HEADER TRANSFERASE 08-FEB-17 5UQM TITLE CLOSTRIDIUM DIFFICILE TOXIN B (TCDB) GLUCOSYLTRANSFERASE DOMAIN IN TITLE 2 COMPLEX WITH U2F COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOXIN B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-543; COMPND 5 EC: 3.4.22.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIOIDES DIFFICILE; SOURCE 3 ORGANISM_TAXID: 1496; SOURCE 4 GENE: TOXB, TCDB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 STAR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS GLUCOSYLTRANSFERASE, TOXIN, HYDROLASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.W.ALVIN,D.B.LACY REVDAT 5 04-OCT-23 5UQM 1 LINK REVDAT 4 11-DEC-19 5UQM 1 REMARK REVDAT 3 20-SEP-17 5UQM 1 REMARK REVDAT 2 14-JUN-17 5UQM 1 JRNL REVDAT 1 10-MAY-17 5UQM 0 JRNL AUTH J.W.ALVIN,D.B.LACY JRNL TITL CLOSTRIDIUM DIFFICILE TOXIN GLUCOSYLTRANSFERASE DOMAINS IN JRNL TITL 2 COMPLEX WITH A NON-HYDROLYZABLE UDP-GLUCOSE ANALOGUE. JRNL REF J. STRUCT. BIOL. V. 198 203 2017 JRNL REFN ESSN 1095-8657 JRNL PMID 28433497 JRNL DOI 10.1016/J.JSB.2017.04.006 REMARK 2 REMARK 2 RESOLUTION. 2.03 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 42208 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 42.2877 - 4.8904 0.98 3143 157 0.2004 0.2597 REMARK 3 2 4.8904 - 3.8825 0.99 2970 148 0.1562 0.1745 REMARK 3 3 3.8825 - 3.3920 1.00 2931 146 0.1748 0.2219 REMARK 3 4 3.3920 - 3.0820 1.00 2898 143 0.1982 0.2237 REMARK 3 5 3.0820 - 2.8611 1.00 2900 145 0.1985 0.2287 REMARK 3 6 2.8611 - 2.6924 1.00 2847 141 0.2168 0.2071 REMARK 3 7 2.6924 - 2.5576 1.00 2872 143 0.2154 0.2692 REMARK 3 8 2.5576 - 2.4463 1.00 2851 141 0.2140 0.2583 REMARK 3 9 2.4463 - 2.3521 1.00 2846 142 0.2181 0.2214 REMARK 3 10 2.3521 - 2.2710 1.00 2838 140 0.2171 0.2428 REMARK 3 11 2.2710 - 2.2000 1.00 2799 139 0.2109 0.2577 REMARK 3 12 2.2000 - 2.1371 1.00 2807 141 0.2293 0.2480 REMARK 3 13 2.1371 - 2.0808 0.99 2813 139 0.2411 0.2527 REMARK 3 14 2.0808 - 2.0301 0.95 2694 134 0.2568 0.2574 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) : 21.430 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 : 0.014 4582 REMARK 3 ANGLE : 1.264 6198 REMARK 3 CHIRALITY : 0.072 678 REMARK 3 PLANARITY : 0.007 801 REMARK 3 DIHEDRAL : 16.346 2778 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.0149 24.1819 -3.4309 REMARK 3 T TENSOR REMARK 3 T11: 0.4380 T22: 0.3936 REMARK 3 T33: 0.6173 T12: 0.1736 REMARK 3 T13: -0.0718 T23: -0.1445 REMARK 3 L TENSOR REMARK 3 L11: 0.5208 L22: 2.1525 REMARK 3 L33: 1.7106 L12: -0.1424 REMARK 3 L13: -0.0379 L23: -1.0655 REMARK 3 S TENSOR REMARK 3 S11: -0.2771 S12: -0.2402 S13: 0.8698 REMARK 3 S21: 0.2588 S22: 0.0288 S23: 0.5994 REMARK 3 S31: -0.6763 S32: -0.6164 S33: -0.0012 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 137 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8438 10.9673 -16.3032 REMARK 3 T TENSOR REMARK 3 T11: 0.1734 T22: 0.3329 REMARK 3 T33: 0.1786 T12: -0.0871 REMARK 3 T13: -0.0894 T23: 0.0708 REMARK 3 L TENSOR REMARK 3 L11: 1.1631 L22: 0.9491 REMARK 3 L33: 1.4960 L12: 0.2454 REMARK 3 L13: -0.4822 L23: 0.3635 REMARK 3 S TENSOR REMARK 3 S11: 0.0566 S12: 0.4016 S13: 0.1889 REMARK 3 S21: -0.1867 S22: -0.1505 S23: -0.0788 REMARK 3 S31: -0.3085 S32: 0.2700 S33: 0.0778 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 138 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7283 -21.6042 -33.2382 REMARK 3 T TENSOR REMARK 3 T11: 0.2997 T22: 0.3454 REMARK 3 T33: 0.4266 T12: 0.0716 REMARK 3 T13: 0.0523 T23: -0.1426 REMARK 3 L TENSOR REMARK 3 L11: 2.0023 L22: 1.4576 REMARK 3 L33: 7.1564 L12: 1.1832 REMARK 3 L13: 0.3862 L23: -0.3069 REMARK 3 S TENSOR REMARK 3 S11: -0.0097 S12: 0.2806 S13: -0.3756 REMARK 3 S21: -0.0078 S22: 0.0268 S23: 0.1012 REMARK 3 S31: 0.6900 S32: -0.1250 S33: -0.0243 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 197 THROUGH 264 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.6641 -14.2299 -15.5774 REMARK 3 T TENSOR REMARK 3 T11: 0.2055 T22: 0.3074 REMARK 3 T33: 0.2747 T12: 0.0500 REMARK 3 T13: 0.0017 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 2.1092 L22: 2.1760 REMARK 3 L33: 2.5201 L12: 0.1169 REMARK 3 L13: 0.6849 L23: 0.7108 REMARK 3 S TENSOR REMARK 3 S11: 0.1007 S12: 0.1475 S13: -0.3084 REMARK 3 S21: 0.1790 S22: -0.0503 S23: -0.1958 REMARK 3 S31: 0.3641 S32: 0.4111 S33: 0.0011 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 265 THROUGH 366 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.9825 13.8009 -33.0425 REMARK 3 T TENSOR REMARK 3 T11: 0.2412 T22: 0.6383 REMARK 3 T33: 0.3096 T12: -0.0976 REMARK 3 T13: 0.0060 T23: 0.0994 REMARK 3 L TENSOR REMARK 3 L11: 0.9790 L22: 0.8390 REMARK 3 L33: 1.8114 L12: -0.1738 REMARK 3 L13: -0.5746 L23: -0.3530 REMARK 3 S TENSOR REMARK 3 S11: 0.0749 S12: 0.3600 S13: 0.1394 REMARK 3 S21: -0.1360 S22: -0.1617 S23: -0.2151 REMARK 3 S31: -0.2398 S32: 0.5368 S33: 0.0359 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 367 THROUGH 455 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.4791 -2.4562 -20.5904 REMARK 3 T TENSOR REMARK 3 T11: 0.1280 T22: 0.2731 REMARK 3 T33: 0.2262 T12: -0.0158 REMARK 3 T13: 0.0037 T23: -0.0656 REMARK 3 L TENSOR REMARK 3 L11: 1.1434 L22: 2.5656 REMARK 3 L33: 1.7155 L12: 0.8198 REMARK 3 L13: 0.4514 L23: 1.0044 REMARK 3 S TENSOR REMARK 3 S11: -0.0182 S12: 0.1962 S13: -0.0598 REMARK 3 S21: -0.0012 S22: -0.1517 S23: 0.2595 REMARK 3 S31: 0.1223 S32: -0.1275 S33: 0.1257 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 456 THROUGH 507 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.0124 7.7415 -22.9141 REMARK 3 T TENSOR REMARK 3 T11: 0.1604 T22: 0.2826 REMARK 3 T33: 0.2096 T12: -0.0075 REMARK 3 T13: -0.0386 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 1.8147 L22: 1.0964 REMARK 3 L33: 1.6429 L12: -0.7728 REMARK 3 L13: -0.5388 L23: 0.1437 REMARK 3 S TENSOR REMARK 3 S11: -0.0327 S12: 0.4392 S13: 0.0735 REMARK 3 S21: -0.0754 S22: -0.1390 S23: 0.1968 REMARK 3 S31: -0.1832 S32: -0.1048 S33: 0.1949 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 508 THROUGH 543 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0026 -7.9874 -39.8371 REMARK 3 T TENSOR REMARK 3 T11: 0.2767 T22: 0.5756 REMARK 3 T33: 0.2774 T12: 0.0226 REMARK 3 T13: 0.0277 T23: -0.0810 REMARK 3 L TENSOR REMARK 3 L11: 0.5408 L22: 4.1771 REMARK 3 L33: 3.0089 L12: 0.1361 REMARK 3 L13: 0.1023 L23: 3.5863 REMARK 3 S TENSOR REMARK 3 S11: 0.0383 S12: 0.2810 S13: -0.1619 REMARK 3 S21: -0.2954 S22: -0.2589 S23: 0.0382 REMARK 3 S31: -0.0309 S32: 0.0453 S33: 0.2070 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 5UQM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1000225977. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6-6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42362 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 53.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 2BVL REMARK 200 REMARK 200 REMARK: SHORT BARS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 0.2 AMMONIUM SULFATE, PEG REMARK 280 8K 16-34%, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 162.99000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.95500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.95500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 81.49500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.95500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.95500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 244.48500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.95500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.95500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 81.49500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.95500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.95500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 244.48500 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 162.99000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 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 908 O HOH A 950 1.12 REMARK 500 HZ3 LYS A 391 O HOH A 701 1.36 REMARK 500 HH11 ARG A 262 O HOH A 715 1.52 REMARK 500 HE ARG A 499 O HOH A 710 1.55 REMARK 500 O ILE A 58 HG1 THR A 62 1.56 REMARK 500 HZ3 LYS A 322 O HOH A 721 1.58 REMARK 500 OE2 GLU A 21 HH TYR A 59 1.58 REMARK 500 O HOH A 880 O HOH A 945 1.82 REMARK 500 NZ LYS A 391 O HOH A 701 1.91 REMARK 500 OD2 ASP A 57 O HOH A 702 2.00 REMARK 500 O GLU A 318 O HOH A 703 2.05 REMARK 500 O LYS A 322 O HOH A 704 2.06 REMARK 500 OD2 ASP A 336 O HOH A 705 2.08 REMARK 500 O HOH A 921 O HOH A 931 2.10 REMARK 500 O HOH A 887 O HOH A 940 2.11 REMARK 500 O HOH A 913 O HOH A 970 2.11 REMARK 500 O GLY A 67 O HOH A 706 2.13 REMARK 500 OG SER A 275 O HOH A 707 2.17 REMARK 500 OG SER A 38 O HOH A 708 2.19 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 O PHE A 17 HG1 THR A 19 7465 1.47 REMARK 500 OD2 ASP A 22 HD21 ASN A 197 7555 1.58 REMARK 500 O PHE A 17 OG1 THR A 19 7465 1.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 247 C LYS A 247 O -0.132 REMARK 500 ASP A 442 CA ASP A 442 CB -0.139 REMARK 500 GLY A 444 C GLY A 444 O -0.146 REMARK 500 GLU A 515 CD GLU A 515 OE1 -0.066 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 168 CA - C - O ANGL. DEV. = -12.8 DEGREES REMARK 500 TYR A 168 CA - C - N ANGL. DEV. = 13.5 DEGREES REMARK 500 ASN A 169 C - N - CA ANGL. DEV. = -24.3 DEGREES REMARK 500 ASP A 339 CB - CA - C ANGL. DEV. = -15.4 DEGREES REMARK 500 ASP A 442 CB - CG - OD1 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASP A 442 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES 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 13 30.61 -92.27 REMARK 500 ASN A 160 32.16 -93.06 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 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 288 OD2 REMARK 620 2 GLU A 515 OE1 95.9 REMARK 620 3 U2F A 602 O2B 160.1 96.5 REMARK 620 4 U2F A 602 O2A 80.0 162.0 83.5 REMARK 620 5 HOH A 725 O 96.3 84.8 100.3 112.9 REMARK 620 6 HOH A 790 O 86.2 83.3 79.8 79.0 168.0 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 MN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U2F A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UQN RELATED DB: PDB REMARK 900 RELATED ID: 5UQK RELATED DB: PDB REMARK 900 RELATED ID: 5UQL RELATED DB: PDB REMARK 900 RELATED ID: 5UQT RELATED DB: PDB DBREF 5UQM A 1 543 UNP P18177 TOXB_CLODI 1 543 SEQADV 5UQM MET A -19 UNP P18177 INITIATING METHIONINE SEQADV 5UQM GLY A -18 UNP P18177 EXPRESSION TAG SEQADV 5UQM SER A -17 UNP P18177 EXPRESSION TAG SEQADV 5UQM SER A -16 UNP P18177 EXPRESSION TAG SEQADV 5UQM HIS A -15 UNP P18177 EXPRESSION TAG SEQADV 5UQM HIS A -14 UNP P18177 EXPRESSION TAG SEQADV 5UQM HIS A -13 UNP P18177 EXPRESSION TAG SEQADV 5UQM HIS A -12 UNP P18177 EXPRESSION TAG SEQADV 5UQM HIS A -11 UNP P18177 EXPRESSION TAG SEQADV 5UQM HIS A -10 UNP P18177 EXPRESSION TAG SEQADV 5UQM SER A -9 UNP P18177 EXPRESSION TAG SEQADV 5UQM SER A -8 UNP P18177 EXPRESSION TAG SEQADV 5UQM GLY A -7 UNP P18177 EXPRESSION TAG SEQADV 5UQM LEU A -6 UNP P18177 EXPRESSION TAG SEQADV 5UQM VAL A -5 UNP P18177 EXPRESSION TAG SEQADV 5UQM PRO A -4 UNP P18177 EXPRESSION TAG SEQADV 5UQM ARG A -3 UNP P18177 EXPRESSION TAG SEQADV 5UQM GLY A -2 UNP P18177 EXPRESSION TAG SEQADV 5UQM SER A -1 UNP P18177 EXPRESSION TAG SEQADV 5UQM HIS A 0 UNP P18177 EXPRESSION TAG SEQRES 1 A 563 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 563 LEU VAL PRO ARG GLY SER HIS MET SER LEU VAL ASN ARG SEQRES 3 A 563 LYS GLN LEU GLU LYS MET ALA ASN VAL ARG PHE ARG THR SEQRES 4 A 563 GLN GLU ASP GLU TYR VAL ALA ILE LEU ASP ALA LEU GLU SEQRES 5 A 563 GLU TYR HIS ASN MET SER GLU ASN THR VAL VAL GLU LYS SEQRES 6 A 563 TYR LEU LYS LEU LYS ASP ILE ASN SER LEU THR ASP ILE SEQRES 7 A 563 TYR ILE ASP THR TYR LYS LYS SER GLY ARG ASN LYS ALA SEQRES 8 A 563 LEU LYS LYS PHE LYS GLU TYR LEU VAL THR GLU VAL LEU SEQRES 9 A 563 GLU LEU LYS ASN ASN ASN LEU THR PRO VAL GLU LYS ASN SEQRES 10 A 563 LEU HIS PHE VAL TRP ILE GLY GLY GLN ILE ASN ASP THR SEQRES 11 A 563 ALA ILE ASN TYR ILE ASN GLN TRP LYS ASP VAL ASN SER SEQRES 12 A 563 ASP TYR ASN VAL ASN VAL PHE TYR ASP SER ASN ALA PHE SEQRES 13 A 563 LEU ILE ASN THR LEU LYS LYS THR VAL VAL GLU SER ALA SEQRES 14 A 563 ILE ASN ASP THR LEU GLU SER PHE ARG GLU ASN LEU ASN SEQRES 15 A 563 ASP PRO ARG PHE ASP TYR ASN LYS PHE PHE ARG LYS ARG SEQRES 16 A 563 MET GLU ILE ILE TYR ASP LYS GLN LYS ASN PHE ILE ASN SEQRES 17 A 563 TYR TYR LYS ALA GLN ARG GLU GLU ASN PRO GLU LEU ILE SEQRES 18 A 563 ILE ASP ASP ILE VAL LYS THR TYR LEU SER ASN GLU TYR SEQRES 19 A 563 SER LYS GLU ILE ASP GLU LEU ASN THR TYR ILE GLU GLU SEQRES 20 A 563 SER LEU ASN LYS ILE THR GLN ASN SER GLY ASN ASP VAL SEQRES 21 A 563 ARG ASN PHE GLU GLU PHE LYS ASN GLY GLU SER PHE ASN SEQRES 22 A 563 LEU TYR GLU GLN GLU LEU VAL GLU ARG TRP ASN LEU ALA SEQRES 23 A 563 ALA ALA SER ASP ILE LEU ARG ILE SER ALA LEU LYS GLU SEQRES 24 A 563 ILE GLY GLY MET TYR LEU ASP VAL ASP MET LEU PRO GLY SEQRES 25 A 563 ILE GLN PRO ASP LEU PHE GLU SER ILE GLU LYS PRO SER SEQRES 26 A 563 SER VAL THR VAL ASP PHE TRP GLU MET THR LYS LEU GLU SEQRES 27 A 563 ALA ILE MET LYS TYR LYS GLU TYR ILE PRO GLU TYR THR SEQRES 28 A 563 SER GLU HIS PHE ASP MET LEU ASP GLU GLU VAL GLN SER SEQRES 29 A 563 SER PHE GLU SER VAL LEU ALA SER LYS SER ASP LYS SER SEQRES 30 A 563 GLU ILE PHE SER SER LEU GLY ASP MET GLU ALA SER PRO SEQRES 31 A 563 LEU GLU VAL LYS ILE ALA PHE ASN SER LYS GLY ILE ILE SEQRES 32 A 563 ASN GLN GLY LEU ILE SER VAL LYS ASP SER TYR CYS SER SEQRES 33 A 563 ASN LEU ILE VAL LYS GLN ILE GLU ASN ARG TYR LYS ILE SEQRES 34 A 563 LEU ASN ASN SER LEU ASN PRO ALA ILE SER GLU ASP ASN SEQRES 35 A 563 ASP PHE ASN THR THR THR ASN THR PHE ILE ASP SER ILE SEQRES 36 A 563 MET ALA GLU ALA ASN ALA ASP ASN GLY ARG PHE MET MET SEQRES 37 A 563 GLU LEU GLY LYS TYR LEU ARG VAL GLY PHE PHE PRO ASP SEQRES 38 A 563 VAL LYS THR THR ILE ASN LEU SER GLY PRO GLU ALA TYR SEQRES 39 A 563 ALA ALA ALA TYR GLN ASP LEU LEU MET PHE LYS GLU GLY SEQRES 40 A 563 SER MET ASN ILE HIS LEU ILE GLU ALA ASP LEU ARG ASN SEQRES 41 A 563 PHE GLU ILE SER LYS THR ASN ILE SER GLN SER THR GLU SEQRES 42 A 563 GLN GLU MET ALA SER LEU TRP SER PHE ASP ASP ALA ARG SEQRES 43 A 563 ALA LYS ALA GLN PHE GLU GLU TYR LYS ARG ASN TYR PHE SEQRES 44 A 563 GLU GLY SER LEU HET MN A 601 1 HET U2F A 602 57 HET SO4 A 603 5 HET SO4 A 604 5 HETNAM MN MANGANESE (II) ION HETNAM U2F URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE HETNAM SO4 SULFATE ION FORMUL 2 MN MN 2+ FORMUL 3 U2F C15 H23 F N2 O16 P2 FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 HOH *270(H2 O) HELIX 1 AA1 ASN A 5 ALA A 13 1 9 HELIX 2 AA2 GLU A 21 HIS A 35 1 15 HELIX 3 AA3 THR A 41 TYR A 63 1 23 HELIX 4 AA4 ARG A 68 ASN A 90 1 23 HELIX 5 AA5 ASN A 108 ASN A 122 1 15 HELIX 6 AA6 LEU A 137 PHE A 157 1 21 HELIX 7 AA7 ASP A 167 ASN A 197 1 31 HELIX 8 AA8 ILE A 201 SER A 215 1 15 HELIX 9 AA9 GLU A 217 GLN A 234 1 18 HELIX 10 AB1 PHE A 243 GLY A 249 1 7 HELIX 11 AB2 SER A 251 GLU A 261 1 11 HELIX 12 AB3 ASN A 264 GLY A 281 1 18 HELIX 13 AB4 THR A 308 GLU A 325 1 18 HELIX 14 AB5 HIS A 334 LEU A 338 5 5 HELIX 15 AB6 ASP A 339 SER A 352 1 14 HELIX 16 AB7 ASP A 355 ILE A 359 5 5 HELIX 17 AB8 SER A 393 GLU A 420 1 28 HELIX 18 AB9 ASP A 423 GLU A 438 1 16 HELIX 19 AC1 ASN A 443 GLY A 451 1 9 HELIX 20 AC2 LYS A 452 VAL A 456 5 5 HELIX 21 AC3 LYS A 463 SER A 469 1 7 HELIX 22 AC4 GLY A 470 PHE A 484 1 15 HELIX 23 AC5 ILE A 494 ASN A 500 1 7 HELIX 24 AC6 SER A 504 THR A 506 5 3 HELIX 25 AC7 GLU A 513 ALA A 517 5 5 HELIX 26 AC8 ASP A 523 GLU A 540 1 18 SHEET 1 AA1 2 THR A 92 PRO A 93 0 SHEET 2 AA1 2 GLU A 367 ALA A 368 -1 O ALA A 368 N THR A 92 SHEET 1 AA2 6 GLY A 237 ASP A 239 0 SHEET 2 AA2 6 ASN A 126 TYR A 131 1 N VAL A 129 O ASN A 238 SHEET 3 AA2 6 ASN A 97 VAL A 101 1 N PHE A 100 O PHE A 130 SHEET 4 AA2 6 GLY A 282 LEU A 285 1 O MET A 283 N HIS A 99 SHEET 5 AA2 6 GLY A 381 SER A 389 -1 O SER A 389 N GLY A 282 SHEET 6 AA2 6 LYS A 374 ASN A 378 -1 N LYS A 374 O ILE A 388 SHEET 1 AA3 2 LEU A 290 PRO A 291 0 SHEET 2 AA3 2 ILE A 508 SER A 509 -1 O SER A 509 N LEU A 290 LINK OD2 ASP A 288 MN MN A 601 1555 1555 2.41 LINK OE1 GLU A 515 MN MN A 601 1555 1555 2.60 LINK MN MN A 601 O2B U2F A 602 1555 1555 2.34 LINK MN MN A 601 O2A U2F A 602 1555 1555 2.09 LINK MN MN A 601 O HOH A 725 1555 1555 2.16 LINK MN MN A 601 O HOH A 790 1555 1555 2.23 SITE 1 AC1 5 ASP A 288 GLU A 515 U2F A 602 HOH A 725 SITE 2 AC1 5 HOH A 790 SITE 1 AC2 27 VAL A 101 TRP A 102 ILE A 103 ASN A 139 SITE 2 AC2 27 LEU A 265 ALA A 266 SER A 269 ASP A 270 SITE 3 AC2 27 ARG A 273 TYR A 284 ASP A 286 VAL A 287 SITE 4 AC2 27 ASP A 288 ILE A 383 ASN A 384 GLN A 385 SITE 5 AC2 27 THR A 465 GLY A 470 GLU A 515 SER A 518 SITE 6 AC2 27 LEU A 519 TRP A 520 MN A 601 HOH A 733 SITE 7 AC2 27 HOH A 752 HOH A 757 HOH A 790 SITE 1 AC3 5 SER A 518 SER A 521 PHE A 522 ASP A 523 SITE 2 AC3 5 ARG A 526 SITE 1 AC4 2 ARG A 526 GLN A 530 CRYST1 61.910 61.910 325.980 90.00 90.00 90.00 P 41 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 0.016152 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016152 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003068 0.00000