HEADER SUGAR BINDING PROTEIN 16-JUN-16 5GGJ TITLE CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN PROTEIN O-MANNOSE TITLE 2 BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE IN COMPLEX WITH MAN-ALPHA- TITLE 3 PNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN O-LINKED-MANNOSE BETA-1,2-N- COMPND 3 ACETYLGLUCOSAMINYLTRANSFERASE 1; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: UNP RESIDUES 92-250; COMPND 6 SYNONYM: POMGNT1,UDP-GLCNAC:ALPHA-D-MANNOSIDE BETA-1,2-N- COMPND 7 ACETYLGLUCOSAMINYLTRANSFERASE I.2,GNT I.2; COMPND 8 EC: 2.4.1.-; COMPND 9 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: POMGNT1, MGAT1.2, UNQ746/PRO1475; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS GLYCOSYLTRANSFEREASE, O-MANNOSYLATION, ALPHA-DYSTROGLYCAN, SUGAR KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.KUWABARA,T.SENDA,R.KATO REVDAT 4 08-NOV-23 5GGJ 1 HETSYN REVDAT 3 29-JUL-20 5GGJ 1 COMPND JRNL REMARK HETNAM REVDAT 3 2 1 SITE REVDAT 2 31-AUG-16 5GGJ 1 JRNL REVDAT 1 10-AUG-16 5GGJ 0 JRNL AUTH N.KUWABARA,H.MANYA,T.YAMADA,H.TATENO,M.KANAGAWA,K.KOBAYASHI, JRNL AUTH 2 K.AKASAKA-MANYA,Y.HIROSE,M.MIZUNO,M.IKEGUCHI,T.TODA, JRNL AUTH 3 J.HIRABAYASHI,T.SENDA,T.ENDO,R.KATO JRNL TITL CARBOHYDRATE-BINDING DOMAIN OF THE POMGNT1 STEM REGION JRNL TITL 2 MODULATES O-MANNOSYLATION SITES OF ALPHA-DYSTROGLYCAN JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 9280 2016 JRNL REFN ESSN 1091-6490 JRNL PMID 27493216 JRNL DOI 10.1073/PNAS.1525545113 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 62371 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.210 REMARK 3 FREE R VALUE TEST SET COUNT : 3819 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 19.1771 - 4.2561 0.99 4282 150 0.1664 0.1692 REMARK 3 2 4.2561 - 3.3843 1.00 4278 136 0.1615 0.1796 REMARK 3 3 3.3843 - 2.9582 1.00 4289 143 0.1689 0.1826 REMARK 3 4 2.9582 - 2.6886 1.00 4288 146 0.1740 0.1889 REMARK 3 5 2.6886 - 2.4963 1.00 4295 147 0.1757 0.2002 REMARK 3 6 2.4963 - 2.3494 1.00 4295 141 0.1753 0.2394 REMARK 3 7 2.3494 - 2.2319 1.00 4280 134 0.1737 0.2200 REMARK 3 8 2.2319 - 2.1349 1.00 4305 144 0.1770 0.1902 REMARK 3 9 2.1349 - 2.0528 1.00 4303 144 0.1766 0.2244 REMARK 3 10 2.0528 - 1.9820 1.00 4254 136 0.1782 0.1795 REMARK 3 11 1.9820 - 1.9201 1.00 4301 144 0.1783 0.2114 REMARK 3 12 1.9201 - 1.8653 1.00 4363 144 0.1935 0.2421 REMARK 3 13 1.8653 - 1.8162 1.00 4251 142 0.2041 0.2591 REMARK 3 14 1.8162 - 1.7719 1.00 4309 144 0.2070 0.2648 REMARK 3 15 1.7719 - 1.7317 1.00 4261 143 0.2095 0.2237 REMARK 3 16 1.7317 - 1.6949 1.00 4324 140 0.2030 0.2399 REMARK 3 17 1.6949 - 1.6610 1.00 4300 146 0.2123 0.2417 REMARK 3 18 1.6610 - 1.6296 1.00 4311 139 0.2118 0.2415 REMARK 3 19 1.6296 - 1.6006 1.00 4289 144 0.2250 0.2255 REMARK 3 20 1.6006 - 1.5734 1.00 4248 143 0.2307 0.2307 REMARK 3 21 1.5734 - 1.5481 1.00 4330 142 0.2411 0.2503 REMARK 3 22 1.5481 - 1.5243 1.00 4281 140 0.2700 0.3261 REMARK 3 23 1.5243 - 1.5018 1.00 4301 145 0.2762 0.2760 REMARK 3 24 1.5018 - 1.4807 1.00 4309 140 0.2924 0.2731 REMARK 3 25 1.4807 - 1.4607 1.00 4313 142 0.3042 0.3109 REMARK 3 26 1.4607 - 1.4417 1.00 4296 144 0.3305 0.3509 REMARK 3 27 1.4417 - 1.4237 0.81 3467 116 0.3726 0.4092 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.280 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 2428 REMARK 3 ANGLE : 1.013 3296 REMARK 3 CHIRALITY : 0.094 378 REMARK 3 PLANARITY : 0.006 417 REMARK 3 DIHEDRAL : 22.008 884 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 116 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6579 10.1307 7.9963 REMARK 3 T TENSOR REMARK 3 T11: 0.1953 T22: 0.2526 REMARK 3 T33: 0.1414 T12: 0.0681 REMARK 3 T13: -0.0326 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 1.2089 L22: 3.6273 REMARK 3 L33: 1.8864 L12: -0.6107 REMARK 3 L13: -0.3557 L23: 1.0757 REMARK 3 S TENSOR REMARK 3 S11: 0.0470 S12: 0.0328 S13: -0.0108 REMARK 3 S21: -0.2334 S22: -0.2069 S23: 0.5403 REMARK 3 S31: -0.2831 S32: -0.3492 S33: 0.1046 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 117 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3560 5.2172 -0.7544 REMARK 3 T TENSOR REMARK 3 T11: 0.3383 T22: 0.2419 REMARK 3 T33: 0.1861 T12: 0.1055 REMARK 3 T13: -0.0576 T23: -0.0399 REMARK 3 L TENSOR REMARK 3 L11: 0.2053 L22: 0.7419 REMARK 3 L33: 0.7844 L12: -0.0956 REMARK 3 L13: 0.1924 L23: -0.7530 REMARK 3 S TENSOR REMARK 3 S11: 0.4414 S12: 0.3593 S13: -0.1856 REMARK 3 S21: -1.1928 S22: -0.5549 S23: 0.4024 REMARK 3 S31: -0.0355 S32: -0.2233 S33: 0.1113 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 130 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.3558 5.1567 11.6977 REMARK 3 T TENSOR REMARK 3 T11: 0.1233 T22: 0.1610 REMARK 3 T33: 0.1039 T12: 0.0222 REMARK 3 T13: -0.0026 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 0.8027 L22: 2.7506 REMARK 3 L33: 0.3517 L12: -0.4044 REMARK 3 L13: -0.0113 L23: 0.1774 REMARK 3 S TENSOR REMARK 3 S11: 0.0127 S12: -0.0292 S13: 0.0496 REMARK 3 S21: -0.0513 S22: -0.0108 S23: -0.1461 REMARK 3 S31: -0.0365 S32: -0.0057 S33: 0.0009 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 187 THROUGH 208 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.8842 -3.5723 18.4166 REMARK 3 T TENSOR REMARK 3 T11: 0.1593 T22: 0.2001 REMARK 3 T33: 0.1431 T12: 0.0028 REMARK 3 T13: 0.0056 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.5046 L22: 1.5238 REMARK 3 L33: 2.0507 L12: -0.4671 REMARK 3 L13: 0.2475 L23: 0.1906 REMARK 3 S TENSOR REMARK 3 S11: 0.0985 S12: -0.1679 S13: -0.0246 REMARK 3 S21: 0.2822 S22: -0.0309 S23: 0.0686 REMARK 3 S31: 0.0253 S32: -0.0362 S33: -0.0130 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 209 THROUGH 237 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.5112 0.0152 14.8221 REMARK 3 T TENSOR REMARK 3 T11: 0.1165 T22: 0.2074 REMARK 3 T33: 0.1906 T12: 0.0286 REMARK 3 T13: -0.0012 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 1.3539 L22: 2.3609 REMARK 3 L33: 1.9174 L12: -0.8871 REMARK 3 L13: -0.4475 L23: 0.1789 REMARK 3 S TENSOR REMARK 3 S11: -0.0515 S12: -0.0614 S13: -0.2230 REMARK 3 S21: 0.0668 S22: -0.0581 S23: 0.4447 REMARK 3 S31: 0.0144 S32: -0.2402 S33: 0.0056 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 238 THROUGH 249 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.8073 15.4642 17.5128 REMARK 3 T TENSOR REMARK 3 T11: 0.2129 T22: 0.2476 REMARK 3 T33: 0.1412 T12: 0.0708 REMARK 3 T13: 0.0135 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 2.4010 L22: 7.6906 REMARK 3 L33: 3.5516 L12: 1.4270 REMARK 3 L13: 0.9730 L23: 4.3423 REMARK 3 S TENSOR REMARK 3 S11: 0.0724 S12: -0.1582 S13: 0.2044 REMARK 3 S21: -0.1256 S22: -0.2602 S23: 0.3321 REMARK 3 S31: -0.3806 S32: -0.3212 S33: 0.1503 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 97 THROUGH 116 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3664 13.9986 33.0945 REMARK 3 T TENSOR REMARK 3 T11: 0.1800 T22: 0.2514 REMARK 3 T33: 0.1922 T12: 0.0848 REMARK 3 T13: 0.0281 T23: -0.0221 REMARK 3 L TENSOR REMARK 3 L11: 4.9869 L22: 2.6846 REMARK 3 L33: 1.4505 L12: 0.6207 REMARK 3 L13: 0.9159 L23: 0.2215 REMARK 3 S TENSOR REMARK 3 S11: 0.1206 S12: 0.6052 S13: -0.2122 REMARK 3 S21: -0.2206 S22: -0.0175 S23: -0.4305 REMARK 3 S31: 0.2296 S32: 0.5271 S33: -0.1354 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 117 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.3040 6.4215 33.4036 REMARK 3 T TENSOR REMARK 3 T11: 0.3176 T22: 0.3208 REMARK 3 T33: 0.3529 T12: 0.0598 REMARK 3 T13: -0.0240 T23: -0.0754 REMARK 3 L TENSOR REMARK 3 L11: 0.0586 L22: 2.7085 REMARK 3 L33: 0.8736 L12: -0.2119 REMARK 3 L13: -0.2158 L23: 0.9943 REMARK 3 S TENSOR REMARK 3 S11: 0.1991 S12: 0.9039 S13: -1.1488 REMARK 3 S21: -0.3203 S22: -0.2762 S23: 0.0282 REMARK 3 S31: 0.2859 S32: 0.0636 S33: -0.0138 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 130 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2830 13.0880 44.8101 REMARK 3 T TENSOR REMARK 3 T11: 0.2230 T22: 0.2149 REMARK 3 T33: 0.1771 T12: 0.0740 REMARK 3 T13: -0.0444 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 2.4909 L22: 2.8898 REMARK 3 L33: 1.1322 L12: 0.0782 REMARK 3 L13: 0.8349 L23: 0.1024 REMARK 3 S TENSOR REMARK 3 S11: 0.1098 S12: -0.4343 S13: -0.3767 REMARK 3 S21: 0.4248 S22: 0.0736 S23: -0.3459 REMARK 3 S31: 0.3487 S32: 0.1131 S33: -0.0645 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 150 THROUGH 166 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.9509 17.3611 46.4242 REMARK 3 T TENSOR REMARK 3 T11: 0.1750 T22: 0.1798 REMARK 3 T33: 0.1559 T12: 0.0156 REMARK 3 T13: 0.0231 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 5.3180 L22: 1.3245 REMARK 3 L33: 2.0806 L12: 0.0326 REMARK 3 L13: 2.9523 L23: 0.4636 REMARK 3 S TENSOR REMARK 3 S11: -0.0492 S12: -0.3754 S13: -0.3890 REMARK 3 S21: 0.2156 S22: 0.0679 S23: 0.1521 REMARK 3 S31: 0.0942 S32: -0.2897 S33: 0.0049 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 167 THROUGH 226 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.3667 23.5993 39.4823 REMARK 3 T TENSOR REMARK 3 T11: 0.1448 T22: 0.1503 REMARK 3 T33: 0.1095 T12: 0.0182 REMARK 3 T13: 0.0075 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 1.8062 L22: 1.1649 REMARK 3 L33: 0.5638 L12: 0.2815 REMARK 3 L13: 0.3409 L23: 0.4216 REMARK 3 S TENSOR REMARK 3 S11: -0.0005 S12: 0.0043 S13: 0.0708 REMARK 3 S21: -0.0044 S22: -0.0560 S23: 0.0285 REMARK 3 S31: -0.0267 S32: 0.0589 S33: 0.0430 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 227 THROUGH 248 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5631 21.0040 30.6608 REMARK 3 T TENSOR REMARK 3 T11: 0.2402 T22: 0.2140 REMARK 3 T33: 0.1323 T12: 0.0593 REMARK 3 T13: 0.0477 T23: -0.0246 REMARK 3 L TENSOR REMARK 3 L11: 3.8905 L22: 2.2636 REMARK 3 L33: 1.4330 L12: 0.2702 REMARK 3 L13: 1.0573 L23: 0.2674 REMARK 3 S TENSOR REMARK 3 S11: 0.1151 S12: 0.2516 S13: 0.3417 REMARK 3 S21: -0.2489 S22: -0.0935 S23: -0.0283 REMARK 3 S31: -0.1539 S32: 0.0861 S33: -0.0118 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE FACTOR FILE CONTAINS REMARK 3 FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5GGJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000738. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 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 MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62431 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 19.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.98000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 5GGG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, PEG-6000, PH 8.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 34.74500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.74500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.41500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 612 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 618 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 GLY A 87 REMARK 465 PRO A 88 REMARK 465 LEU A 89 REMARK 465 GLY A 90 REMARK 465 SER A 91 REMARK 465 GLY A 92 REMARK 465 SER A 93 REMARK 465 GLY A 94 REMARK 465 PRO A 95 REMARK 465 ARG A 96 REMARK 465 GLU A 250 REMARK 465 GLY B 87 REMARK 465 PRO B 88 REMARK 465 LEU B 89 REMARK 465 GLY B 90 REMARK 465 SER B 91 REMARK 465 GLY B 92 REMARK 465 SER B 93 REMARK 465 GLY B 94 REMARK 465 PRO B 95 REMARK 465 ARG B 96 REMARK 465 ALA B 249 REMARK 465 GLU B 250 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 97 CG CD NE CZ NH1 NH2 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 HOH A 536 O HOH A 549 2.08 REMARK 500 O HOH A 447 O HOH A 460 2.09 REMARK 500 O HOH B 516 O HOH B 534 2.14 REMARK 500 O HOH B 527 O HOH B 547 2.15 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 OE1 GLU A 123 O HOH B 519 1554 1.97 REMARK 500 O HOH A 614 O HOH B 580 3546 2.15 REMARK 500 O HOH A 614 O HOH B 584 3546 2.17 REMARK 500 O HOH A 561 O HOH A 561 2655 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 HIS A 155 -21.43 84.53 REMARK 500 ASP A 179 -77.16 73.21 REMARK 500 SER A 248 -156.45 -155.42 REMARK 500 THR B 140 -44.36 66.60 REMARK 500 HIS B 155 -10.65 79.83 REMARK 500 ASP B 179 -70.74 71.49 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 622 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 623 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH A 624 DISTANCE = 8.46 ANGSTROMS REMARK 525 HOH B 585 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH B 586 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH B 587 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH B 588 DISTANCE = 7.48 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GGF RELATED DB: PDB REMARK 900 RELATED ID: 5GGG RELATED DB: PDB REMARK 900 RELATED ID: 5GGI RELATED DB: PDB REMARK 900 RELATED ID: 5GGK RELATED DB: PDB REMARK 900 RELATED ID: 5GGL RELATED DB: PDB REMARK 900 RELATED ID: 5GGN RELATED DB: PDB REMARK 900 RELATED ID: 5GGO RELATED DB: PDB REMARK 900 RELATED ID: 5GGP RELATED DB: PDB DBREF 5GGJ A 92 250 UNP Q8WZA1 PMGT1_HUMAN 92 250 DBREF 5GGJ B 92 250 UNP Q8WZA1 PMGT1_HUMAN 92 250 SEQADV 5GGJ GLY A 87 UNP Q8WZA1 EXPRESSION TAG SEQADV 5GGJ PRO A 88 UNP Q8WZA1 EXPRESSION TAG SEQADV 5GGJ LEU A 89 UNP Q8WZA1 EXPRESSION TAG SEQADV 5GGJ GLY A 90 UNP Q8WZA1 EXPRESSION TAG SEQADV 5GGJ SER A 91 UNP Q8WZA1 EXPRESSION TAG SEQADV 5GGJ GLY B 87 UNP Q8WZA1 EXPRESSION TAG SEQADV 5GGJ PRO B 88 UNP Q8WZA1 EXPRESSION TAG SEQADV 5GGJ LEU B 89 UNP Q8WZA1 EXPRESSION TAG SEQADV 5GGJ GLY B 90 UNP Q8WZA1 EXPRESSION TAG SEQADV 5GGJ SER B 91 UNP Q8WZA1 EXPRESSION TAG SEQRES 1 A 164 GLY PRO LEU GLY SER GLY SER GLY PRO ARG ARG VAL LEU SEQRES 2 A 164 ASP VAL GLU VAL TYR SER SER ARG SER LYS VAL TYR VAL SEQRES 3 A 164 ALA VAL ASP GLY THR THR VAL LEU GLU ASP GLU ALA ARG SEQRES 4 A 164 GLU GLN GLY ARG GLY ILE HIS VAL ILE VAL LEU ASN GLN SEQRES 5 A 164 ALA THR GLY HIS VAL MET ALA LYS ARG VAL PHE ASP THR SEQRES 6 A 164 TYR SER PRO HIS GLU ASP GLU ALA MET VAL LEU PHE LEU SEQRES 7 A 164 ASN MET VAL ALA PRO GLY ARG VAL LEU ILE CYS THR VAL SEQRES 8 A 164 LYS ASP GLU GLY SER PHE HIS LEU LYS ASP THR ALA LYS SEQRES 9 A 164 ALA LEU LEU ARG SER LEU GLY SER GLN ALA GLY PRO ALA SEQRES 10 A 164 LEU GLY TRP ARG ASP THR TRP ALA PHE VAL GLY ARG LYS SEQRES 11 A 164 GLY GLY PRO VAL PHE GLY GLU LYS HIS SER LYS SER PRO SEQRES 12 A 164 ALA LEU SER SER TRP GLY ASP PRO VAL LEU LEU LYS THR SEQRES 13 A 164 ASP VAL PRO LEU SER SER ALA GLU SEQRES 1 B 164 GLY PRO LEU GLY SER GLY SER GLY PRO ARG ARG VAL LEU SEQRES 2 B 164 ASP VAL GLU VAL TYR SER SER ARG SER LYS VAL TYR VAL SEQRES 3 B 164 ALA VAL ASP GLY THR THR VAL LEU GLU ASP GLU ALA ARG SEQRES 4 B 164 GLU GLN GLY ARG GLY ILE HIS VAL ILE VAL LEU ASN GLN SEQRES 5 B 164 ALA THR GLY HIS VAL MET ALA LYS ARG VAL PHE ASP THR SEQRES 6 B 164 TYR SER PRO HIS GLU ASP GLU ALA MET VAL LEU PHE LEU SEQRES 7 B 164 ASN MET VAL ALA PRO GLY ARG VAL LEU ILE CYS THR VAL SEQRES 8 B 164 LYS ASP GLU GLY SER PHE HIS LEU LYS ASP THR ALA LYS SEQRES 9 B 164 ALA LEU LEU ARG SER LEU GLY SER GLN ALA GLY PRO ALA SEQRES 10 B 164 LEU GLY TRP ARG ASP THR TRP ALA PHE VAL GLY ARG LYS SEQRES 11 B 164 GLY GLY PRO VAL PHE GLY GLU LYS HIS SER LYS SER PRO SEQRES 12 B 164 ALA LEU SER SER TRP GLY ASP PRO VAL LEU LEU LYS THR SEQRES 13 B 164 ASP VAL PRO LEU SER SER ALA GLU HET PNA A 301 21 HET PNA B 301 21 HETNAM PNA 4-NITROPHENYL ALPHA-D-MANNOPYRANOSIDE HETSYN PNA 4'-NITROPHENYL-ALPHA-D-MANNOPYRANOSIDE; 4-NITROPHENYL HETSYN 2 PNA ALPHA-D-MANNOSIDE; 4-NITROPHENYL D-MANNOSIDE; 4- HETSYN 3 PNA NITROPHENYL MANNOSIDE FORMUL 3 PNA 2(C12 H15 N O8) FORMUL 5 HOH *412(H2 O) HELIX 1 AA1 HIS A 155 MET A 166 1 12 HELIX 2 AA2 LYS A 186 LEU A 196 1 11 HELIX 3 AA3 ALA A 200 LEU A 204 5 5 HELIX 4 AA4 HIS B 155 MET B 166 1 12 HELIX 5 AA5 LYS B 186 LEU B 196 1 11 HELIX 6 AA6 ALA B 200 LEU B 204 5 5 SHEET 1 AA1 4 THR A 117 ASP A 122 0 SHEET 2 AA1 4 VAL A 110 VAL A 114 -1 N VAL A 114 O THR A 117 SHEET 3 AA1 4 VAL A 98 SER A 105 -1 N GLU A 102 O ALA A 113 SHEET 4 AA1 4 VAL A 238 PRO A 245 -1 O LEU A 240 N VAL A 103 SHEET 1 AA2 5 VAL A 143 PHE A 149 0 SHEET 2 AA2 5 GLY A 130 LEU A 136 -1 N VAL A 135 O MET A 144 SHEET 3 AA2 5 VAL A 172 LYS A 178 -1 O THR A 176 N HIS A 132 SHEET 4 AA2 5 THR A 209 ARG A 215 -1 O GLY A 214 N LEU A 173 SHEET 5 AA2 5 VAL A 220 SER A 226 -1 O GLY A 222 N VAL A 213 SHEET 1 AA3 4 THR B 117 ASP B 122 0 SHEET 2 AA3 4 VAL B 110 VAL B 114 -1 N VAL B 112 O VAL B 119 SHEET 3 AA3 4 VAL B 98 SER B 105 -1 N TYR B 104 O TYR B 111 SHEET 4 AA3 4 VAL B 238 PRO B 245 -1 O VAL B 244 N LEU B 99 SHEET 1 AA4 5 VAL B 143 PHE B 149 0 SHEET 2 AA4 5 GLY B 130 LEU B 136 -1 N VAL B 135 O MET B 144 SHEET 3 AA4 5 VAL B 172 LYS B 178 -1 O THR B 176 N HIS B 132 SHEET 4 AA4 5 THR B 209 ARG B 215 -1 O GLY B 214 N LEU B 173 SHEET 5 AA4 5 VAL B 220 SER B 226 -1 O PHE B 221 N VAL B 213 CISPEP 1 GLY A 218 PRO A 219 0 -0.62 CISPEP 2 GLY B 218 PRO B 219 0 -2.82 CRYST1 69.490 88.830 53.533 90.00 90.00 90.00 P 21 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 0.014391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011257 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018680 0.00000