 522 C1 NAG B 702 1555 1555 1.45 CISPEP 1 ASP A 57 PRO A 58 0 1.67 CISPEP 2 GLN A 92 PRO A 93 0 -3.90 CISPEP 3 THR A 96 PRO A 97 0 -5.67 CISPEP 4 ASN A 159 PRO A 160 0 2.66 CISPEP 5 SER A 259 PRO A 260 0 -0.20 CISPEP 6 LYS B 549 PRO B 550 0 3.10 CRYST1 96.109 96.109 371.613 90.00 90.00 120.00 P 32 1 2 6 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 0.010405 0.006007 0.000000 0.00000 SCALE2 0.000000 0.012014 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002691 0.00000