HEADER TRANSFERASE 20-SEP-17 6EJ8 TITLE HUMAN XYLOSYLTRANSFERASE 1 IN COMPLEX WITH PEPTIDE QEEEGSGGGQGG COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSYLTRANSFERASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPTIDE O-XYLOSYLTRANSFERASE 1,XYLOSYLTRANSFERASE I,XYLT-I; COMPND 5 EC: 2.4.2.26; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN AMBP; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: XYLT1, XT1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCEP-PU; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS PROTEOGLYCAN, GLYCOSYLTRANSFERASE, GOLGI, XYLOSYLTRANSFERASE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.C.BRIGGS,E.HOHENESTER REVDAT 5 23-OCT-24 6EJ8 1 REMARK REVDAT 4 17-JAN-24 6EJ8 1 HETSYN REVDAT 3 29-JUL-20 6EJ8 1 COMPND REMARK HETNAM SITE REVDAT 2 13-JUN-18 6EJ8 1 JRNL REVDAT 1 02-MAY-18 6EJ8 0 JRNL AUTH D.C.BRIGGS,E.HOHENESTER JRNL TITL STRUCTURAL BASIS FOR THE INITIATION OF GLYCOSAMINOGLYCAN JRNL TITL 2 BIOSYNTHESIS BY HUMAN XYLOSYLTRANSFERASE 1. JRNL REF STRUCTURE V. 26 801 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 29681470 JRNL DOI 10.1016/J.STR.2018.03.014 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 53548 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 2612 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 57.3467 - 5.5754 0.99 2876 135 0.1899 0.1968 REMARK 3 2 5.5754 - 4.4259 0.99 2762 128 0.1372 0.1564 REMARK 3 3 4.4259 - 3.8665 0.99 2717 129 0.1429 0.1850 REMARK 3 4 3.8665 - 3.5131 0.99 2663 155 0.1618 0.1709 REMARK 3 5 3.5131 - 3.2613 1.00 2693 147 0.1901 0.2153 REMARK 3 6 3.2613 - 3.0690 1.00 2687 140 0.2031 0.2486 REMARK 3 7 3.0690 - 2.9153 1.00 2673 131 0.2008 0.2448 REMARK 3 8 2.9153 - 2.7884 1.00 2663 145 0.2154 0.2588 REMARK 3 9 2.7884 - 2.6811 1.00 2655 157 0.2251 0.2687 REMARK 3 10 2.6811 - 2.5886 1.00 2680 116 0.2274 0.2433 REMARK 3 11 2.5886 - 2.5076 1.00 2662 121 0.2263 0.2836 REMARK 3 12 2.5076 - 2.4360 1.00 2667 148 0.2420 0.2766 REMARK 3 13 2.4360 - 2.3718 1.00 2666 143 0.2524 0.3003 REMARK 3 14 2.3718 - 2.3140 1.00 2631 126 0.2465 0.2517 REMARK 3 15 2.3140 - 2.2614 1.00 2654 143 0.2520 0.3256 REMARK 3 16 2.2614 - 2.2132 1.00 2661 120 0.2763 0.3037 REMARK 3 17 2.2132 - 2.1690 1.00 2603 164 0.2849 0.3095 REMARK 3 18 2.1690 - 2.1280 1.00 2676 139 0.2964 0.3052 REMARK 3 19 2.1280 - 2.0900 1.00 2647 125 0.3253 0.3435 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.37 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 : 0.004 5830 REMARK 3 ANGLE : 0.538 7929 REMARK 3 CHIRALITY : 0.042 849 REMARK 3 PLANARITY : 0.003 1020 REMARK 3 DIHEDRAL : 12.589 3432 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 252 THROUGH 349 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.4855 19.0743 55.7387 REMARK 3 T TENSOR REMARK 3 T11: 0.2680 T22: 0.2971 REMARK 3 T33: 0.2429 T12: 0.0279 REMARK 3 T13: -0.0130 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 1.8780 L22: 2.0167 REMARK 3 L33: 0.7937 L12: -0.3349 REMARK 3 L13: -0.2106 L23: -0.0388 REMARK 3 S TENSOR REMARK 3 S11: -0.0522 S12: 0.0255 S13: -0.3195 REMARK 3 S21: 0.0615 S22: 0.0454 S23: 0.1212 REMARK 3 S31: 0.0237 S32: -0.0990 S33: 0.0022 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 350 THROUGH 628 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9040 22.9294 57.9291 REMARK 3 T TENSOR REMARK 3 T11: 0.2543 T22: 0.2906 REMARK 3 T33: 0.3211 T12: 0.0234 REMARK 3 T13: -0.0104 T23: 0.0129 REMARK 3 L TENSOR REMARK 3 L11: 1.0413 L22: 2.0950 REMARK 3 L33: 0.6292 L12: 0.0334 REMARK 3 L13: 0.0986 L23: 0.1627 REMARK 3 S TENSOR REMARK 3 S11: -0.0274 S12: -0.1182 S13: -0.1741 REMARK 3 S21: 0.1064 S22: 0.0060 S23: -0.0566 REMARK 3 S31: 0.0378 S32: -0.0025 S33: 0.0248 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 629 THROUGH 736 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4273 60.9049 54.1056 REMARK 3 T TENSOR REMARK 3 T11: 0.2790 T22: 0.2056 REMARK 3 T33: 0.2588 T12: 0.0158 REMARK 3 T13: -0.0619 T23: -0.0395 REMARK 3 L TENSOR REMARK 3 L11: 1.4361 L22: 1.4041 REMARK 3 L33: 2.2377 L12: 0.2844 REMARK 3 L13: -0.2044 L23: -0.6082 REMARK 3 S TENSOR REMARK 3 S11: 0.0513 S12: -0.0021 S13: 0.1636 REMARK 3 S21: 0.0233 S22: -0.0279 S23: 0.0409 REMARK 3 S31: -0.3487 S32: -0.0131 S33: -0.0301 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 737 THROUGH 790 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.8729 50.2152 74.7841 REMARK 3 T TENSOR REMARK 3 T11: 0.3860 T22: 0.4388 REMARK 3 T33: 0.4437 T12: -0.0130 REMARK 3 T13: 0.0429 T23: -0.0359 REMARK 3 L TENSOR REMARK 3 L11: 2.9339 L22: 2.7370 REMARK 3 L33: 2.3815 L12: -0.5863 REMARK 3 L13: -0.2856 L23: 0.2522 REMARK 3 S TENSOR REMARK 3 S11: 0.1851 S12: -0.3073 S13: 0.0194 REMARK 3 S21: 0.1884 S22: -0.0708 S23: 0.2173 REMARK 3 S31: 0.0142 S32: -0.1290 S33: -0.0085 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 791 THROUGH 959 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.1398 58.1263 65.3349 REMARK 3 T TENSOR REMARK 3 T11: 0.3689 T22: 0.3808 REMARK 3 T33: 0.4183 T12: 0.0530 REMARK 3 T13: -0.0266 T23: -0.0843 REMARK 3 L TENSOR REMARK 3 L11: 1.3306 L22: 1.5835 REMARK 3 L33: 1.2921 L12: -0.0019 REMARK 3 L13: -0.3975 L23: 0.1826 REMARK 3 S TENSOR REMARK 3 S11: 0.0515 S12: -0.1077 S13: 0.0490 REMARK 3 S21: 0.1681 S22: -0.1292 S23: 0.3072 REMARK 3 S31: -0.3724 S32: -0.2984 S33: 0.0382 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 211 THROUGH 219 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.4238 21.4866 70.6412 REMARK 3 T TENSOR REMARK 3 T11: 0.5586 T22: 0.5052 REMARK 3 T33: 0.4836 T12: -0.0411 REMARK 3 T13: -0.0098 T23: 0.0384 REMARK 3 L TENSOR REMARK 3 L11: 0.3130 L22: 0.7669 REMARK 3 L33: 0.4128 L12: 0.4899 REMARK 3 L13: 0.3551 L23: 0.5568 REMARK 3 S TENSOR REMARK 3 S11: 0.2008 S12: -0.5520 S13: -0.1040 REMARK 3 S21: 0.0776 S22: 0.1046 S23: -0.1254 REMARK 3 S31: 0.2037 S32: -0.1689 S33: -0.2308 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 6EJ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JAN-17 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 : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9282 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53618 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 57.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 1.26600 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: 2GAK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 55-65% MORPHEUS PRECIPITANT MIX 2 REMARK 280 (PEG8000 AND ETHYLENE GLYCOL) 0.1M BICINE/TRIS BUFFER AT PH 7.5 REMARK 280 0.1M OF NPS MIX (0.033M OF EACH), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 33.65500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.42500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.34000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.42500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.65500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.34000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 ARG A 205 REMARK 465 ALA A 206 REMARK 465 LEU A 207 REMARK 465 ALA A 208 REMARK 465 ALA A 209 REMARK 465 PRO A 210 REMARK 465 LEU A 211 REMARK 465 VAL A 212 REMARK 465 HIS A 213 REMARK 465 HIS A 214 REMARK 465 HIS A 215 REMARK 465 HIS A 216 REMARK 465 HIS A 217 REMARK 465 HIS A 218 REMARK 465 ALA A 219 REMARK 465 LEU A 220 REMARK 465 ASP A 221 REMARK 465 GLU A 222 REMARK 465 ASN A 223 REMARK 465 LEU A 224 REMARK 465 TYR A 225 REMARK 465 PHE A 226 REMARK 465 GLN A 227 REMARK 465 GLY A 228 REMARK 465 ALA A 229 REMARK 465 LEU A 230 REMARK 465 ALA A 231 REMARK 465 ASP A 232 REMARK 465 VAL A 233 REMARK 465 SER A 234 REMARK 465 ARG A 235 REMARK 465 PRO A 236 REMARK 465 PRO A 237 REMARK 465 HIS A 238 REMARK 465 ALA A 239 REMARK 465 ARG A 240 REMARK 465 LYS A 241 REMARK 465 THR A 242 REMARK 465 GLY A 243 REMARK 465 GLY A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 PRO A 247 REMARK 465 GLU A 248 REMARK 465 THR A 249 REMARK 465 LYS A 250 REMARK 465 TYR A 251 REMARK 465 VAL A 311 REMARK 465 PRO A 731 REMARK 465 SER A 732 REMARK 465 ASP A 733 REMARK 465 PHE A 734 REMARK 465 GLN B 210 REMARK 465 GLY B 220 REMARK 465 GLY B 221 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 ASP A 252 CG OD1 OD2 REMARK 470 GLN A 253 CG CD OE1 NE2 REMARK 470 LYS A 256 CG CD CE NZ REMARK 470 LYS A 262 CD CE NZ REMARK 470 LYS A 272 CE NZ REMARK 470 LYS A 274 CD CE NZ REMARK 470 GLU A 282 CD OE1 OE2 REMARK 470 ARG A 286 NE CZ NH1 NH2 REMARK 470 LYS A 296 CE NZ REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 ASN A 308 CG OD1 ND2 REMARK 470 ASN A 310 CG OD1 ND2 REMARK 470 GLN A 312 CG CD OE1 NE2 REMARK 470 ASP A 314 CG OD1 OD2 REMARK 470 GLU A 315 CG CD OE1 OE2 REMARK 470 ASP A 316 CG OD1 OD2 REMARK 470 ARG A 453 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 457 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 558 CE NZ REMARK 470 LYS A 566 CG CD CE NZ REMARK 470 LYS A 723 CD CE NZ REMARK 470 LYS A 726 CG CD CE NZ REMARK 470 SER A 729 OG REMARK 470 PRO A 730 CG CD REMARK 470 LYS A 774 CG CD CE NZ REMARK 470 LEU A 863 CG CD1 CD2 REMARK 470 ARG A 864 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 865 CG OD1 ND2 REMARK 470 GLU A 869 CG CD OE1 OE2 REMARK 470 ARG A 892 CD NE CZ NH1 NH2 REMARK 470 ARG A 893 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 211 CG CD OE1 OE2 REMARK 470 GLU B 212 CG CD OE1 OE2 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 HG CYS A 257 HG CYS A 285 0.57 REMARK 500 SG CYS A 301 HG CYS A 542 0.88 REMARK 500 SG CYS A 257 HG CYS A 285 0.90 REMARK 500 HG CYS A 257 SG CYS A 285 1.19 REMARK 500 ND2 ASN A 777 C1 NAG A 1001 1.64 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 GLN A 253 128.80 -176.23 REMARK 500 ALA A 307 -72.72 -84.68 REMARK 500 ASN A 308 94.75 68.12 REMARK 500 SER A 364 72.93 -112.45 REMARK 500 ARG A 453 -155.36 -158.71 REMARK 500 SER A 530 -12.37 -146.61 REMARK 500 ASN A 548 118.94 -171.73 REMARK 500 ASN A 556 68.86 -151.75 REMARK 500 ASN A 605 111.16 -165.27 REMARK 500 TRP A 829 -6.75 71.71 REMARK 500 VAL A 832 -60.23 -120.29 REMARK 500 LEU A 881 65.82 -118.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG A 1001 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1002 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 375 O REMARK 620 2 TYR A 378 O 82.5 REMARK 620 3 VAL A 381 O 91.4 91.4 REMARK 620 4 HOH A1219 O 166.2 110.9 91.4 REMARK 620 5 HOH A1317 O 85.6 85.6 176.1 92.0 REMARK 620 6 HOH A1322 O 90.1 172.5 87.3 76.5 95.3 REMARK 620 N 1 2 3 4 5 DBREF 6EJ8 A 232 959 UNP Q86Y38 XYLT1_HUMAN 232 959 DBREF 6EJ8 B 210 221 UNP P02760 AMBP_HUMAN 210 221 SEQADV 6EJ8 ARG A 205 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 ALA A 206 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 LEU A 207 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 ALA A 208 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 ALA A 209 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 PRO A 210 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 LEU A 211 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 VAL A 212 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 HIS A 213 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 HIS A 214 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 HIS A 215 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 HIS A 216 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 HIS A 217 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 HIS A 218 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 ALA A 219 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 LEU A 220 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 ASP A 221 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 GLU A 222 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 ASN A 223 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 LEU A 224 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 TYR A 225 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 PHE A 226 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 GLN A 227 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 GLY A 228 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 ALA A 229 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 LEU A 230 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 ALA A 231 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJ8 GLY B 220 UNP P02760 LEU 220 ENGINEERED MUTATION SEQADV 6EJ8 GLY B 221 UNP P02760 VAL 221 ENGINEERED MUTATION SEQRES 1 A 755 ARG ALA LEU ALA ALA PRO LEU VAL HIS HIS HIS HIS HIS SEQRES 2 A 755 HIS ALA LEU ASP GLU ASN LEU TYR PHE GLN GLY ALA LEU SEQRES 3 A 755 ALA ASP VAL SER ARG PRO PRO HIS ALA ARG LYS THR GLY SEQRES 4 A 755 GLY SER SER PRO GLU THR LYS TYR ASP GLN PRO PRO LYS SEQRES 5 A 755 CYS ASP ILE SER GLY LYS GLU ALA ILE SER ALA LEU SER SEQRES 6 A 755 ARG ALA LYS SER LYS HIS CYS ARG GLN GLU ILE GLY GLU SEQRES 7 A 755 THR TYR CYS ARG HIS LYS LEU GLY LEU LEU MET PRO GLU SEQRES 8 A 755 LYS VAL THR ARG PHE CYS PRO LEU GLU GLY LYS ALA ASN SEQRES 9 A 755 LYS ASN VAL GLN TRP ASP GLU ASP SER VAL GLU TYR MET SEQRES 10 A 755 PRO ALA ASN PRO VAL ARG ILE ALA PHE VAL LEU VAL VAL SEQRES 11 A 755 HIS GLY ARG ALA SER ARG GLN LEU GLN ARG MET PHE LYS SEQRES 12 A 755 ALA ILE TYR HIS LYS ASP HIS PHE TYR TYR ILE HIS VAL SEQRES 13 A 755 ASP LYS ARG SER ASN TYR LEU HIS ARG GLN VAL LEU GLN SEQRES 14 A 755 VAL SER ARG GLN TYR SER ASN VAL ARG VAL THR PRO TRP SEQRES 15 A 755 ARG MET ALA THR ILE TRP GLY GLY ALA SER LEU LEU SER SEQRES 16 A 755 THR TYR LEU GLN SER MET ARG ASP LEU LEU GLU MET THR SEQRES 17 A 755 ASP TRP PRO TRP ASP PHE PHE ILE ASN LEU SER ALA ALA SEQRES 18 A 755 ASP TYR PRO ILE ARG THR ASN ASP GLN LEU VAL ALA PHE SEQRES 19 A 755 LEU SER ARG TYR ARG ASP MET ASN PHE LEU LYS SER HIS SEQRES 20 A 755 GLY ARG ASP ASN ALA ARG PHE ILE ARG LYS GLN GLY LEU SEQRES 21 A 755 ASP ARG LEU PHE LEU GLU CYS ASP ALA HIS MET TRP ARG SEQRES 22 A 755 LEU GLY ASP ARG ARG ILE PRO GLU GLY ILE ALA VAL ASP SEQRES 23 A 755 GLY GLY SER ASP TRP PHE LEU LEU ASN ARG ARG PHE VAL SEQRES 24 A 755 GLU TYR VAL THR PHE SER THR ASP ASP LEU VAL THR LYS SEQRES 25 A 755 MET LYS GLN PHE TYR SER TYR THR LEU LEU PRO ALA GLU SEQRES 26 A 755 SER PHE PHE HIS THR VAL LEU GLU ASN SER PRO HIS CYS SEQRES 27 A 755 ASP THR MET VAL ASP ASN ASN LEU ARG ILE THR ASN TRP SEQRES 28 A 755 ASN ARG LYS LEU GLY CYS LYS CYS GLN TYR LYS HIS ILE SEQRES 29 A 755 VAL ASP TRP CYS GLY CYS SER PRO ASN ASP PHE LYS PRO SEQRES 30 A 755 GLN ASP PHE HIS ARG PHE GLN GLN THR ALA ARG PRO THR SEQRES 31 A 755 PHE PHE ALA ARG LYS PHE GLU ALA VAL VAL ASN GLN GLU SEQRES 32 A 755 ILE ILE GLY GLN LEU ASP TYR TYR LEU TYR GLY ASN TYR SEQRES 33 A 755 PRO ALA GLY THR PRO GLY LEU ARG SER TYR TRP GLU ASN SEQRES 34 A 755 VAL TYR ASP GLU PRO ASP GLY ILE HIS SER LEU SER ASP SEQRES 35 A 755 VAL THR LEU THR LEU TYR HIS SER PHE ALA ARG LEU GLY SEQRES 36 A 755 LEU ARG ARG ALA GLU THR SER LEU HIS THR ASP GLY GLU SEQRES 37 A 755 ASN SER CYS ARG TYR TYR PRO MET GLY HIS PRO ALA SER SEQRES 38 A 755 VAL HIS LEU TYR PHE LEU ALA ASP ARG PHE GLN GLY PHE SEQRES 39 A 755 LEU ILE LYS HIS HIS ALA THR ASN LEU ALA VAL SER LYS SEQRES 40 A 755 LEU GLU THR LEU GLU THR TRP VAL MET PRO LYS LYS VAL SEQRES 41 A 755 PHE LYS ILE ALA SER PRO PRO SER ASP PHE GLY ARG LEU SEQRES 42 A 755 GLN PHE SER GLU VAL GLY THR ASP TRP ASP ALA LYS GLU SEQRES 43 A 755 ARG LEU PHE ARG ASN PHE GLY GLY LEU LEU GLY PRO MET SEQRES 44 A 755 ASP GLU PRO VAL GLY MET GLN LYS TRP GLY LYS GLY PRO SEQRES 45 A 755 ASN VAL THR VAL THR VAL ILE TRP VAL ASP PRO VAL ASN SEQRES 46 A 755 VAL ILE ALA ALA THR TYR ASP ILE LEU ILE GLU SER THR SEQRES 47 A 755 ALA GLU PHE THR HIS TYR LYS PRO PRO LEU ASN LEU PRO SEQRES 48 A 755 LEU ARG PRO GLY VAL TRP THR VAL LYS ILE LEU HIS HIS SEQRES 49 A 755 TRP VAL PRO VAL ALA GLU THR LYS PHE LEU VAL ALA PRO SEQRES 50 A 755 LEU THR PHE SER ASN ARG GLN PRO ILE LYS PRO GLU GLU SEQRES 51 A 755 ALA LEU LYS LEU HIS ASN GLY PRO LEU ARG ASN ALA TYR SEQRES 52 A 755 MET GLU GLN SER PHE GLN SER LEU ASN PRO VAL LEU SER SEQRES 53 A 755 LEU PRO ILE ASN PRO ALA GLN VAL GLU GLN ALA ARG ARG SEQRES 54 A 755 ASN ALA ALA SER THR GLY THR ALA LEU GLU GLY TRP LEU SEQRES 55 A 755 ASP SER LEU VAL GLY GLY MET TRP THR ALA MET ASP ILE SEQRES 56 A 755 CYS ALA THR GLY PRO THR ALA CYS PRO VAL MET GLN THR SEQRES 57 A 755 CYS SER GLN THR ALA TRP SER SER PHE SER PRO ASP PRO SEQRES 58 A 755 LYS SER GLU LEU GLY ALA VAL LYS PRO ASP GLY ARG LEU SEQRES 59 A 755 ARG SEQRES 1 B 12 GLN GLU GLU GLU GLY SER GLY GLY GLY GLN GLY GLY HET NAG A1001 27 HET NA A1002 1 HET PO4 A1003 5 HET PO4 A1004 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION 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 C8 H15 N O6 FORMUL 4 NA NA 1+ FORMUL 5 PO4 2(O4 P 3-) FORMUL 7 HOH *232(H2 O) HELIX 1 AA1 GLY A 261 ALA A 271 1 11 HELIX 2 AA2 SER A 273 LEU A 289 1 17 HELIX 3 AA3 ASP A 314 TYR A 320 5 7 HELIX 4 AA4 ALA A 338 TYR A 350 1 13 HELIX 5 AA5 SER A 364 TYR A 378 1 15 HELIX 6 AA6 ALA A 395 MET A 411 1 17 HELIX 7 AA7 THR A 431 TYR A 442 1 12 HELIX 8 AA8 ASP A 454 GLY A 463 1 10 HELIX 9 AA9 ARG A 500 SER A 509 1 10 HELIX 10 AB1 ASP A 511 TYR A 521 1 11 HELIX 11 AB2 SER A 522 THR A 524 5 3 HELIX 12 AB3 LEU A 526 GLU A 529 5 4 HELIX 13 AB4 SER A 530 SER A 539 1 10 HELIX 14 AB5 HIS A 541 ASP A 543 5 3 HELIX 15 AB6 ASN A 556 CYS A 561 1 6 HELIX 16 AB7 LYS A 580 GLN A 589 5 10 HELIX 17 AB8 GLN A 606 GLY A 618 1 13 HELIX 18 AB9 PRO A 638 LEU A 644 5 7 HELIX 19 AC1 SER A 645 LEU A 667 1 23 HELIX 20 AC2 LYS A 851 HIS A 859 1 9 HELIX 21 AC3 PHE A 872 SER A 874 5 3 HELIX 22 AC4 LEU A 875 SER A 880 1 6 HELIX 23 AC5 ASN A 884 ALA A 896 1 13 HELIX 24 AC6 THR A 898 MET A 913 1 16 HELIX 25 AC7 THR A 932 THR A 936 5 5 HELIX 26 AC8 ASP A 944 GLU A 948 5 5 SHEET 1 AA1 5 VAL A 381 VAL A 383 0 SHEET 2 AA1 5 PHE A 355 VAL A 360 1 N TYR A 356 O ARG A 382 SHEET 3 AA1 5 ILE A 328 VAL A 334 1 N PHE A 330 O PHE A 355 SHEET 4 AA1 5 PHE A 418 LEU A 422 1 O ILE A 420 N VAL A 331 SHEET 5 AA1 5 LEU A 497 ASN A 499 -1 O LEU A 498 N PHE A 419 SHEET 1 AA2 3 ASP A 426 PRO A 428 0 SHEET 2 AA2 3 PHE A 596 ARG A 598 -1 O ALA A 597 N TYR A 427 SHEET 3 AA2 3 ARG A 551 THR A 553 1 N ILE A 552 O ARG A 598 SHEET 1 AA3 2 ASN A 446 LEU A 448 0 SHEET 2 AA3 2 MET A 545 ASP A 547 1 O VAL A 546 N ASN A 446 SHEET 1 AA4 2 ARG A 466 GLU A 470 0 SHEET 2 AA4 2 MET A 475 ASP A 480 -1 O GLY A 479 N LEU A 467 SHEET 1 AA5 5 SER A 629 ASP A 636 0 SHEET 2 AA5 5 TYR A 677 LEU A 691 -1 O LEU A 688 N GLU A 632 SHEET 3 AA5 5 ARG A 694 ASN A 706 -1 O GLN A 696 N TYR A 689 SHEET 4 AA5 5 LYS A 711 PRO A 721 -1 O LYS A 711 N ASN A 706 SHEET 5 AA5 5 TRP A 914 ALA A 921 -1 O THR A 915 N MET A 720 SHEET 1 AA6 5 LYS A 726 ILE A 727 0 SHEET 2 AA6 5 VAL A 830 VAL A 839 -1 O GLU A 834 N LYS A 726 SHEET 3 AA6 5 GLY A 819 HIS A 827 -1 N VAL A 823 O THR A 835 SHEET 4 AA6 5 VAL A 778 VAL A 785 -1 N VAL A 785 O THR A 822 SHEET 5 AA6 5 ILE A 791 ILE A 799 -1 O ILE A 799 N VAL A 778 SHEET 1 AA7 3 LEU A 737 GLY A 743 0 SHEET 2 AA7 3 VAL A 767 TRP A 772 -1 O MET A 769 N GLU A 741 SHEET 3 AA7 3 PHE A 805 TYR A 808 -1 O THR A 806 N GLN A 770 SHEET 1 AA8 2 TRP A 746 ASP A 747 0 SHEET 2 AA8 2 LEU A 752 PHE A 753 -1 O LEU A 752 N ASP A 747 SHEET 1 AA9 2 PHE A 844 SER A 845 0 SHEET 2 AA9 2 GLN A 848 PRO A 849 -1 O GLN A 848 N SER A 845 SSBOND 1 CYS A 257 CYS A 285 1555 1555 2.03 SSBOND 2 CYS A 301 CYS A 542 1555 1555 2.05 SSBOND 3 CYS A 561 CYS A 574 1555 1555 2.04 SSBOND 4 CYS A 563 CYS A 572 1555 1555 2.04 SSBOND 5 CYS A 675 CYS A 927 1555 1555 2.04 SSBOND 6 CYS A 920 CYS A 933 1555 1555 2.04 LINK O SER A 375 NA NA A1002 1555 1555 2.38 LINK O TYR A 378 NA NA A1002 1555 1555 2.39 LINK O VAL A 381 NA NA A1002 1555 1555 2.39 LINK NA NA A1002 O HOH A1219 1555 1555 2.64 LINK NA NA A1002 O HOH A1317 1555 1555 2.50 LINK NA NA A1002 O HOH A1322 1555 1555 2.57 CISPEP 1 ARG A 598 LYS A 599 0 -1.41 CISPEP 2 LEU A 814 PRO A 815 0 -3.98 CRYST1 67.310 86.680 152.850 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014857 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011537 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006542 0.00000