HEADER HYDROLASE/HYDROLASE INHIBITOR 09-DEC-13 4NXS TITLE CRYSTAL STRUCTURE OF HUMAN ALPHA-GALACTOSIDASE A IN COMPLEX WITH 1- TITLE 2 DEOXYGALACTONOJIRIMYCIN-PFPHT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALPHA-D-GALACTOSIDASE A, ALPHA-D-GALACTOSIDE COMPND 5 GALACTOHYDROLASE, MELIBIASE; COMPND 6 EC: 3.2.1.22; 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 GENE: GLA; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS PHARMACOLOGICAL CHAPERONE, DRUG DELIVERY SYSTEMS, ENZYME ACTIVATION, KEYWDS 2 ENZYME STABILITY, HUMANS, LYSOSOMES, MOLECULAR CHAPERONES, PROTEIN KEYWDS 3 BINDING, ALPHA-GALACTOSIDASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, KEYWDS 4 FABRY DISEASE, GLA GENE, ARYLTHIOUREA EXPDTA X-RAY DIFFRACTION AUTHOR J.L.JOHNSON,J.E.DRURY,R.L.LIEBERMAN REVDAT 5 20-SEP-23 4NXS 1 HETSYN REVDAT 4 29-JUL-20 4NXS 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 22-NOV-17 4NXS 1 REMARK REVDAT 2 30-JUL-14 4NXS 1 JRNL REVDAT 1 11-JUN-14 4NXS 0 JRNL AUTH Y.YU,T.MENA-BARRAGAN,K.HIGAKI,J.L.JOHNSON,J.E.DRURY, JRNL AUTH 2 R.L.LIEBERMAN,N.NAKASONE,H.NINOMIYA,T.TSUKIMURA,H.SAKURABA, JRNL AUTH 3 Y.SUZUKI,E.NANBA,C.O.MELLET,J.M.GARCIA FERNANDEZ,K.OHNO JRNL TITL MOLECULAR BASIS OF 1-DEOXYGALACTONOJIRIMYCIN ARYLTHIOUREA JRNL TITL 2 BINDING TO HUMAN ALPHA-GALACTOSIDASE A: PHARMACOLOGICAL JRNL TITL 3 CHAPERONING EFFICACY ON FABRY DISEASE MUTANTS. JRNL REF ACS CHEM.BIOL. V. 9 1460 2014 JRNL REFN ISSN 1554-8929 JRNL PMID 24783948 JRNL DOI 10.1021/CB500143H REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 33736 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1992 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 38.6872 - 6.1366 0.99 2494 160 0.2020 0.2500 REMARK 3 2 6.1366 - 4.8739 0.99 2362 153 0.1725 0.1958 REMARK 3 3 4.8739 - 4.2587 0.98 2313 142 0.1369 0.1577 REMARK 3 4 4.2587 - 3.8697 0.99 2321 141 0.1443 0.1846 REMARK 3 5 3.8697 - 3.5925 0.99 2321 145 0.1733 0.2162 REMARK 3 6 3.5925 - 3.3809 1.00 2298 143 0.1869 0.2474 REMARK 3 7 3.3809 - 3.2116 0.99 2301 145 0.2038 0.2594 REMARK 3 8 3.2116 - 3.0719 0.99 2291 144 0.2150 0.2703 REMARK 3 9 3.0719 - 2.9537 0.99 2267 143 0.2121 0.2728 REMARK 3 10 2.9537 - 2.8518 0.98 2255 139 0.2269 0.2891 REMARK 3 11 2.8518 - 2.7626 0.97 2226 137 0.2351 0.2776 REMARK 3 12 2.7626 - 2.6837 0.96 2202 137 0.2260 0.2975 REMARK 3 13 2.6837 - 2.6131 0.93 2130 135 0.2319 0.2857 REMARK 3 14 2.6131 - 2.5493 0.85 1963 128 0.2659 0.3310 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.76 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 : 0.003 6630 REMARK 3 ANGLE : 0.895 9010 REMARK 3 CHIRALITY : 0.044 938 REMARK 3 PLANARITY : 0.003 1157 REMARK 3 DIHEDRAL : 16.471 2410 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.7420 -7.5056 6.3900 REMARK 3 T TENSOR REMARK 3 T11: 0.4355 T22: 0.2836 REMARK 3 T33: 0.3329 T12: 0.0137 REMARK 3 T13: 0.0034 T23: 0.0096 REMARK 3 L TENSOR REMARK 3 L11: 2.6216 L22: 2.9884 REMARK 3 L33: 1.5247 L12: -0.0015 REMARK 3 L13: -0.0132 L23: -0.0173 REMARK 3 S TENSOR REMARK 3 S11: -0.0693 S12: -0.3797 S13: 0.2454 REMARK 3 S21: 0.3628 S22: 0.0420 S23: 0.2294 REMARK 3 S31: -0.3499 S32: 0.0458 S33: -0.0266 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 116 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.6489 -1.2646 3.4155 REMARK 3 T TENSOR REMARK 3 T11: 0.4548 T22: 0.4502 REMARK 3 T33: 0.3155 T12: 0.0422 REMARK 3 T13: -0.0135 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 2.7586 L22: 3.4389 REMARK 3 L33: 2.8169 L12: -0.3368 REMARK 3 L13: 0.2268 L23: 0.3406 REMARK 3 S TENSOR REMARK 3 S11: -0.2309 S12: -0.2355 S13: 0.2844 REMARK 3 S21: 0.1966 S22: 0.0630 S23: 0.3397 REMARK 3 S31: -0.5677 S32: -0.3498 S33: 0.1512 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 117 THROUGH 388 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.3232 -20.3642 -4.4848 REMARK 3 T TENSOR REMARK 3 T11: 0.2937 T22: 0.3577 REMARK 3 T33: 0.2868 T12: -0.0333 REMARK 3 T13: -0.0093 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 0.6976 L22: 1.9115 REMARK 3 L33: 1.5446 L12: -0.2412 REMARK 3 L13: 0.0816 L23: 0.3211 REMARK 3 S TENSOR REMARK 3 S11: -0.0252 S12: 0.0188 S13: 0.0334 REMARK 3 S21: -0.1845 S22: -0.0189 S23: 0.1873 REMARK 3 S31: -0.1417 S32: -0.1608 S33: 0.0395 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 389 THROUGH 421 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.8405 -37.5910 -5.7544 REMARK 3 T TENSOR REMARK 3 T11: 0.3795 T22: 0.4704 REMARK 3 T33: 0.3095 T12: 0.0245 REMARK 3 T13: -0.0207 T23: 0.0125 REMARK 3 L TENSOR REMARK 3 L11: 3.2907 L22: 3.9216 REMARK 3 L33: 3.1710 L12: -1.3235 REMARK 3 L13: -0.1164 L23: 3.3218 REMARK 3 S TENSOR REMARK 3 S11: 0.0346 S12: 0.2945 S13: -0.0340 REMARK 3 S21: 0.0672 S22: 0.1852 S23: -0.2120 REMARK 3 S31: 0.3677 S32: 0.4836 S33: -0.2576 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 32 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 54.8057 -49.0765 23.2044 REMARK 3 T TENSOR REMARK 3 T11: 0.3926 T22: 0.4059 REMARK 3 T33: 0.3593 T12: 0.0171 REMARK 3 T13: 0.0694 T23: 0.0531 REMARK 3 L TENSOR REMARK 3 L11: 2.4008 L22: 2.3833 REMARK 3 L33: 2.5921 L12: -0.9037 REMARK 3 L13: -0.0519 L23: 0.8356 REMARK 3 S TENSOR REMARK 3 S11: -0.2537 S12: -0.0057 S13: -0.2919 REMARK 3 S21: -0.0351 S22: -0.0106 S23: -0.0353 REMARK 3 S31: 0.5359 S32: 0.2433 S33: 0.1714 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 79 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): 55.0169 -57.3826 24.9418 REMARK 3 T TENSOR REMARK 3 T11: 0.7149 T22: 0.4732 REMARK 3 T33: 0.4566 T12: 0.0607 REMARK 3 T13: 0.1083 T23: 0.0856 REMARK 3 L TENSOR REMARK 3 L11: 2.4017 L22: 2.3052 REMARK 3 L33: 2.6334 L12: -1.0226 REMARK 3 L13: -0.1677 L23: 1.0086 REMARK 3 S TENSOR REMARK 3 S11: -0.2343 S12: -0.2326 S13: -0.5332 REMARK 3 S21: 0.3906 S22: 0.0634 S23: -0.0114 REMARK 3 S31: 0.7601 S32: 0.3688 S33: 0.2026 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 116 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.8158 -59.2677 27.3634 REMARK 3 T TENSOR REMARK 3 T11: 0.7361 T22: 0.4357 REMARK 3 T33: 0.4538 T12: 0.0482 REMARK 3 T13: 0.1092 T23: 0.0752 REMARK 3 L TENSOR REMARK 3 L11: 2.3733 L22: 1.9834 REMARK 3 L33: 2.2677 L12: -0.8979 REMARK 3 L13: -0.9823 L23: -0.2453 REMARK 3 S TENSOR REMARK 3 S11: -0.2728 S12: -0.2198 S13: -0.8001 REMARK 3 S21: 0.2574 S22: -0.0267 S23: 0.0775 REMARK 3 S31: 1.0123 S32: 0.2143 S33: 0.3305 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 152 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.7603 -59.3916 32.2973 REMARK 3 T TENSOR REMARK 3 T11: 0.8116 T22: 0.4111 REMARK 3 T33: 0.5978 T12: -0.0617 REMARK 3 T13: 0.2225 T23: 0.0794 REMARK 3 L TENSOR REMARK 3 L11: 2.7641 L22: 2.6639 REMARK 3 L33: 2.1723 L12: 0.1725 REMARK 3 L13: -0.6139 L23: 0.0706 REMARK 3 S TENSOR REMARK 3 S11: -0.3889 S12: 0.0466 S13: -0.6792 REMARK 3 S21: 0.3197 S22: 0.1073 S23: 0.3301 REMARK 3 S31: 0.7482 S32: -0.1477 S33: 0.2989 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 216 THROUGH 235 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.7012 -48.2348 31.7594 REMARK 3 T TENSOR REMARK 3 T11: 0.6087 T22: 0.5160 REMARK 3 T33: 0.5101 T12: -0.1252 REMARK 3 T13: 0.1460 T23: 0.0256 REMARK 3 L TENSOR REMARK 3 L11: 2.0886 L22: 2.6110 REMARK 3 L33: 3.6887 L12: -0.6962 REMARK 3 L13: -0.6831 L23: -0.5627 REMARK 3 S TENSOR REMARK 3 S11: -0.2257 S12: -0.1439 S13: -0.6038 REMARK 3 S21: 0.3216 S22: -0.0787 S23: 0.5720 REMARK 3 S31: 0.6041 S32: -0.2929 S33: 0.1732 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 236 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.8262 -36.6351 27.2455 REMARK 3 T TENSOR REMARK 3 T11: 0.3292 T22: 0.4038 REMARK 3 T33: 0.2873 T12: -0.0944 REMARK 3 T13: 0.0191 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 1.9227 L22: 2.3283 REMARK 3 L33: 3.2681 L12: -0.9944 REMARK 3 L13: -0.7086 L23: 0.1090 REMARK 3 S TENSOR REMARK 3 S11: -0.0889 S12: 0.0225 S13: -0.3768 REMARK 3 S21: 0.0444 S22: -0.0869 S23: 0.2090 REMARK 3 S31: 0.2478 S32: -0.2673 S33: 0.0897 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 290 THROUGH 320 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.4401 -35.5650 28.0677 REMARK 3 T TENSOR REMARK 3 T11: 0.3625 T22: 0.3549 REMARK 3 T33: 0.2927 T12: -0.0419 REMARK 3 T13: 0.0033 T23: 0.0277 REMARK 3 L TENSOR REMARK 3 L11: 1.9230 L22: 2.2870 REMARK 3 L33: 2.5738 L12: -1.0544 REMARK 3 L13: -0.9647 L23: 0.7665 REMARK 3 S TENSOR REMARK 3 S11: 0.0106 S12: -0.1002 S13: 0.1245 REMARK 3 S21: 0.0656 S22: 0.0564 S23: -0.1498 REMARK 3 S31: -0.0429 S32: 0.3359 S33: -0.0120 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 321 THROUGH 388 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.3104 -24.2999 35.4186 REMARK 3 T TENSOR REMARK 3 T11: 0.4152 T22: 0.4439 REMARK 3 T33: 0.3000 T12: -0.0324 REMARK 3 T13: 0.0548 T23: -0.0428 REMARK 3 L TENSOR REMARK 3 L11: 1.7588 L22: 2.0254 REMARK 3 L33: 2.4183 L12: -0.8353 REMARK 3 L13: -0.7047 L23: 0.1870 REMARK 3 S TENSOR REMARK 3 S11: 0.1005 S12: -0.5013 S13: 0.0938 REMARK 3 S21: 0.4321 S22: 0.0312 S23: 0.0844 REMARK 3 S31: -0.2079 S32: -0.2659 S33: -0.0381 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 389 THROUGH 422 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.3195 -17.1079 37.3823 REMARK 3 T TENSOR REMARK 3 T11: 0.5882 T22: 0.4439 REMARK 3 T33: 0.4183 T12: -0.0791 REMARK 3 T13: 0.1116 T23: -0.0388 REMARK 3 L TENSOR REMARK 3 L11: 2.3258 L22: 1.6034 REMARK 3 L33: 4.0090 L12: -0.1990 REMARK 3 L13: -0.6766 L23: -0.1987 REMARK 3 S TENSOR REMARK 3 S11: 0.0435 S12: -0.2836 S13: 0.3700 REMARK 3 S21: 0.2839 S22: -0.0535 S23: 0.0050 REMARK 3 S31: -0.6127 S32: -0.0274 S33: -0.0009 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 3686 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4NXS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083789. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33831 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.549 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 (%) : 96.8 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.47100 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 2.5.5 REMARK 200 STARTING MODEL: PDB ENTRY 3GXN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M ACETATE PH 4.5, 0.215 M AMMONIUM REMARK 280 SULFATE, AND 24% PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 144.92133 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 72.46067 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 0.00000 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 72.46067 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 144.92133 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: 5130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 GLN A 422 REMARK 465 MET A 423 REMARK 465 SER A 424 REMARK 465 LEU A 425 REMARK 465 LYS A 426 REMARK 465 ASP A 427 REMARK 465 LEU A 428 REMARK 465 LEU A 429 REMARK 465 MET B 423 REMARK 465 SER B 424 REMARK 465 LEU B 425 REMARK 465 LYS B 426 REMARK 465 ASP B 427 REMARK 465 LEU B 428 REMARK 465 LEU B 429 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 MET A 51 -128.44 47.81 REMARK 500 ASP A 92 -157.86 -89.37 REMARK 500 CYS A 94 33.24 80.07 REMARK 500 ASP A 101 -177.21 -68.80 REMARK 500 ASP A 266 -177.95 79.49 REMARK 500 ASN A 272 -127.52 -98.93 REMARK 500 GLU A 358 41.35 -104.38 REMARK 500 MET B 51 -128.90 47.82 REMARK 500 ASP B 92 -157.78 -90.15 REMARK 500 CYS B 94 34.11 79.73 REMARK 500 ASP B 101 -175.32 -68.59 REMARK 500 ASP B 266 -178.90 79.26 REMARK 500 ASN B 272 -128.64 -99.28 REMARK 500 GLU B 358 41.59 -105.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 4NXS A 32 429 UNP P06280 AGAL_HUMAN 32 429 DBREF 4NXS B 32 429 UNP P06280 AGAL_HUMAN 32 429 SEQRES 1 A 398 LEU ASP ASN GLY LEU ALA ARG THR PRO THR MET GLY TRP SEQRES 2 A 398 LEU HIS TRP GLU ARG PHE MET CYS ASN LEU ASP CYS GLN SEQRES 3 A 398 GLU GLU PRO ASP SER CYS ILE SER GLU LYS LEU PHE MET SEQRES 4 A 398 GLU MET ALA GLU LEU MET VAL SER GLU GLY TRP LYS ASP SEQRES 5 A 398 ALA GLY TYR GLU TYR LEU CYS ILE ASP ASP CYS TRP MET SEQRES 6 A 398 ALA PRO GLN ARG ASP SER GLU GLY ARG LEU GLN ALA ASP SEQRES 7 A 398 PRO GLN ARG PHE PRO HIS GLY ILE ARG GLN LEU ALA ASN SEQRES 8 A 398 TYR VAL HIS SER LYS GLY LEU LYS LEU GLY ILE TYR ALA SEQRES 9 A 398 ASP VAL GLY ASN LYS THR CYS ALA GLY PHE PRO GLY SER SEQRES 10 A 398 PHE GLY TYR TYR ASP ILE ASP ALA GLN THR PHE ALA ASP SEQRES 11 A 398 TRP GLY VAL ASP LEU LEU LYS PHE ASP GLY CYS TYR CYS SEQRES 12 A 398 ASP SER LEU GLU ASN LEU ALA ASP GLY TYR LYS HIS MET SEQRES 13 A 398 SER LEU ALA LEU ASN ARG THR GLY ARG SER ILE VAL TYR SEQRES 14 A 398 SER CYS GLU TRP PRO LEU TYR MET TRP PRO PHE GLN LYS SEQRES 15 A 398 PRO ASN TYR THR GLU ILE ARG GLN TYR CYS ASN HIS TRP SEQRES 16 A 398 ARG ASN PHE ALA ASP ILE ASP ASP SER TRP LYS SER ILE SEQRES 17 A 398 LYS SER ILE LEU ASP TRP THR SER PHE ASN GLN GLU ARG SEQRES 18 A 398 ILE VAL ASP VAL ALA GLY PRO GLY GLY TRP ASN ASP PRO SEQRES 19 A 398 ASP MET LEU VAL ILE GLY ASN PHE GLY LEU SER TRP ASN SEQRES 20 A 398 GLN GLN VAL THR GLN MET ALA LEU TRP ALA ILE MET ALA SEQRES 21 A 398 ALA PRO LEU PHE MET SER ASN ASP LEU ARG HIS ILE SER SEQRES 22 A 398 PRO GLN ALA LYS ALA LEU LEU GLN ASP LYS ASP VAL ILE SEQRES 23 A 398 ALA ILE ASN GLN ASP PRO LEU GLY LYS GLN GLY TYR GLN SEQRES 24 A 398 LEU ARG GLN GLY ASP ASN PHE GLU VAL TRP GLU ARG PRO SEQRES 25 A 398 LEU SER GLY LEU ALA TRP ALA VAL ALA MET ILE ASN ARG SEQRES 26 A 398 GLN GLU ILE GLY GLY PRO ARG SER TYR THR ILE ALA VAL SEQRES 27 A 398 ALA SER LEU GLY LYS GLY VAL ALA CYS ASN PRO ALA CYS SEQRES 28 A 398 PHE ILE THR GLN LEU LEU PRO VAL LYS ARG LYS LEU GLY SEQRES 29 A 398 PHE TYR GLU TRP THR SER ARG LEU ARG SER HIS ILE ASN SEQRES 30 A 398 PRO THR GLY THR VAL LEU LEU GLN LEU GLU ASN THR MET SEQRES 31 A 398 GLN MET SER LEU LYS ASP LEU LEU SEQRES 1 B 398 LEU ASP ASN GLY LEU ALA ARG THR PRO THR MET GLY TRP SEQRES 2 B 398 LEU HIS TRP GLU ARG PHE MET CYS ASN LEU ASP CYS GLN SEQRES 3 B 398 GLU GLU PRO ASP SER CYS ILE SER GLU LYS LEU PHE MET SEQRES 4 B 398 GLU MET ALA GLU LEU MET VAL SER GLU GLY TRP LYS ASP SEQRES 5 B 398 ALA GLY TYR GLU TYR LEU CYS ILE ASP ASP CYS TRP MET SEQRES 6 B 398 ALA PRO GLN ARG ASP SER GLU GLY ARG LEU GLN ALA ASP SEQRES 7 B 398 PRO GLN ARG PHE PRO HIS GLY ILE ARG GLN LEU ALA ASN SEQRES 8 B 398 TYR VAL HIS SER LYS GLY LEU LYS LEU GLY ILE TYR ALA SEQRES 9 B 398 ASP VAL GLY ASN LYS THR CYS ALA GLY PHE PRO GLY SER SEQRES 10 B 398 PHE GLY TYR TYR ASP ILE ASP ALA GLN THR PHE ALA ASP SEQRES 11 B 398 TRP GLY VAL ASP LEU LEU LYS PHE ASP GLY CYS TYR CYS SEQRES 12 B 398 ASP SER LEU GLU ASN LEU ALA ASP GLY TYR LYS HIS MET SEQRES 13 B 398 SER LEU ALA LEU ASN ARG THR GLY ARG SER ILE VAL TYR SEQRES 14 B 398 SER CYS GLU TRP PRO LEU TYR MET TRP PRO PHE GLN LYS SEQRES 15 B 398 PRO ASN TYR THR GLU ILE ARG GLN TYR CYS ASN HIS TRP SEQRES 16 B 398 ARG ASN PHE ALA ASP ILE ASP ASP SER TRP LYS SER ILE SEQRES 17 B 398 LYS SER ILE LEU ASP TRP THR SER PHE ASN GLN GLU ARG SEQRES 18 B 398 ILE VAL ASP VAL ALA GLY PRO GLY GLY TRP ASN ASP PRO SEQRES 19 B 398 ASP MET LEU VAL ILE GLY ASN PHE GLY LEU SER TRP ASN SEQRES 20 B 398 GLN GLN VAL THR GLN MET ALA LEU TRP ALA ILE MET ALA SEQRES 21 B 398 ALA PRO LEU PHE MET SER ASN ASP LEU ARG HIS ILE SER SEQRES 22 B 398 PRO GLN ALA LYS ALA LEU LEU GLN ASP LYS ASP VAL ILE SEQRES 23 B 398 ALA ILE ASN GLN ASP PRO LEU GLY LYS GLN GLY TYR GLN SEQRES 24 B 398 LEU ARG GLN GLY ASP ASN PHE GLU VAL TRP GLU ARG PRO SEQRES 25 B 398 LEU SER GLY LEU ALA TRP ALA VAL ALA MET ILE ASN ARG SEQRES 26 B 398 GLN GLU ILE GLY GLY PRO ARG SER TYR THR ILE ALA VAL SEQRES 27 B 398 ALA SER LEU GLY LYS GLY VAL ALA CYS ASN PRO ALA CYS SEQRES 28 B 398 PHE ILE THR GLN LEU LEU PRO VAL LYS ARG LYS LEU GLY SEQRES 29 B 398 PHE TYR GLU TRP THR SER ARG LEU ARG SER HIS ILE ASN SEQRES 30 B 398 PRO THR GLY THR VAL LEU LEU GLN LEU GLU ASN THR MET SEQRES 31 B 398 GLN MET SER LEU LYS ASP LEU LEU MODRES 4NXS ASN B 139 ASN GLYCOSYLATION SITE MODRES 4NXS ASN A 192 ASN GLYCOSYLATION SITE MODRES 4NXS ASN A 139 ASN GLYCOSYLATION SITE MODRES 4NXS ASN B 192 ASN GLYCOSYLATION SITE MODRES 4NXS ASN B 215 ASN GLYCOSYLATION SITE MODRES 4NXS ASN A 215 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET SO4 A 501 5 HET SO4 A 502 5 HET SO4 A 503 5 HET NAG A 506 14 HET NAG A 507 14 HET 2OZ A 508 21 HET SO4 B 501 5 HET SO4 B 502 5 HET NAG B 505 14 HET NAG B 506 14 HET 2OZ B 507 21 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION HETNAM 2OZ (2R,3S,4R,5S)-N-(4-FLUOROPHENYL)-3,4,5-TRIHYDROXY-2- HETNAM 2 2OZ (HYDROXYMETHYL)PIPERIDINE-1-CARBOTHIOAMIDE 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 8(C8 H15 N O6) FORMUL 5 SO4 5(O4 S 2-) FORMUL 10 2OZ 2(C13 H17 F N2 O4 S) FORMUL 16 HOH *96(H2 O) HELIX 1 1 HIS A 46 MET A 51 1 6 HELIX 2 2 SER A 65 GLU A 79 1 15 HELIX 3 3 GLY A 116 LYS A 127 1 12 HELIX 4 4 TYR A 151 GLY A 163 1 13 HELIX 5 5 SER A 176 ARG A 193 1 18 HELIX 6 6 ASN A 215 CYS A 223 1 9 HELIX 7 7 SER A 235 ASN A 249 1 15 HELIX 8 8 ASN A 249 VAL A 254 1 6 HELIX 9 9 SER A 276 MET A 290 1 15 HELIX 10 10 SER A 304 GLN A 312 1 9 HELIX 11 11 ASP A 313 GLN A 321 1 9 HELIX 12 12 ALA A 370 VAL A 376 5 7 HELIX 13 13 HIS B 46 MET B 51 1 6 HELIX 14 14 SER B 65 GLU B 79 1 15 HELIX 15 15 HIS B 115 LYS B 127 1 13 HELIX 16 16 TYR B 151 GLY B 163 1 13 HELIX 17 17 SER B 176 ARG B 193 1 18 HELIX 18 18 ASN B 215 CYS B 223 1 9 HELIX 19 19 SER B 235 ASN B 249 1 15 HELIX 20 20 ASN B 249 VAL B 254 1 6 HELIX 21 21 SER B 276 MET B 290 1 15 HELIX 22 22 SER B 304 GLN B 312 1 9 HELIX 23 23 ASP B 313 GLN B 321 1 9 HELIX 24 24 ALA B 370 VAL B 376 5 7 SHEET 1 A 8 TRP A 262 ASP A 264 0 SHEET 2 A 8 HIS A 225 ARG A 227 1 N TRP A 226 O ASP A 264 SHEET 3 A 8 VAL A 199 CYS A 202 1 N CYS A 202 O ARG A 227 SHEET 4 A 8 LEU A 166 ASP A 170 1 N LEU A 167 O SER A 201 SHEET 5 A 8 LYS A 130 ASP A 136 1 N ILE A 133 O LYS A 168 SHEET 6 A 8 TYR A 88 CYS A 90 1 N LEU A 89 O LYS A 130 SHEET 7 A 8 MET A 42 LEU A 45 1 N TRP A 44 O CYS A 90 SHEET 8 A 8 LEU A 294 MET A 296 1 O MET A 296 N LEU A 45 SHEET 1 B 6 TYR A 329 GLY A 334 0 SHEET 2 B 6 PHE A 337 PRO A 343 -1 O VAL A 339 N ARG A 332 SHEET 3 B 6 ALA A 348 ASN A 355 -1 O ALA A 352 N TRP A 340 SHEET 4 B 6 THR A 412 ASN A 419 -1 O LEU A 417 N TRP A 349 SHEET 5 B 6 ALA A 381 LEU A 388 -1 N LEU A 387 O LEU A 414 SHEET 6 B 6 ARG A 392 GLU A 398 -1 O TYR A 397 N CYS A 382 SHEET 1 C 2 ARG A 363 ALA A 368 0 SHEET 2 C 2 ARG A 402 ILE A 407 -1 O SER A 405 N TYR A 365 SHEET 1 D 8 TRP B 262 ASP B 264 0 SHEET 2 D 8 HIS B 225 ARG B 227 1 N TRP B 226 O ASP B 264 SHEET 3 D 8 VAL B 199 CYS B 202 1 N CYS B 202 O HIS B 225 SHEET 4 D 8 LEU B 166 ASP B 170 1 N PHE B 169 O SER B 201 SHEET 5 D 8 LYS B 130 ASP B 136 1 N ALA B 135 O ASP B 170 SHEET 6 D 8 TYR B 88 CYS B 90 1 N LEU B 89 O LYS B 130 SHEET 7 D 8 MET B 42 LEU B 45 1 N TRP B 44 O TYR B 88 SHEET 8 D 8 LEU B 294 MET B 296 1 O MET B 296 N LEU B 45 SHEET 1 E 6 TYR B 329 GLY B 334 0 SHEET 2 E 6 PHE B 337 PRO B 343 -1 O VAL B 339 N ARG B 332 SHEET 3 E 6 ALA B 348 ASN B 355 -1 O ALA B 352 N TRP B 340 SHEET 4 E 6 THR B 412 THR B 420 -1 O LEU B 417 N TRP B 349 SHEET 5 E 6 ALA B 381 LEU B 388 -1 N LEU B 387 O LEU B 414 SHEET 6 E 6 ARG B 392 GLU B 398 -1 O TYR B 397 N CYS B 382 SHEET 1 F 2 ARG B 363 ALA B 368 0 SHEET 2 F 2 ARG B 402 ILE B 407 -1 O SER B 405 N TYR B 365 SSBOND 1 CYS A 52 CYS A 94 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 63 1555 1555 2.03 SSBOND 3 CYS A 142 CYS A 172 1555 1555 2.03 SSBOND 4 CYS A 202 CYS A 223 1555 1555 2.03 SSBOND 5 CYS A 378 CYS A 382 1555 1555 2.03 SSBOND 6 CYS B 52 CYS B 94 1555 1555 2.03 SSBOND 7 CYS B 56 CYS B 63 1555 1555 2.03 SSBOND 8 CYS B 142 CYS B 172 1555 1555 2.03 SSBOND 9 CYS B 202 CYS B 223 1555 1555 2.03 SSBOND 10 CYS B 378 CYS B 382 1555 1555 2.03 LINK ND2 ASN A 139 C1 NAG A 506 1555 1555 1.44 LINK ND2 ASN A 192 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 215 C1 NAG A 507 1555 1555 1.46 LINK ND2 ASN B 139 C1 NAG B 506 1555 1555 1.43 LINK ND2 ASN B 192 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN B 215 C1 NAG B 505 1555 1555 1.46 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 CISPEP 1 ASN A 379 PRO A 380 0 1.04 CISPEP 2 LEU A 388 PRO A 389 0 2.64 CISPEP 3 ASN B 379 PRO B 380 0 -1.89 CISPEP 4 LEU B 388 PRO B 389 0 3.05 CRYST1 90.783 90.783 217.382 90.00 90.00 120.00 P 32 2 1 12 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 0.011015 0.006360 0.000000 0.00000 SCALE2 0.000000 0.012719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004600 0.00000