PDB Short entry for 6EJA HEADER TRANSFERASE 20-SEP-17 6EJA TITLE HUMAN XYLOSYLTRANSFERASE 1 IN COMPLEX WITH PEPTIDE QEEEYSGGGQGG COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSYLTRANSFERASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 232-959; COMPND 5 SYNONYM: PEPTIDE O-XYLOSYLTRANSFERASE 1,XYLOSYLTRANSFERASE I,XYLT-I; COMPND 6 EC: 2.4.2.26; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROTEIN AMBP; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 210-221; COMPND 12 SYNONYM: BIKUNIN; COMPND 13 ENGINEERED: YES; COMPND 14 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: HEK293FS; 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 3 17-JAN-24 6EJA 1 REMARK REVDAT 2 13-JUN-18 6EJA 1 JRNL REVDAT 1 02-MAY-18 6EJA 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. 1.94 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 64173 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 3183 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 40.1925 - 5.5126 0.95 2754 146 0.1883 0.2014 REMARK 3 2 5.5126 - 4.3772 0.97 2679 145 0.1430 0.1727 REMARK 3 3 4.3772 - 3.8244 0.97 2659 142 0.1432 0.1650 REMARK 3 4 3.8244 - 3.4750 0.99 2666 140 0.1610 0.1972 REMARK 3 5 3.4750 - 3.2260 0.99 2692 133 0.1781 0.2062 REMARK 3 6 3.2260 - 3.0359 0.99 2691 117 0.1987 0.2417 REMARK 3 7 3.0359 - 2.8839 0.99 2628 144 0.1908 0.2103 REMARK 3 8 2.8839 - 2.7584 0.99 2639 160 0.1900 0.2050 REMARK 3 9 2.7584 - 2.6522 1.00 2683 129 0.1960 0.2325 REMARK 3 10 2.6522 - 2.5607 1.00 2661 146 0.1957 0.2342 REMARK 3 11 2.5607 - 2.4807 1.00 2657 144 0.1979 0.2551 REMARK 3 12 2.4807 - 2.4098 0.99 2625 153 0.2067 0.2384 REMARK 3 13 2.4098 - 2.3463 0.99 2665 139 0.2128 0.2615 REMARK 3 14 2.3463 - 2.2891 0.99 2605 132 0.2033 0.2588 REMARK 3 15 2.2891 - 2.2371 0.98 2620 135 0.2091 0.2266 REMARK 3 16 2.2371 - 2.1894 0.99 2642 130 0.2214 0.2452 REMARK 3 17 2.1894 - 2.1457 0.99 2595 142 0.2239 0.2654 REMARK 3 18 2.1457 - 2.1052 0.99 2664 148 0.2422 0.2299 REMARK 3 19 2.1052 - 2.0676 0.99 2640 126 0.2616 0.2796 REMARK 3 20 2.0676 - 2.0325 0.99 2636 137 0.2673 0.3124 REMARK 3 21 2.0325 - 1.9997 0.99 2630 124 0.2846 0.3472 REMARK 3 22 1.9997 - 1.9690 1.00 2656 130 0.3094 0.3411 REMARK 3 23 1.9690 - 1.9400 0.99 2603 141 0.3330 0.3408 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.54 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 5718 REMARK 3 ANGLE : 0.631 7793 REMARK 3 CHIRALITY : 0.043 835 REMARK 3 PLANARITY : 0.004 1008 REMARK 3 DIHEDRAL : 11.292 3372 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 253 THROUGH 349 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.6871 18.8070 54.3647 REMARK 3 T TENSOR REMARK 3 T11: 0.3729 T22: 0.3817 REMARK 3 T33: 0.3444 T12: 0.0356 REMARK 3 T13: -0.0136 T23: -0.0168 REMARK 3 L TENSOR REMARK 3 L11: 2.1164 L22: 2.3377 REMARK 3 L33: 0.9030 L12: 0.0178 REMARK 3 L13: -0.1928 L23: -0.0887 REMARK 3 S TENSOR REMARK 3 S11: -0.0655 S12: 0.0310 S13: -0.3408 REMARK 3 S21: 0.0440 S22: 0.0566 S23: 0.2674 REMARK 3 S31: 0.0639 S32: -0.1415 S33: 0.0174 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 350 THROUGH 606 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.4917 21.2359 56.7630 REMARK 3 T TENSOR REMARK 3 T11: 0.3592 T22: 0.3938 REMARK 3 T33: 0.3922 T12: 0.0372 REMARK 3 T13: 0.0031 T23: 0.0245 REMARK 3 L TENSOR REMARK 3 L11: 1.4730 L22: 2.4749 REMARK 3 L33: 0.6915 L12: 0.2594 REMARK 3 L13: 0.0518 L23: 0.0845 REMARK 3 S TENSOR REMARK 3 S11: -0.0266 S12: -0.2570 S13: -0.2369 REMARK 3 S21: 0.1980 S22: -0.0183 S23: -0.0158 REMARK 3 S31: 0.0387 S32: -0.0496 S33: 0.0543 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 607 THROUGH 959 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.9730 56.2525 62.3909 REMARK 3 T TENSOR REMARK 3 T11: 0.4258 T22: 0.3791 REMARK 3 T33: 0.3778 T12: 0.0240 REMARK 3 T13: -0.0345 T23: -0.0707 REMARK 3 L TENSOR REMARK 3 L11: 1.0820 L22: 1.4771 REMARK 3 L33: 1.3672 L12: 0.2664 REMARK 3 L13: -0.1417 L23: 0.0672 REMARK 3 S TENSOR REMARK 3 S11: -0.0060 S12: -0.1662 S13: 0.1108 REMARK 3 S21: 0.2027 S22: -0.0477 S23: 0.2432 REMARK 3 S31: -0.2855 S32: -0.2226 S33: 0.0418 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 213 THROUGH 219 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9261 20.5986 69.2099 REMARK 3 T TENSOR REMARK 3 T11: 0.8509 T22: 0.6857 REMARK 3 T33: 0.6222 T12: -0.1391 REMARK 3 T13: 0.1231 T23: 0.0663 REMARK 3 L TENSOR REMARK 3 L11: 4.7401 L22: 6.7175 REMARK 3 L33: 6.4821 L12: -5.4933 REMARK 3 L13: -0.9971 L23: 0.5677 REMARK 3 S TENSOR REMARK 3 S11: -0.4133 S12: -0.6715 S13: -1.6026 REMARK 3 S21: 0.5482 S22: 0.0329 S23: 0.2639 REMARK 3 S31: 0.5139 S32: 0.3614 S33: 0.3920 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 6EJA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006663. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-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 : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64274 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 43.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 1.21900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 2GAM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 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 33.28000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.61000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.61000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.28000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.98000 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: 1300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 ASP A 252 REMARK 465 VAL A 311 REMARK 465 GLN A 312 REMARK 465 TRP A 313 REMARK 465 ASP A 314 REMARK 465 GLU A 315 REMARK 465 ASP A 316 REMARK 465 PRO A 730 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 GLU B 211 REMARK 465 GLU B 212 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 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 CG CD CE NZ REMARK 470 LYS A 274 CD CE NZ REMARK 470 ARG A 286 NE CZ NH1 NH2 REMARK 470 LYS A 296 CE NZ REMARK 470 LYS A 306 CG CD CE NZ REMARK 470 ASN A 308 CG OD1 ND2 REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 ARG A 441 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 457 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 461 CG CD CE NZ REMARK 470 ARG A 482 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 485 CG CD OE1 OE2 REMARK 470 ARG A 501 CD NE CZ NH1 NH2 REMARK 470 GLU A 504 CD OE1 OE2 REMARK 470 LYS A 558 CG CD CE NZ REMARK 470 LYS A 562 CG CD CE NZ REMARK 470 LYS A 566 CG CD CE NZ REMARK 470 THR A 590 OG1 CG2 REMARK 470 LYS A 723 CD CE NZ REMARK 470 LYS A 726 CG CD CE NZ 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 GLN A 873 CG CD OE1 NE2 REMARK 470 LEU A 879 CG CD1 CD2 REMARK 470 ARG A 892 CD NE CZ NH1 NH2 REMARK 470 ARG A 893 CG CD NE CZ NH1 NH2 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 HE2 HIS A 541 OD1 ASP A 670 1545 1.54 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 ALA A 307 -70.77 -81.68 REMARK 500 ASN A 308 74.58 64.53 REMARK 500 SER A 364 72.11 -113.41 REMARK 500 ARG A 453 -151.95 -100.61 REMARK 500 SER A 530 -20.08 -148.65 REMARK 500 ASN A 556 89.27 -154.18 REMARK 500 CYS A 561 68.82 -115.94 REMARK 500 REMARK 500 REMARK: NULL 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 A1001 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 101.1 89.3 REMARK 620 4 HOH A1127 O 168.7 102.3 89.3 REMARK 620 5 HOH A1291 O 83.3 86.3 173.4 86.8 REMARK 620 6 HOH A1302 O 97.8 179.6 91.0 77.4 93.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1001 DBREF 6EJA A 232 959 UNP Q86Y38 XYLT1_HUMAN 232 959 DBREF 6EJA B 210 221 UNP P02760 AMBP_HUMAN 210 221 SEQADV 6EJA ALA A 209 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA PRO A 210 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA LEU A 211 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA VAL A 212 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA HIS A 213 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA HIS A 214 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA HIS A 215 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA HIS A 216 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA HIS A 217 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA HIS A 218 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA ALA A 219 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA LEU A 220 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA ASP A 221 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA GLU A 222 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA ASN A 223 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA LEU A 224 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA TYR A 225 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA PHE A 226 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA GLN A 227 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA GLY A 228 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA ALA A 229 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA LEU A 230 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA ALA A 231 UNP Q86Y38 EXPRESSION TAG SEQADV 6EJA TYR B 214 UNP P02760 GLY 214 ENGINEERED MUTATION SEQADV 6EJA GLY B 220 UNP P02760 LEU 220 ENGINEERED MUTATION SEQADV 6EJA GLY B 221 UNP P02760 VAL 221 ENGINEERED MUTATION SEQRES 1 A 751 ALA PRO LEU VAL HIS HIS HIS HIS HIS HIS ALA LEU ASP SEQRES 2 A 751 GLU ASN LEU TYR PHE GLN GLY ALA LEU ALA ASP VAL SER SEQRES 3 A 751 ARG PRO PRO HIS ALA ARG LYS THR GLY GLY SER SER PRO SEQRES 4 A 751 GLU THR LYS TYR ASP GLN PRO PRO LYS CYS ASP ILE SER SEQRES 5 A 751 GLY LYS GLU ALA ILE SER ALA LEU SER ARG ALA LYS SER SEQRES 6 A 751 LYS HIS CYS ARG GLN GLU ILE GLY GLU THR TYR CYS ARG SEQRES 7 A 751 HIS LYS LEU GLY LEU LEU MET PRO GLU LYS VAL THR ARG SEQRES 8 A 751 PHE CYS PRO LEU GLU GLY LYS ALA ASN LYS ASN VAL GLN SEQRES 9 A 751 TRP ASP GLU ASP SER VAL GLU TYR MET PRO ALA ASN PRO SEQRES 10 A 751 VAL ARG ILE ALA PHE VAL LEU VAL VAL HIS GLY ARG ALA SEQRES 11 A 751 SER ARG GLN LEU GLN ARG MET PHE LYS ALA ILE TYR HIS SEQRES 12 A 751 LYS ASP HIS PHE TYR TYR ILE HIS VAL ASP LYS ARG SER SEQRES 13 A 751 ASN TYR LEU HIS ARG GLN VAL LEU GLN VAL SER ARG GLN SEQRES 14 A 751 TYR SER ASN VAL ARG VAL THR PRO TRP ARG MET ALA THR SEQRES 15 A 751 ILE TRP GLY GLY ALA SER LEU LEU SER THR TYR LEU GLN SEQRES 16 A 751 SER MET ARG ASP LEU LEU GLU MET THR ASP TRP PRO TRP SEQRES 17 A 751 ASP PHE PHE ILE ASN LEU SER ALA ALA ASP TYR PRO ILE SEQRES 18 A 751 ARG THR ASN ASP GLN LEU VAL ALA PHE LEU SER ARG TYR SEQRES 19 A 751 ARG ASP MET ASN PHE LEU LYS SER HIS GLY ARG ASP ASN SEQRES 20 A 751 ALA ARG PHE ILE ARG LYS GLN GLY LEU ASP ARG LEU PHE SEQRES 21 A 751 LEU GLU CYS ASP ALA HIS MET TRP ARG LEU GLY ASP ARG SEQRES 22 A 751 ARG ILE PRO GLU GLY ILE ALA VAL ASP GLY GLY SER ASP SEQRES 23 A 751 TRP PHE LEU LEU ASN ARG ARG PHE VAL GLU TYR VAL THR SEQRES 24 A 751 PHE SER THR ASP ASP LEU VAL THR LYS MET LYS GLN PHE SEQRES 25 A 751 TYR SER TYR THR LEU LEU PRO ALA GLU SER PHE PHE HIS SEQRES 26 A 751 THR VAL LEU GLU ASN SER PRO HIS CYS ASP THR MET VAL SEQRES 27 A 751 ASP ASN ASN LEU ARG ILE THR ASN TRP ASN ARG LYS LEU SEQRES 28 A 751 GLY CYS LYS CYS GLN TYR LYS HIS ILE VAL ASP TRP CYS SEQRES 29 A 751 GLY CYS SER PRO ASN ASP PHE LYS PRO GLN ASP PHE HIS SEQRES 30 A 751 ARG PHE GLN GLN THR ALA ARG PRO THR PHE PHE ALA ARG SEQRES 31 A 751 LYS PHE GLU ALA VAL VAL ASN GLN GLU ILE ILE GLY GLN SEQRES 32 A 751 LEU ASP TYR TYR LEU TYR GLY ASN TYR PRO ALA GLY THR SEQRES 33 A 751 PRO GLY LEU ARG SER TYR TRP GLU ASN VAL TYR ASP GLU SEQRES 34 A 751 PRO ASP GLY ILE HIS SER LEU SER ASP VAL THR LEU THR SEQRES 35 A 751 LEU TYR HIS SER PHE ALA ARG LEU GLY LEU ARG ARG ALA SEQRES 36 A 751 GLU THR SER LEU HIS THR ASP GLY GLU ASN SER CYS ARG SEQRES 37 A 751 TYR TYR PRO MET GLY HIS PRO ALA SER VAL HIS LEU TYR SEQRES 38 A 751 PHE LEU ALA ASP ARG PHE GLN GLY PHE LEU ILE LYS HIS SEQRES 39 A 751 HIS ALA THR ASN LEU ALA VAL SER LYS LEU GLU THR LEU SEQRES 40 A 751 GLU THR TRP VAL MET PRO LYS LYS VAL PHE LYS ILE ALA SEQRES 41 A 751 SER PRO PRO SER ASP PHE GLY ARG LEU GLN PHE SER GLU SEQRES 42 A 751 VAL GLY THR ASP TRP ASP ALA LYS GLU ARG LEU PHE ARG SEQRES 43 A 751 ASN PHE GLY GLY LEU LEU GLY PRO MET ASP GLU PRO VAL SEQRES 44 A 751 GLY MET GLN LYS TRP GLY LYS GLY PRO ASN VAL THR VAL SEQRES 45 A 751 THR VAL ILE TRP VAL ASP PRO VAL ASN VAL ILE ALA ALA SEQRES 46 A 751 THR TYR ASP ILE LEU ILE GLU SER THR ALA GLU PHE THR SEQRES 47 A 751 HIS TYR LYS PRO PRO LEU ASN LEU PRO LEU ARG PRO GLY SEQRES 48 A 751 VAL TRP THR VAL LYS ILE LEU HIS HIS TRP VAL PRO VAL SEQRES 49 A 751 ALA GLU THR LYS PHE LEU VAL ALA PRO LEU THR PHE SER SEQRES 50 A 751 ASN ARG GLN PRO ILE LYS PRO GLU GLU ALA LEU LYS LEU SEQRES 51 A 751 HIS ASN GLY PRO LEU ARG ASN ALA TYR MET GLU GLN SER SEQRES 52 A 751 PHE GLN SER LEU ASN PRO VAL LEU SER LEU PRO ILE ASN SEQRES 53 A 751 PRO ALA GLN VAL GLU GLN ALA ARG ARG ASN ALA ALA SER SEQRES 54 A 751 THR GLY THR ALA LEU GLU GLY TRP LEU ASP SER LEU VAL SEQRES 55 A 751 GLY GLY MET TRP THR ALA MET ASP ILE CYS ALA THR GLY SEQRES 56 A 751 PRO THR ALA CYS PRO VAL MET GLN THR CYS SER GLN THR SEQRES 57 A 751 ALA TRP SER SER PHE SER PRO ASP PRO LYS SER GLU LEU SEQRES 58 A 751 GLY ALA VAL LYS PRO ASP GLY ARG LEU ARG SEQRES 1 B 12 GLN GLU GLU GLU TYR SER GLY GLY GLY GLN GLY GLY HET NA A1001 1 HETNAM NA SODIUM ION FORMUL 3 NA NA 1+ FORMUL 4 HOH *225(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 ALA A 338 TYR A 350 1 13 HELIX 4 AA4 SER A 364 TYR A 378 1 15 HELIX 5 AA5 ALA A 395 MET A 411 1 17 HELIX 6 AA6 THR A 431 TYR A 442 1 12 HELIX 7 AA7 ASP A 454 GLN A 462 1 9 HELIX 8 AA8 ARG A 500 SER A 509 1 10 HELIX 9 AA9 ASP A 511 SER A 522 1 12 HELIX 10 AB1 LEU A 526 GLU A 529 5 4 HELIX 11 AB2 SER A 530 SER A 539 1 10 HELIX 12 AB3 HIS A 541 ASP A 543 5 3 HELIX 13 AB4 ASN A 556 CYS A 561 1 6 HELIX 14 AB5 LYS A 580 GLN A 589 5 10 HELIX 15 AB6 GLN A 606 GLY A 618 1 13 HELIX 16 AB7 PRO A 638 LEU A 644 5 7 HELIX 17 AB8 SER A 645 SER A 666 1 22 HELIX 18 AB9 LYS A 851 ASN A 860 1 10 HELIX 19 AC1 PHE A 872 ASN A 876 5 5 HELIX 20 AC2 ASN A 884 ALA A 896 1 13 HELIX 21 AC3 THR A 898 MET A 913 1 16 HELIX 22 AC4 SER A 934 THR A 936 5 3 HELIX 23 AC5 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 LEU A 332 O HIS A 359 SHEET 4 AA1 5 PHE A 418 SER A 423 1 O PHE A 418 N ALA A 329 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 CYS A 471 0 SHEET 2 AA4 2 HIS A 474 ASP A 480 -1 O GLY A 479 N LEU A 467 SHEET 1 AA5 6 SER A 629 ASP A 636 0 SHEET 2 AA5 6 TYR A 677 LEU A 691 -1 O LEU A 688 N GLU A 632 SHEET 3 AA5 6 ARG A 694 ASN A 706 -1 O GLN A 696 N TYR A 689 SHEET 4 AA5 6 LYS A 711 PRO A 721 -1 O LYS A 711 N ASN A 706 SHEET 5 AA5 6 TRP A 914 ALA A 921 -1 O ASP A 918 N TRP A 718 SHEET 6 AA5 6 GLN A 931 THR A 932 1 O GLN A 931 N ALA A 921 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 ILE A 825 O ALA A 833 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 2.04 SSBOND 2 CYS A 276 CYS A 471 1555 1555 2.04 SSBOND 3 CYS A 301 CYS A 542 1555 1555 2.05 SSBOND 4 CYS A 561 CYS A 574 1555 1555 2.03 SSBOND 5 CYS A 563 CYS A 572 1555 1555 2.04 SSBOND 6 CYS A 675 CYS A 927 1555 1555 2.04 SSBOND 7 CYS A 920 CYS A 933 1555 1555 2.04 LINK O SER A 375 NA NA A1001 1555 1555 2.34 LINK O TYR A 378 NA NA A1001 1555 1555 2.48 LINK O VAL A 381 NA NA A1001 1555 1555 2.32 LINK NA NA A1001 O HOH A1127 1555 1555 2.63 LINK NA NA A1001 O HOH A1291 1555 1555 2.50 LINK NA NA A1001 O HOH A1302 1555 1555 2.76 CISPEP 1 ARG A 598 LYS A 599 0 5.63 CISPEP 2 LEU A 814 PRO A 815 0 -3.41 SITE 1 AC1 6 SER A 375 TYR A 378 VAL A 381 HOH A1127 SITE 2 AC1 6 HOH A1291 HOH A1302 CRYST1 66.560 85.960 151.220 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 0.015024 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006613 0.00000