HEADER HYDROLASE 29-JUN-19 6PKH TITLE ZEBRAFISH N-ACETYLGLUCOSAMINE-1-PHOSPHODIESTER ALPHA-N- TITLE 2 ACETYLGLUCOSAMINIDASE (NAGPA) CATALYTIC DOMAIN AUTO-INHIBITED BY PRO- TITLE 3 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLGLUCOSAMINE-1-PHOSPHODIESTER ALPHA-N- COMPND 3 ACETYLGLUCOSAMINIDASE; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: NAGPA; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS UNCOVERING ENZYME, MANNOSE 6-PHOSPHATE, GLYCOSIDASE, PRO-PEPTIDE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.GORELIK,K.ILLES,B.NAGAR REVDAT 5 11-OCT-23 6PKH 1 HETSYN LINK REVDAT 4 29-JUL-20 6PKH 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 15-APR-20 6PKH 1 JRNL REVDAT 2 11-MAR-20 6PKH 1 JRNL REVDAT 1 19-FEB-20 6PKH 0 JRNL AUTH A.GORELIK,K.ILLES,B.NAGAR JRNL TITL CRYSTAL STRUCTURE OF THE MANNOSE-6-PHOSPHATE UNCOVERING JRNL TITL 2 ENZYME. JRNL REF STRUCTURE V. 28 426 2020 JRNL REFN ISSN 0969-2126 JRNL PMID 32109365 JRNL DOI 10.1016/J.STR.2020.02.001 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 68.6 REMARK 3 NUMBER OF REFLECTIONS : 52393 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.540 REMARK 3 FREE R VALUE TEST SET COUNT : 2904 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 35.0348 - 4.4116 0.99 3407 198 0.1400 0.1602 REMARK 3 2 4.4116 - 3.5026 0.98 3364 195 0.1051 0.1181 REMARK 3 3 3.5026 - 3.0602 0.97 3346 195 0.1153 0.1614 REMARK 3 4 3.0602 - 2.7805 0.98 3401 200 0.1271 0.1809 REMARK 3 5 2.7805 - 2.5813 0.98 3351 198 0.1361 0.1889 REMARK 3 6 2.5813 - 2.4291 0.98 3387 201 0.1380 0.1807 REMARK 3 7 2.4291 - 2.3075 0.98 3369 197 0.1328 0.1790 REMARK 3 8 2.3075 - 2.2071 0.93 3193 193 0.1477 0.1751 REMARK 3 9 2.2071 - 2.1221 0.91 3120 178 0.1363 0.2109 REMARK 3 10 2.1221 - 2.0489 0.84 2877 167 0.1388 0.1933 REMARK 3 11 2.0489 - 1.9848 0.76 2619 158 0.1478 0.1701 REMARK 3 12 1.9848 - 1.9281 0.68 2333 139 0.1667 0.1957 REMARK 3 13 1.9281 - 1.8773 0.61 2106 122 0.1917 0.2228 REMARK 3 14 1.8773 - 1.8315 0.54 1846 109 0.1748 0.1963 REMARK 3 15 1.8315 - 1.7899 0.47 1622 92 0.1810 0.2084 REMARK 3 16 1.7899 - 1.7518 0.43 1479 86 0.1888 0.1887 REMARK 3 17 1.7518 - 1.7168 0.39 1332 79 0.2123 0.2219 REMARK 3 18 1.7168 - 1.6844 0.32 1107 66 0.2144 0.2340 REMARK 3 19 1.6844 - 1.6543 0.27 945 55 0.2560 0.2308 REMARK 3 20 1.6543 - 1.6263 0.22 748 44 0.2731 0.2796 REMARK 3 21 1.6263 - 1.6000 0.16 537 32 0.3042 0.3208 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.410 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 2517 REMARK 3 ANGLE : 0.915 3435 REMARK 3 CHIRALITY : 0.054 395 REMARK 3 PLANARITY : 0.006 444 REMARK 3 DIHEDRAL : 10.210 1506 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 30 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.5772 44.0270 38.7585 REMARK 3 T TENSOR REMARK 3 T11: 0.1172 T22: 0.1668 REMARK 3 T33: 0.0960 T12: 0.0170 REMARK 3 T13: -0.0119 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.2152 L22: 0.4003 REMARK 3 L33: 0.2166 L12: -0.1260 REMARK 3 L13: 0.0776 L23: 0.1444 REMARK 3 S TENSOR REMARK 3 S11: 0.1568 S12: 0.2973 S13: -0.0413 REMARK 3 S21: -0.1592 S22: -0.1320 S23: 0.0838 REMARK 3 S31: 0.0219 S32: -0.0376 S33: 0.0056 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 50 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0508 57.2722 59.2184 REMARK 3 T TENSOR REMARK 3 T11: 0.1380 T22: 0.1589 REMARK 3 T33: 0.0936 T12: 0.0466 REMARK 3 T13: 0.0105 T23: -0.0465 REMARK 3 L TENSOR REMARK 3 L11: 0.1226 L22: 0.6699 REMARK 3 L33: 0.5517 L12: 0.2629 REMARK 3 L13: 0.0324 L23: -0.0659 REMARK 3 S TENSOR REMARK 3 S11: -0.0193 S12: -0.1582 S13: 0.1242 REMARK 3 S21: 0.2030 S22: 0.1089 S23: 0.0538 REMARK 3 S31: -0.0602 S32: -0.0681 S33: 0.4614 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 80 THROUGH 106 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.5644 33.6783 60.4892 REMARK 3 T TENSOR REMARK 3 T11: 0.1116 T22: 0.1643 REMARK 3 T33: 0.1350 T12: 0.0047 REMARK 3 T13: -0.0247 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 1.0543 L22: 0.8946 REMARK 3 L33: 0.6473 L12: -0.2227 REMARK 3 L13: -0.1652 L23: -0.5632 REMARK 3 S TENSOR REMARK 3 S11: -0.0777 S12: -0.1819 S13: -0.1936 REMARK 3 S21: -0.0889 S22: 0.0147 S23: 0.1648 REMARK 3 S31: -0.0188 S32: -0.2465 S33: -0.0508 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 107 THROUGH 160 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.8969 52.0792 46.1475 REMARK 3 T TENSOR REMARK 3 T11: 0.0908 T22: 0.0985 REMARK 3 T33: 0.1313 T12: -0.0107 REMARK 3 T13: -0.0019 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 0.8519 L22: 0.9318 REMARK 3 L33: 0.7458 L12: -0.3925 REMARK 3 L13: -0.3023 L23: -0.1192 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: 0.0167 S13: 0.1444 REMARK 3 S21: 0.0258 S22: -0.0095 S23: -0.1270 REMARK 3 S31: -0.0692 S32: 0.0022 S33: -0.0002 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 161 THROUGH 190 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.7165 59.9670 50.7282 REMARK 3 T TENSOR REMARK 3 T11: 0.0887 T22: 0.0920 REMARK 3 T33: 0.1472 T12: -0.0005 REMARK 3 T13: 0.0085 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.2458 L22: 0.9088 REMARK 3 L33: 0.6315 L12: -0.3652 REMARK 3 L13: 0.1828 L23: -0.4806 REMARK 3 S TENSOR REMARK 3 S11: 0.0273 S12: -0.0228 S13: 0.3290 REMARK 3 S21: 0.0923 S22: -0.0267 S23: -0.0348 REMARK 3 S31: -0.1303 S32: -0.0782 S33: 0.0016 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 191 THROUGH 221 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.0777 57.7593 53.6012 REMARK 3 T TENSOR REMARK 3 T11: 0.0969 T22: 0.0709 REMARK 3 T33: 0.1215 T12: 0.0201 REMARK 3 T13: 0.0192 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 0.6635 L22: 0.4126 REMARK 3 L33: 0.3767 L12: -0.1664 REMARK 3 L13: 0.0731 L23: 0.2382 REMARK 3 S TENSOR REMARK 3 S11: -0.0216 S12: -0.1017 S13: 0.3124 REMARK 3 S21: 0.1183 S22: 0.0866 S23: 0.0314 REMARK 3 S31: -0.1655 S32: -0.0345 S33: 0.0130 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 222 THROUGH 265 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6607 43.7486 51.3557 REMARK 3 T TENSOR REMARK 3 T11: 0.0671 T22: 0.1025 REMARK 3 T33: 0.0836 T12: 0.0116 REMARK 3 T13: -0.0014 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 0.6634 L22: 1.2321 REMARK 3 L33: 0.3406 L12: -0.3926 REMARK 3 L13: -0.3415 L23: -0.2049 REMARK 3 S TENSOR REMARK 3 S11: 0.0032 S12: -0.0440 S13: -0.0834 REMARK 3 S21: 0.0259 S22: 0.0226 S23: 0.2216 REMARK 3 S31: 0.0121 S32: -0.1443 S33: 0.0347 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 266 THROUGH 299 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3630 38.9053 55.3999 REMARK 3 T TENSOR REMARK 3 T11: 0.0931 T22: 0.0978 REMARK 3 T33: 0.0679 T12: 0.0074 REMARK 3 T13: 0.0058 T23: 0.0223 REMARK 3 L TENSOR REMARK 3 L11: 0.7930 L22: 0.7074 REMARK 3 L33: 0.2663 L12: -0.2719 REMARK 3 L13: 0.2702 L23: 0.1047 REMARK 3 S TENSOR REMARK 3 S11: -0.0274 S12: -0.0813 S13: -0.1372 REMARK 3 S21: 0.1033 S22: 0.0327 S23: 0.0564 REMARK 3 S31: 0.0392 S32: -0.0128 S33: 0.0155 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 300 THROUGH 319 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.5489 37.0447 47.2559 REMARK 3 T TENSOR REMARK 3 T11: 0.1018 T22: 0.1082 REMARK 3 T33: 0.1078 T12: 0.0104 REMARK 3 T13: -0.0150 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.3198 L22: 0.4270 REMARK 3 L33: 0.0427 L12: -0.3483 REMARK 3 L13: 0.0984 L23: -0.1324 REMARK 3 S TENSOR REMARK 3 S11: -0.0080 S12: 0.1243 S13: 0.0686 REMARK 3 S21: -0.0023 S22: 0.0080 S23: -0.0601 REMARK 3 S31: 0.0692 S32: 0.1126 S33: -0.0012 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 320 THROUGH 336 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.1911 44.6093 48.6782 REMARK 3 T TENSOR REMARK 3 T11: 0.0909 T22: 0.1008 REMARK 3 T33: 0.1191 T12: 0.0220 REMARK 3 T13: -0.0236 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.5620 L22: 0.2969 REMARK 3 L33: 0.7732 L12: -0.0854 REMARK 3 L13: -0.2255 L23: -0.4113 REMARK 3 S TENSOR REMARK 3 S11: -0.0477 S12: -0.0352 S13: 0.1088 REMARK 3 S21: 0.0679 S22: 0.0747 S23: -0.1729 REMARK 3 S31: 0.0126 S32: 0.1829 S33: -0.0096 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 6PKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242680. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38530 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 93.8 REMARK 200 DATA REDUNDANCY : 15.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 6PKG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, HEPES PH 7.5, CRYO REMARK 280 -PROTECTED WITH SODIUM MALONATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 54.64400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.97700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.97700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.32200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.97700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.97700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 81.96600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.97700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.97700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.32200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.97700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.97700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 81.96600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 54.64400 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: 4330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 17.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 109.28800 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 671 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 922 LIES ON A SPECIAL POSITION. 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 ASP A 16 REMARK 465 ARG A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 HIS A 20 REMARK 465 HIS A 21 REMARK 465 HIS A 22 REMARK 465 HIS A 23 REMARK 465 LYS A 24 REMARK 465 LEU A 25 REMARK 465 LYS A 26 REMARK 465 ASP A 27 REMARK 465 ILE A 28 REMARK 465 ARG A 29 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 HD1 HIS A 126 O HOH A 504 1.46 REMARK 500 HZ3 LYS A 320 O HOH A 511 1.55 REMARK 500 HH12 ARG A 169 O HOH A 506 1.58 REMARK 500 O HOH A 506 O HOH A 722 1.80 REMARK 500 O HOH A 723 O HOH A 844 1.89 REMARK 500 O HOH A 799 O HOH A 839 1.97 REMARK 500 O HOH A 782 O HOH A 800 1.98 REMARK 500 O HOH A 832 O HOH A 873 2.08 REMARK 500 O HOH A 515 O HOH A 793 2.10 REMARK 500 O HOH A 540 O HOH A 752 2.10 REMARK 500 OD1 ASN A 83 O HOH A 501 2.12 REMARK 500 O HOH A 815 O HOH A 884 2.13 REMARK 500 O HOH A 578 O HOH A 863 2.14 REMARK 500 O HOH A 537 O HOH A 789 2.16 REMARK 500 O HOH A 541 O HOH A 832 2.18 REMARK 500 O HOH A 524 O HOH A 876 2.19 REMARK 500 O HOH A 632 O HOH A 863 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 504 O HOH A 779 6565 1.92 REMARK 500 O HOH A 917 O HOH A 924 3655 1.96 REMARK 500 O HOH A 773 O HOH A 784 3555 2.01 REMARK 500 O HOH A 808 O HOH A 808 7556 2.10 REMARK 500 O HOH A 539 O HOH A 804 6465 2.13 REMARK 500 O HOH A 522 O HOH A 769 7556 2.14 REMARK 500 O HOH A 540 O HOH A 542 4454 2.15 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 ASP A 35 76.68 -109.48 REMARK 500 LYS A 42 -132.46 -114.74 REMARK 500 VAL A 212 124.58 95.63 REMARK 500 ILE A 327 -161.92 -118.14 REMARK 500 SER A 328 -114.57 -108.67 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 A 926 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 927 DISTANCE = 6.62 ANGSTROMS DBREF 6PKH A 26 336 UNP F1QSF9 F1QSF9_DANRE 45 355 SEQADV 6PKH ASP A 16 UNP F1QSF9 EXPRESSION TAG SEQADV 6PKH ARG A 17 UNP F1QSF9 EXPRESSION TAG SEQADV 6PKH HIS A 18 UNP F1QSF9 EXPRESSION TAG SEQADV 6PKH HIS A 19 UNP F1QSF9 EXPRESSION TAG SEQADV 6PKH HIS A 20 UNP F1QSF9 EXPRESSION TAG SEQADV 6PKH HIS A 21 UNP F1QSF9 EXPRESSION TAG SEQADV 6PKH HIS A 22 UNP F1QSF9 EXPRESSION TAG SEQADV 6PKH HIS A 23 UNP F1QSF9 EXPRESSION TAG SEQADV 6PKH LYS A 24 UNP F1QSF9 EXPRESSION TAG SEQADV 6PKH LEU A 25 UNP F1QSF9 EXPRESSION TAG SEQRES 1 A 321 ASP ARG HIS HIS HIS HIS HIS HIS LYS LEU LYS ASP ILE SEQRES 2 A 321 ARG HIS SER SER ASP ASP ASP LEU LEU LEU PRO TYR THR SEQRES 3 A 321 LYS SER HIS GLY PRO SER HIS SER HIS ARG TYR VAL ARG SEQRES 4 A 321 ASP CYS GLN PRO VAL ALA HIS GLY THR VAL THR HIS GLU SEQRES 5 A 321 THR GLN ALA ALA SER LYS HIS SER ASN SER PRO VAL LEU SEQRES 6 A 321 GLU SER ASN ILE PHE ILE SER ASP ILE THR ASP ASP SER SEQRES 7 A 321 GLY THR HIS ARG TRP VAL SER GLY HIS ILE THR GLU VAL SEQRES 8 A 321 HIS ASP PRO LEU ARG SER VAL SER VAL LEU GLU PRO GLY SEQRES 9 A 321 GLY PRO GLY GLY CYS ALA HIS ASN HIS ARG GLU LEU VAL SEQRES 10 A 321 GLU VAL THR ALA LYS THR ARG LYS CYS LEU VAL ALA GLN SEQRES 11 A 321 ASN GLY GLY TYR PHE ASP THR HIS THR GLY GLN CYS LEU SEQRES 12 A 321 GLY ASN ILE ILE SER ASP GLY LYS LEU VAL ARG ASN SER SEQRES 13 A 321 GLY GLY ILE GLN ASN ALA GLN PHE GLY ILE ARG LYS ASP SEQRES 14 A 321 GLY THR LEU VAL PHE GLY TYR LEU SER GLU ASP ASP ILE SEQRES 15 A 321 LEU ASP GLN GLU ASN PRO PHE VAL GLN LEU ILE SER GLY SEQRES 16 A 321 VAL VAL TRP LEU LEU ARG LYS GLY GLU ILE TYR ILE ASN SEQRES 17 A 321 GLU SER ILE GLN ALA GLU CYS ASP LYS THR GLN GLU THR SEQRES 18 A 321 GLY ASN PHE ARG HIS PHE VAL ASP VAL ILE SER ALA ARG SEQRES 19 A 321 THR ALA VAL GLY HIS ASP LYS GLU GLY LYS LEU ILE LEU SEQRES 20 A 321 PHE HIS VAL ASP GLY GLN THR ASP VAL ARG GLY MET ASN SEQRES 21 A 321 LEU TRP GLN VAL ALA LYS PHE LEU LYS ASP GLN ASN VAL SEQRES 22 A 321 MET ASN ALA ILE ASN LEU ASP GLY GLY GLY SER ALA THR SEQRES 23 A 321 TYR VAL LEU ASN GLY SER LEU ALA SER TYR PRO SER ASP SEQRES 24 A 321 HIS CYS ASN PRO SER LYS TRP ARG CYS PRO ARG ALA ILE SEQRES 25 A 321 SER THR VAL LEU CYS ILE HIS GLU ARG HET NAG B 1 26 HET NAG B 2 27 HET BMA B 3 21 HET MAN B 4 22 HET FUC B 5 21 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE 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 BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 2 MAN C6 H12 O6 FORMUL 2 FUC C6 H12 O5 FORMUL 3 HOH *427(H2 O) HELIX 1 AA1 SER A 49 GLN A 57 1 9 HELIX 2 AA2 PRO A 58 GLY A 62 5 5 HELIX 3 AA3 ASP A 108 SER A 112 1 5 HELIX 4 AA4 GLY A 123 ASN A 127 5 5 HELIX 5 AA5 LEU A 131 THR A 138 1 8 HELIX 6 AA6 SER A 193 ASP A 199 1 7 HELIX 7 AA7 TYR A 221 CYS A 230 1 10 HELIX 8 AA8 GLN A 234 VAL A 245 1 12 HELIX 9 AA9 ASN A 275 GLN A 286 1 12 HELIX 10 AB1 GLY A 296 ALA A 300 5 5 SHEET 1 AA1 4 HIS A 66 ALA A 70 0 SHEET 2 AA1 4 THR A 186 GLY A 190 -1 O LEU A 187 N GLN A 69 SHEET 3 AA1 4 GLN A 178 ARG A 182 -1 N GLY A 180 O VAL A 188 SHEET 4 AA1 4 PHE A 204 SER A 209 -1 O VAL A 205 N ILE A 181 SHEET 1 AA2 7 LEU A 80 THR A 90 0 SHEET 2 AA2 7 HIS A 96 VAL A 106 -1 O GLU A 105 N GLU A 81 SHEET 3 AA2 7 LEU A 260 VAL A 265 -1 O LEU A 262 N THR A 104 SHEET 4 AA2 7 ARG A 249 ASP A 255 -1 N GLY A 253 O ILE A 261 SHEET 5 AA2 7 VAL A 288 ASN A 293 -1 O MET A 289 N HIS A 254 SHEET 6 AA2 7 TRP A 213 ARG A 216 -1 N LEU A 215 O ALA A 291 SHEET 7 AA2 7 GLU A 219 ILE A 220 -1 O GLU A 219 N ARG A 216 SHEET 1 AA3 5 VAL A 113 LEU A 116 0 SHEET 2 AA3 5 VAL A 330 ILE A 333 -1 O VAL A 330 N LEU A 116 SHEET 3 AA3 5 VAL A 143 ASN A 146 -1 N VAL A 143 O ILE A 333 SHEET 4 AA3 5 TYR A 302 LEU A 304 -1 O VAL A 303 N ALA A 144 SHEET 5 AA3 5 SER A 307 LEU A 308 -1 O SER A 307 N LEU A 304 SHEET 1 AA4 2 ILE A 161 SER A 163 0 SHEET 2 AA4 2 LYS A 166 ARG A 169 -1 O ARG A 169 N ILE A 161 SSBOND 1 CYS A 124 CYS A 157 1555 1555 2.08 SSBOND 2 CYS A 141 CYS A 332 1555 1555 2.05 SSBOND 3 CYS A 316 CYS A 323 1555 1555 2.05 LINK ND2 ASN A 223 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O6 NAG B 1 C1 FUC B 5 1555 1555 1.45 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.45 LINK O3 BMA B 3 C1 MAN B 4 1555 1555 1.45 CRYST1 73.954 73.954 109.288 90.00 90.00 90.00 P 41 21 2 8 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 0.013522 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013522 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009150 0.00000