HEADER TOXIN 23-MAY-19 6RTG TITLE CRYSTAL STRUCTURE OF THE UDP-BOUND GLYCOSYLTRANSFERASE DOMAIN FROM THE TITLE 2 YGT TOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RTX TOXIN AND CA2+-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA MOLLARETII (STRAIN ATCC 43969 / DSM SOURCE 3 18520 / CIP 103324 / CNY 7263 / WAIP 204); SOURCE 4 ORGANISM_TAXID: 349967; SOURCE 5 STRAIN: ATCC 43969 / DSM 18520 / CIP 103324 / CNY 7263 / WAIP 204; SOURCE 6 GENE: YMOLL0001_37990; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSYLTRANSFERASE DOMAIN, TOXIN, NUCLEOTIDE BINDING EXPDTA X-RAY DIFFRACTION AUTHOR C.WIRTH,X.BOGDANOVIC,W.-C.KAO,C.HUNTE REVDAT 3 15-MAY-24 6RTG 1 REMARK LINK REVDAT 2 01-APR-20 6RTG 1 JRNL REVDAT 1 18-MAR-20 6RTG 0 JRNL AUTH G.S.OST,C.WIRTH,X.BOGDANOVIC,W.C.KAO,B.SCHORCH, JRNL AUTH 2 P.J.K.AKTORIES,P.PAPATHEODOROU,C.SCHWAN,A.SCHLOSSER,T.JANK, JRNL AUTH 3 C.HUNTE,K.AKTORIES JRNL TITL INVERSE CONTROL OF RAB PROTEINS JRNL TITL 2 BYYERSINIAADP-RIBOSYLTRANSFERASE AND GLYCOSYLTRANSFERASE JRNL TITL 3 RELATED TO CLOSTRIDIAL GLUCOSYLATING TOXINS. JRNL REF SCI ADV V. 6 Z2094 2020 JRNL REFN ESSN 2375-2548 JRNL PMID 32195351 JRNL DOI 10.1126/SCIADV.AAZ2094 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 52064 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) : 0.186 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2082 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 45.5734 - 4.6844 1.00 3599 149 0.1730 0.2076 REMARK 3 2 4.6844 - 3.7187 1.00 3409 142 0.1482 0.1783 REMARK 3 3 3.7187 - 3.2488 1.00 3385 142 0.1698 0.2061 REMARK 3 4 3.2488 - 2.9518 1.00 3341 139 0.1851 0.2234 REMARK 3 5 2.9518 - 2.7403 1.00 3343 139 0.1905 0.2063 REMARK 3 6 2.7403 - 2.5787 1.00 3323 139 0.1942 0.2659 REMARK 3 7 2.5787 - 2.4496 1.00 3298 137 0.1987 0.2536 REMARK 3 8 2.4496 - 2.3430 1.00 3297 137 0.1966 0.2273 REMARK 3 9 2.3430 - 2.2528 1.00 3310 138 0.2008 0.2137 REMARK 3 10 2.2528 - 2.1750 1.00 3277 137 0.2107 0.2782 REMARK 3 11 2.1750 - 2.1070 1.00 3298 137 0.2259 0.2684 REMARK 3 12 2.1070 - 2.0468 1.00 3285 137 0.2409 0.2764 REMARK 3 13 2.0468 - 1.9929 1.00 3247 135 0.2618 0.3085 REMARK 3 14 1.9929 - 1.9443 1.00 3299 138 0.2716 0.3238 REMARK 3 15 1.9443 - 1.9001 1.00 3271 136 0.2929 0.3204 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 4298 REMARK 3 ANGLE : 0.640 5827 REMARK 3 CHIRALITY : 0.044 653 REMARK 3 PLANARITY : 0.004 748 REMARK 3 DIHEDRAL : 12.637 2592 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 15 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 86.8126 128.9233 34.3501 REMARK 3 T TENSOR REMARK 3 T11: 0.3918 T22: 0.4100 REMARK 3 T33: 0.3651 T12: 0.1830 REMARK 3 T13: -0.2358 T23: -0.2669 REMARK 3 L TENSOR REMARK 3 L11: 4.3326 L22: 2.8478 REMARK 3 L33: 1.8659 L12: -0.9747 REMARK 3 L13: 0.4449 L23: 0.5884 REMARK 3 S TENSOR REMARK 3 S11: -0.7369 S12: -0.9166 S13: 0.9414 REMARK 3 S21: 0.8717 S22: 0.6070 S23: -0.1116 REMARK 3 S31: -0.0552 S32: 0.0804 S33: 0.0923 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 150 THROUGH 268 ) REMARK 3 ORIGIN FOR THE GROUP (A): 80.5941 116.7770 21.9729 REMARK 3 T TENSOR REMARK 3 T11: 0.2207 T22: 0.2144 REMARK 3 T33: 0.1697 T12: 0.0136 REMARK 3 T13: 0.0246 T23: -0.0364 REMARK 3 L TENSOR REMARK 3 L11: 3.8538 L22: 2.5929 REMARK 3 L33: 0.8489 L12: -1.8515 REMARK 3 L13: -0.2441 L23: 0.1056 REMARK 3 S TENSOR REMARK 3 S11: -0.1873 S12: 0.0425 S13: -0.2482 REMARK 3 S21: 0.1433 S22: 0.0924 S23: 0.2639 REMARK 3 S31: 0.0772 S32: -0.0769 S33: 0.0671 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 269 THROUGH 316 ) REMARK 3 ORIGIN FOR THE GROUP (A): 75.5891 110.2043 15.2554 REMARK 3 T TENSOR REMARK 3 T11: 0.2971 T22: 0.3674 REMARK 3 T33: 0.5518 T12: 0.0044 REMARK 3 T13: -0.0616 T23: -0.1257 REMARK 3 L TENSOR REMARK 3 L11: 8.1591 L22: 0.7374 REMARK 3 L33: 1.1356 L12: -2.3235 REMARK 3 L13: 0.6296 L23: -0.0078 REMARK 3 S TENSOR REMARK 3 S11: 0.2695 S12: 0.7458 S13: -1.1104 REMARK 3 S21: -0.1643 S22: -0.2985 S23: 0.9061 REMARK 3 S31: 0.2376 S32: -0.0893 S33: 0.0126 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 317 THROUGH 357 ) REMARK 3 ORIGIN FOR THE GROUP (A): 107.5751 123.3321 16.7966 REMARK 3 T TENSOR REMARK 3 T11: 0.3380 T22: 0.5088 REMARK 3 T33: 1.0883 T12: 0.0002 REMARK 3 T13: 0.1620 T23: 0.1519 REMARK 3 L TENSOR REMARK 3 L11: 2.4068 L22: 4.9323 REMARK 3 L33: 2.4185 L12: 1.2772 REMARK 3 L13: -0.5144 L23: -0.9843 REMARK 3 S TENSOR REMARK 3 S11: 0.1205 S12: 0.5314 S13: 1.2689 REMARK 3 S21: -0.7403 S22: -0.0898 S23: -1.6927 REMARK 3 S31: -0.2205 S32: 0.6965 S33: 0.0225 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 358 THROUGH 384 ) REMARK 3 ORIGIN FOR THE GROUP (A): 100.7656 128.2510 14.5850 REMARK 3 T TENSOR REMARK 3 T11: 0.4422 T22: 0.3856 REMARK 3 T33: 0.8346 T12: 0.0180 REMARK 3 T13: 0.1520 T23: 0.1898 REMARK 3 L TENSOR REMARK 3 L11: 6.7374 L22: 4.3923 REMARK 3 L33: 4.6353 L12: -0.7573 REMARK 3 L13: 2.3549 L23: -2.5195 REMARK 3 S TENSOR REMARK 3 S11: -0.3917 S12: 1.1184 S13: 0.6056 REMARK 3 S21: -1.0748 S22: -0.2870 S23: -0.8538 REMARK 3 S31: 0.5006 S32: 0.2840 S33: 0.4967 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 385 THROUGH 438 ) REMARK 3 ORIGIN FOR THE GROUP (A): 89.3001 119.1572 13.1158 REMARK 3 T TENSOR REMARK 3 T11: 0.2844 T22: 0.3464 REMARK 3 T33: 0.1686 T12: 0.0615 REMARK 3 T13: 0.0012 T23: 0.0479 REMARK 3 L TENSOR REMARK 3 L11: 4.1785 L22: 1.9444 REMARK 3 L33: 0.9419 L12: -1.8036 REMARK 3 L13: -0.0791 L23: 0.0839 REMARK 3 S TENSOR REMARK 3 S11: 0.2052 S12: 0.6055 S13: 0.2621 REMARK 3 S21: -0.2887 S22: -0.3178 S23: -0.1942 REMARK 3 S31: 0.0925 S32: 0.0715 S33: 0.1110 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 439 THROUGH 518 ) REMARK 3 ORIGIN FOR THE GROUP (A): 73.7632 146.3565 15.6296 REMARK 3 T TENSOR REMARK 3 T11: 0.4225 T22: 0.3725 REMARK 3 T33: 0.8206 T12: 0.0545 REMARK 3 T13: -0.1704 T23: 0.1069 REMARK 3 L TENSOR REMARK 3 L11: 1.5588 L22: 4.8844 REMARK 3 L33: 1.5006 L12: 0.5650 REMARK 3 L13: -0.9862 L23: -0.4117 REMARK 3 S TENSOR REMARK 3 S11: -0.2497 S12: 0.3868 S13: 1.4797 REMARK 3 S21: -0.2487 S22: 0.0424 S23: -0.1761 REMARK 3 S31: -0.3853 S32: -0.1116 S33: 0.1852 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 6RTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102039. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52064 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.40 REMARK 200 R MERGE (I) : 0.18400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.20 REMARK 200 R MERGE FOR SHELL (I) : 2.08300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSHARP, PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: LONG RODS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH 8.5, 200 MM SODIUM REMARK 280 ACETATE AND 15 % PEG 4000, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.87000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 82.13500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 82.13500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.80500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 82.13500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 82.13500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.93500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 82.13500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 82.13500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.80500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 82.13500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 82.13500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 11.93500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 23.87000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 KCAL/MOL 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 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 A1108 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 0 REMARK 465 SER A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 ASP A 4 REMARK 465 LEU A 5 REMARK 465 PRO A 6 REMARK 465 LYS A 7 REMARK 465 SER A 8 REMARK 465 ASN A 9 REMARK 465 LYS A 10 REMARK 465 ASN A 11 REMARK 465 GLN A 151 REMARK 465 GLN A 152 REMARK 465 MET A 231 REMARK 465 ASN A 232 REMARK 465 ALA A 519 REMARK 465 ASP A 520 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 116 CG CD CE NZ REMARK 480 LYS A 120 CE NZ REMARK 480 ASP A 127 CG OD1 OD2 REMARK 480 GLN A 131 CG CD OE1 NE2 REMARK 480 GLU A 138 CG CD OE1 OE2 REMARK 480 GLU A 238 CD OE1 OE2 REMARK 480 ARG A 303 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 363 CG CD OE1 OE2 REMARK 480 ASN A 493 CG OD1 ND2 REMARK 480 LYS A 513 CG CD CE NZ 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 ASN A 13 -2.97 73.97 REMARK 500 ASP A 81 90.20 -161.29 REMARK 500 HIS A 108 34.30 -151.35 REMARK 500 ASP A 127 -143.46 52.22 REMARK 500 ASP A 169 83.83 -155.95 REMARK 500 VAL A 342 -53.54 -130.53 REMARK 500 SER A 379 -13.87 78.29 REMARK 500 SER A 379 -11.66 76.42 REMARK 500 TRP A 432 -31.44 -140.59 REMARK 500 SER A 435 18.11 -146.62 REMARK 500 ASP A 439 -120.61 48.37 REMARK 500 LYS A 474 -124.94 58.22 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 A1108 DISTANCE = 6.83 ANGSTROMS 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 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 213 OD1 REMARK 620 2 GLU A 427 OE1 88.1 REMARK 620 3 UDP A 601 O1A 79.4 162.8 REMARK 620 4 UDP A 601 O1B 165.4 105.8 86.0 REMARK 620 5 HOH A 734 O 91.7 87.4 104.7 93.0 REMARK 620 6 HOH A 786 O 90.1 83.6 84.6 87.5 170.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 603 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 213 OD1 REMARK 620 2 GLU A 426 O 86.5 REMARK 620 3 PHE A 429 O 145.8 78.1 REMARK 620 4 UDP A 601 O1A 61.0 142.4 117.5 REMARK 620 5 HOH A 727 O 112.4 79.5 94.8 128.5 REMARK 620 6 HOH A 786 O 69.7 91.0 80.1 61.4 170.0 REMARK 620 7 HOH A 909 O 120.1 143.4 88.7 73.8 67.7 120.4 REMARK 620 8 HOH A1055 O 89.5 119.7 124.6 81.2 47.4 142.3 44.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 611 DBREF 6RTG A 2 520 UNP C4SH25 C4SH25_YERMW 2 520 SEQADV 6RTG GLY A 0 UNP C4SH25 EXPRESSION TAG SEQADV 6RTG SER A 1 UNP C4SH25 EXPRESSION TAG SEQRES 1 A 521 GLY SER SER THR ASP LEU PRO LYS SER ASN LYS ASN ASN SEQRES 2 A 521 ASN PHE ILE THR HIS ASN LEU HIS THR VAL TRP ILE GLY SEQRES 3 A 521 GLY PRO LEU PRO ASP ILE THR LYS SER TYR LEU LYS VAL SEQRES 4 A 521 TRP ARG ASP ILE ASN PRO ASP TYR THR HIS ILE THR TRP SEQRES 5 A 521 ILE ASP THR ASP ASN LYS PHE VAL ALA LEU TYR ASN ASN SEQRES 6 A 521 ALA VAL LYS GLU LEU ARG GLU TYR THR LEU LYS GLN TYR SEQRES 7 A 521 LEU VAL GLY ASP SER ASN ALA THR ALA ASN ASP TYR TYR SEQRES 8 A 521 ASP GLN ALA VAL GLN ILE GLU ARG GLY VAL ARG GLU ASN SEQRES 9 A 521 VAL TYR LEU PRO HIS GLY ASN ASP ILE GLU ARG ILE LYS SEQRES 10 A 521 THR ILE LYS LYS ILE ALA GLY SER LEU GLY ASP ASN LYS SEQRES 11 A 521 VAL GLN GLU TYR ARG THR LYS ILE GLU THR ILE GLU SER SEQRES 12 A 521 SER PHE VAL GLU MET ILE ASP GLY GLN GLN GLY HIS TYR SEQRES 13 A 521 GLN HIS VAL SER ALA LEU PHE GLU GLN PHE SER GLU MET SEQRES 14 A 521 ASP ASN LEU ARG ALA THR ALA LEU LYS GLN ILE TYR GLU SEQRES 15 A 521 ARG GLU ILE ASN ASP ARG GLY ASN LEU ALA ALA ALA SER SEQRES 16 A 521 ASP ILE LEU ARG LEU VAL ALA LEU GLN THR GLN GLY GLY SEQRES 17 A 521 VAL TYR ILE ASP THR ASP LEU LEU PRO HIS ILE ASP TRP SEQRES 18 A 521 ASP LEU ILE GLU SER THR LYS LEU PHE LEU MET ASN ASP SEQRES 19 A 521 ASN ASN SER VAL GLU ARG VAL TYR SER LYS GLU ILE TYR SEQRES 20 A 521 LEU GLU ILE GLU LYS TYR LYS GLN LEU THR GLY SER LYS SEQRES 21 A 521 THR ASN LYS ILE ARG SER GLY LEU THR LYS SER GLN ILE SEQRES 22 A 521 ASN GLU ILE GLN ARG LEU THR GLU GLU ASN ASN LEU PHE SEQRES 23 A 521 LYS HIS LEU ASN GLU LEU GLU LYS ASN CYS PHE TYR SER SEQRES 24 A 521 ASP ASN SER VAL ARG GLY TRP THR ASN ALA MET LEU ALA SEQRES 25 A 521 CYS ASN GLU ASN ASN GLY PHE MET ASN ALA LEU MET ASP SEQRES 26 A 521 ARG ILE ILE LEU ASN TYR THR ILE LEU ASP GLU PHE ILE SEQRES 27 A 521 ILE SER ASN ILE VAL THR ASP GLY GLU MET LEU ASN PHE SEQRES 28 A 521 THR GLU LYS MET SER ALA GLN PHE GLY LEU ASN ALA GLU SEQRES 29 A 521 HIS GLU GLY SER PHE ILE PRO SER LEU ALA ASN TYR TYR SEQRES 30 A 521 LYS ASP SER ILE VAL PRO ASN SER PRO GLN ALA THR ALA SEQRES 31 A 521 THR LEU PHE MET THR GLY PRO THR VAL LEU ASP THR VAL SEQRES 32 A 521 ILE ARG VAL GLU GLU ALA VAL ARG ARG GLY ILE VAL LYS SEQRES 33 A 521 LYS GLU ALA ILE ALA SER LEU TYR THR VAL GLU GLU THR SEQRES 34 A 521 PHE SER SER TRP SER ILE SER GLN PHE TYR ASP LYS ALA SEQRES 35 A 521 ALA PHE TYR LEU ASP LYS VAL LYS PHE ASP ILE SER LEU SEQRES 36 A 521 ASN SER ALA GLU GLU GLY ILE LEU ARG ASP SER CYS PHE SEQRES 37 A 521 ASP VAL ILE GLN GLN SER LYS GLU GLN ALA THR HIS LEU SEQRES 38 A 521 PRO ASP ILE ALA ILE LYS PHE LEU GLU SER LEU ASN ASN SEQRES 39 A 521 PHE THR TRP LYS GLN LEU GLU LEU LEU ILE LYS ALA SER SEQRES 40 A 521 GLU PHE SER ASP GLN TYR LYS THR LEU ALA THR LEU ALA SEQRES 41 A 521 ASP HET UDP A 601 25 HET MN A 602 1 HET K A 603 1 HET EDO A 604 4 HET EDO A 605 4 HET EDO A 606 4 HET EDO A 607 4 HET EDO A 608 4 HET EDO A 609 4 HET EDO A 610 4 HET EDO A 611 4 HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 UDP C9 H14 N2 O12 P2 FORMUL 3 MN MN 2+ FORMUL 4 K K 1+ FORMUL 5 EDO 8(C2 H6 O2) FORMUL 13 HOH *408(H2 O) HELIX 1 AA1 PRO A 29 ASN A 43 1 15 HELIX 2 AA2 PHE A 58 GLY A 80 1 23 HELIX 3 AA3 THR A 85 GLU A 102 1 18 HELIX 4 AA4 ASN A 110 GLY A 126 1 17 HELIX 5 AA5 ASN A 128 GLY A 150 1 23 HELIX 6 AA6 VAL A 158 GLU A 167 1 10 HELIX 7 AA7 ASP A 169 ASP A 186 1 18 HELIX 8 AA8 ASN A 189 GLY A 206 1 18 HELIX 9 AA9 ASP A 219 SER A 225 1 7 HELIX 10 AB1 SER A 236 GLN A 254 1 19 HELIX 11 AB2 LYS A 259 ILE A 263 5 5 HELIX 12 AB3 THR A 268 GLU A 281 1 14 HELIX 13 AB4 ASN A 316 ASN A 340 1 25 HELIX 14 AB5 THR A 343 PHE A 358 1 16 HELIX 15 AB6 GLU A 363 GLY A 366 5 4 HELIX 16 AB7 SER A 367 LEU A 372 1 6 HELIX 17 AB8 ALA A 373 TYR A 375 5 3 HELIX 18 AB9 SER A 384 ALA A 387 5 4 HELIX 19 AC1 THR A 388 THR A 394 1 7 HELIX 20 AC2 GLY A 395 GLU A 406 1 12 HELIX 21 AC3 VAL A 425 PHE A 429 5 5 HELIX 22 AC4 TYR A 438 PHE A 450 1 13 HELIX 23 AC5 ASN A 455 LYS A 474 1 20 HELIX 24 AC6 PRO A 481 LEU A 491 1 11 HELIX 25 AC7 THR A 495 SER A 509 1 15 HELIX 26 AC8 ASP A 510 LYS A 513 5 4 SHEET 1 AA1 7 TYR A 155 HIS A 157 0 SHEET 2 AA1 7 THR A 47 ILE A 52 1 N ILE A 52 O GLN A 156 SHEET 3 AA1 7 ASN A 18 VAL A 22 1 N LEU A 19 O THR A 47 SHEET 4 AA1 7 GLY A 207 ILE A 210 1 O VAL A 208 N HIS A 20 SHEET 5 AA1 7 THR A 306 CYS A 312 -1 O LEU A 310 N TYR A 209 SHEET 6 AA1 7 PHE A 296 ASP A 299 -1 N TYR A 297 O ALA A 311 SHEET 7 AA1 7 VAL A 414 LYS A 416 1 O LYS A 415 N PHE A 296 LINK OD1 ASP A 213 MN MN A 602 1555 1555 2.25 LINK OD1 ASP A 213 K K A 603 1555 1555 2.61 LINK O GLU A 426 K K A 603 1555 1555 2.94 LINK OE1 GLU A 427 MN MN A 602 1555 1555 2.27 LINK O PHE A 429 K K A 603 1555 1555 2.65 LINK O1A UDP A 601 MN MN A 602 1555 1555 2.28 LINK O1B UDP A 601 MN MN A 602 1555 1555 2.12 LINK O1A UDP A 601 K K A 603 1555 1555 3.04 LINK MN MN A 602 O HOH A 734 1555 1555 2.22 LINK MN MN A 602 O HOH A 786 1555 1555 2.30 LINK K K A 603 O HOH A 727 1555 1555 3.00 LINK K K A 603 O HOH A 786 1555 1555 2.99 LINK K K A 603 O HOH A 909 1555 1555 3.31 LINK K K A 603 O HOH A1055 1555 1555 3.05 SITE 1 AC1 25 VAL A 22 TRP A 23 ILE A 24 LEU A 190 SITE 2 AC1 25 ALA A 191 SER A 194 TYR A 209 ASP A 211 SITE 3 AC1 25 THR A 212 ASP A 213 GLU A 427 SER A 430 SITE 4 AC1 25 SER A 431 TRP A 432 MN A 602 K A 603 SITE 5 AC1 25 EDO A 604 EDO A 605 HOH A 705 HOH A 741 SITE 6 AC1 25 HOH A 771 HOH A 786 HOH A 894 HOH A 909 SITE 7 AC1 25 HOH A 918 SITE 1 AC2 6 ASP A 213 GLU A 427 UDP A 601 K A 603 SITE 2 AC2 6 HOH A 734 HOH A 786 SITE 1 AC3 8 ASP A 213 GLU A 426 PHE A 429 UDP A 601 SITE 2 AC3 8 MN A 602 HOH A 727 HOH A 786 HOH A1055 SITE 1 AC4 5 TRP A 432 UDP A 601 HOH A 705 HOH A 731 SITE 2 AC4 5 HOH A 800 SITE 1 AC5 9 ALA A 191 ASP A 195 THR A 390 GLY A 395 SITE 2 AC5 9 PRO A 396 TRP A 432 UDP A 601 HOH A 703 SITE 3 AC5 9 HOH A 704 SITE 1 AC6 4 LYS A 259 PHE A 429 GLN A 511 HOH A 735 SITE 1 AC7 6 LEU A 36 ARG A 40 HIS A 48 THR A 50 SITE 2 AC7 6 HOH A 711 HOH A 759 SITE 1 AC8 5 TYR A 46 THR A 47 HIS A 48 GLY A 153 SITE 2 AC8 5 HIS A 154 SITE 1 AC9 10 VAL A 302 ARG A 303 GLY A 304 TRP A 305 SITE 2 AC9 10 THR A 306 GLN A 386 LEU A 391 PRO A 396 SITE 3 AC9 10 HOH A 702 HOH A 817 SITE 1 AD1 7 ILE A 52 ASP A 53 THR A 54 ASP A 55 SITE 2 AD1 7 HIS A 157 VAL A 158 SER A 159 SITE 1 AD2 5 ASP A 30 LYS A 33 SER A 34 THR A 256 SITE 2 AD2 5 HOH A 841 CRYST1 164.270 164.270 47.740 90.00 90.00 90.00 P 43 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 0.006088 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020947 0.00000 CONECT 1658 4185 4186 CONECT 3389 4186 CONECT 3402 4185 CONECT 3414 4186 CONECT 4160 4161 4165 4168 CONECT 4161 4160 4162 4166 CONECT 4162 4161 4163 CONECT 4163 4162 4164 4167 CONECT 4164 4163 4165 CONECT 4165 4160 4164 CONECT 4166 4161 CONECT 4167 4163 CONECT 4168 4160 4169 4173 CONECT 4169 4168 4170 4171 CONECT 4170 4169 CONECT 4171 4169 4172 4174 CONECT 4172 4171 4173 4175 CONECT 4173 4168 4172 CONECT 4174 4171 CONECT 4175 4172 4176 CONECT 4176 4175 4177 CONECT 4177 4176 4178 4179 4180 CONECT 4178 4177 4185 4186 CONECT 4179 4177 CONECT 4180 4177 4181 CONECT 4181 4180 4182 4183 4184 CONECT 4182 4181 4185 CONECT 4183 4181 CONECT 4184 4181 CONECT 4185 1658 3402 4178 4182 CONECT 4185 4253 4305 CONECT 4186 1658 3389 3414 4178 CONECT 4186 4246 4305 4430 4577 CONECT 4187 4188 4189 CONECT 4188 4187 CONECT 4189 4187 4190 CONECT 4190 4189 CONECT 4191 4192 4193 CONECT 4192 4191 CONECT 4193 4191 4194 CONECT 4194 4193 CONECT 4195 4196 4197 CONECT 4196 4195 CONECT 4197 4195 4198 CONECT 4198 4197 CONECT 4199 4200 4201 CONECT 4200 4199 CONECT 4201 4199 4202 CONECT 4202 4201 CONECT 4203 4204 4205 CONECT 4204 4203 CONECT 4205 4203 4206 CONECT 4206 4205 CONECT 4207 4208 4209 CONECT 4208 4207 CONECT 4209 4207 4210 CONECT 4210 4209 CONECT 4211 4212 4213 CONECT 4212 4211 CONECT 4213 4211 4214 CONECT 4214 4213 CONECT 4215 4216 4217 CONECT 4216 4215 CONECT 4217 4215 4218 CONECT 4218 4217 CONECT 4246 4186 CONECT 4253 4185 CONECT 4305 4185 4186 CONECT 4430 4186 CONECT 4577 4186 MASTER 491 0 11 26 7 0 28 6 4535 1 70 41 END