HEADER TRANSFERASE 08-FEB-17 5UQK TITLE CLOSTRIDIUM DIFFICILE TOXIN A (TCDA) GLUCOSYLTRANSFERASE DOMAIN IN TITLE 2 COMPLEX WITH U2F COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOXIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-544; 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: TOXA, TCDA; SOURCE 5 EXPRESSION_SYSTEM: BACILLUS MEGATERIUM; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1404; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHIS1622 KEYWDS GLUCOSYLTRANSFERASE, TOXIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.W.ALVIN,D.B.LACY REVDAT 5 04-OCT-23 5UQK 1 LINK REVDAT 4 11-DEC-19 5UQK 1 REMARK LINK REVDAT 3 20-SEP-17 5UQK 1 REMARK REVDAT 2 14-JUN-17 5UQK 1 JRNL REVDAT 1 10-MAY-17 5UQK 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 65417 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 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 31.4148 - 4.4580 1.00 4654 146 0.1713 0.1804 REMARK 3 2 4.4580 - 3.5400 1.00 4580 149 0.1577 0.1685 REMARK 3 3 3.5400 - 3.0929 1.00 4539 139 0.1728 0.2112 REMARK 3 4 3.0929 - 2.8104 1.00 4550 144 0.1814 0.2457 REMARK 3 5 2.8104 - 2.6090 1.00 4545 143 0.1850 0.2260 REMARK 3 6 2.6090 - 2.4553 1.00 4511 142 0.1825 0.2292 REMARK 3 7 2.4553 - 2.3323 1.00 4541 145 0.1829 0.2089 REMARK 3 8 2.3323 - 2.2308 1.00 4528 142 0.1929 0.2174 REMARK 3 9 2.2308 - 2.1450 1.00 4512 141 0.1916 0.2169 REMARK 3 10 2.1450 - 2.0710 1.00 4503 138 0.2072 0.2427 REMARK 3 11 2.0710 - 2.0062 1.00 4510 145 0.2238 0.2501 REMARK 3 12 2.0062 - 1.9489 1.00 4524 141 0.2321 0.2540 REMARK 3 13 1.9489 - 1.8976 1.00 4519 139 0.2830 0.2870 REMARK 3 14 1.8976 - 1.8513 0.98 4406 141 0.2791 0.2682 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.320 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 : 0.021 4699 REMARK 3 ANGLE : 1.598 6398 REMARK 3 CHIRALITY : 0.102 726 REMARK 3 PLANARITY : 0.014 817 REMARK 3 DIHEDRAL : 13.170 2919 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 108 THROUGH 418 ) REMARK 3 ORIGIN FOR THE GROUP (A): 89.2847 75.8855 0.0332 REMARK 3 T TENSOR REMARK 3 T11: 0.2401 T22: 0.2417 REMARK 3 T33: 0.2513 T12: 0.0358 REMARK 3 T13: -0.0190 T23: -0.0426 REMARK 3 L TENSOR REMARK 3 L11: 0.1482 L22: 0.2793 REMARK 3 L33: 0.8908 L12: -0.1926 REMARK 3 L13: 0.2156 L23: 0.2840 REMARK 3 S TENSOR REMARK 3 S11: -0.0492 S12: -0.1482 S13: 0.0252 REMARK 3 S21: -0.0326 S22: -0.1175 S23: -0.0093 REMARK 3 S31: -0.2316 S32: -0.1894 S33: -0.1155 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 419 THROUGH 506 ) REMARK 3 ORIGIN FOR THE GROUP (A): 98.6068 59.2843 -4.9183 REMARK 3 T TENSOR REMARK 3 T11: 0.2214 T22: 0.3158 REMARK 3 T33: 0.2432 T12: -0.0389 REMARK 3 T13: 0.0028 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 0.4481 L22: 0.2408 REMARK 3 L33: 0.5632 L12: -0.3187 REMARK 3 L13: -0.0125 L23: 0.2557 REMARK 3 S TENSOR REMARK 3 S11: -0.0538 S12: 0.1507 S13: -0.0469 REMARK 3 S21: 0.0361 S22: 0.0271 S23: -0.0303 REMARK 3 S31: -0.0287 S32: 0.0135 S33: -0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 507 THROUGH 538 ) REMARK 3 ORIGIN FOR THE GROUP (A): 101.4390 83.1033 -7.6849 REMARK 3 T TENSOR REMARK 3 T11: 0.6354 T22: 0.4460 REMARK 3 T33: 0.5246 T12: -0.0986 REMARK 3 T13: -0.0272 T23: 0.1087 REMARK 3 L TENSOR REMARK 3 L11: 0.6347 L22: 0.0871 REMARK 3 L33: 0.0677 L12: 0.0359 REMARK 3 L13: 0.0801 L23: 0.1095 REMARK 3 S TENSOR REMARK 3 S11: -0.1287 S12: 0.3074 S13: -0.1089 REMARK 3 S21: 0.1722 S22: 0.0190 S23: -0.0202 REMARK 3 S31: -0.3346 S32: 0.0803 S33: -0.0114 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 79.4458 41.1625 -12.7958 REMARK 3 T TENSOR REMARK 3 T11: 0.2622 T22: 0.3856 REMARK 3 T33: 0.3285 T12: -0.0450 REMARK 3 T13: 0.0298 T23: -0.0300 REMARK 3 L TENSOR REMARK 3 L11: 0.1757 L22: 0.5944 REMARK 3 L33: 0.6684 L12: 0.0686 REMARK 3 L13: 0.5121 L23: 0.3448 REMARK 3 S TENSOR REMARK 3 S11: 0.0735 S12: -0.1055 S13: -0.0160 REMARK 3 S21: 0.0450 S22: -0.1098 S23: 0.1931 REMARK 3 S31: 0.1989 S32: -0.1125 S33: -0.0074 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 5UQK 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_1000225952. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7-8.5 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-D 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65449 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 31.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.4000 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: 3SRZ REMARK 200 REMARK 200 REMARK: LONG, HEXAGONAL BARS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 0.2 M L-PROLINE, PEG 3350 REMARK 280 10-25%, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.04933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.02467 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.03700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 11.01233 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.06167 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: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 1 REMARK 465 GLY A 539 REMARK 465 GLY A 540 REMARK 465 SER A 541 REMARK 465 LEU A 542 REMARK 465 SER A 543 REMARK 465 GLU A 544 REMARK 465 PRO A 545 REMARK 465 HIS A 546 REMARK 465 ALA A 547 REMARK 465 GLY A 548 REMARK 465 LEU A 549 REMARK 465 ARG A 550 REMARK 465 GLY A 551 REMARK 465 SER A 552 REMARK 465 HIS A 553 REMARK 465 HIS A 554 REMARK 465 HIS A 555 REMARK 465 HIS A 556 REMARK 465 HIS A 557 REMARK 465 HIS A 558 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 HH21 ARG A 261 O HOH A 707 1.31 REMARK 500 CB SER A 517 O HOH A 705 1.36 REMARK 500 NH1 ARG A 302 O ILE A 306 1.36 REMARK 500 HB3 SER A 517 O HOH A 705 1.45 REMARK 500 HH21 ARG A 215 O HOH A 711 1.53 REMARK 500 O HOH A 906 O HOH A 955 1.58 REMARK 500 CE LYS A 532 OD1 ASP A 536 1.62 REMARK 500 CE LYS A 532 OD2 ASP A 536 1.65 REMARK 500 CE LYS A 532 CG ASP A 536 1.77 REMARK 500 O HOH A 926 O HOH A 1058 1.82 REMARK 500 OD1 ASN A 43 O HOH A 701 1.84 REMARK 500 O LEU A 308 O HOH A 702 1.85 REMARK 500 NH1 ARG A 17 O HOH A 703 1.90 REMARK 500 ND2 ASN A 41 O HOH A 704 1.91 REMARK 500 O HOH A 1051 O HOH A 1113 1.92 REMARK 500 O HOH A 1052 O HOH A 1053 1.92 REMARK 500 O HOH A 1049 O HOH A 1081 1.93 REMARK 500 O HOH A 1004 O HOH A 1065 1.99 REMARK 500 O PHE A 334 CD1 LEU A 337 2.01 REMARK 500 O HOH A 1023 O HOH A 1045 2.04 REMARK 500 O HOH A 1166 O HOH A 1168 2.04 REMARK 500 OG SER A 517 O HOH A 705 2.04 REMARK 500 O HOH A 909 O HOH A 1046 2.06 REMARK 500 O HOH A 832 O HOH A 1096 2.06 REMARK 500 O HOH A 855 O HOH A 953 2.07 REMARK 500 O LEU A 296 CD1 ILE A 348 2.08 REMARK 500 O HOH A 1020 O HOH A 1095 2.10 REMARK 500 OD1 ASN A 404 O HOH A 706 2.12 REMARK 500 NH2 ARG A 261 O HOH A 707 2.12 REMARK 500 OE1 GLU A 441 O HOH A 708 2.12 REMARK 500 O HOH A 923 O HOH A 1070 2.15 REMARK 500 O HOH A 1016 O HOH A 1114 2.17 REMARK 500 OE1 GLU A 146 O HOH A 709 2.17 REMARK 500 O HOH A 717 O HOH A 841 2.18 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 HH TYR A 14 OE1 GLN A 248 3664 1.57 REMARK 500 OH TYR A 14 OE1 GLN A 248 3664 2.11 REMARK 500 OE1 GLU A 8 OG1 THR A 38 2654 2.12 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 ARG A 302 CZ ARG A 302 NH1 0.091 REMARK 500 ARG A 302 CZ ARG A 302 NH2 0.093 REMARK 500 ARG A 310 CZ ARG A 310 NH1 0.081 REMARK 500 ARG A 310 CZ ARG A 310 NH2 0.093 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 SER A 88 CA - C - O ANGL. DEV. = -20.0 DEGREES REMARK 500 LYS A 127 CA - C - O ANGL. DEV. = -15.5 DEGREES REMARK 500 LYS A 127 CA - C - O ANGL. DEV. = -15.6 DEGREES REMARK 500 GLU A 133 N - CA - CB ANGL. DEV. = -11.3 DEGREES REMARK 500 SER A 419 CA - C - O ANGL. DEV. = -17.5 DEGREES REMARK 500 SER A 419 CA - C - O ANGL. DEV. = -17.7 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 ASN A 242 -163.48 -119.60 REMARK 500 ASN A 242 -163.46 -119.64 REMARK 500 GLU A 363 -134.26 53.17 REMARK 500 GLU A 363 -134.97 53.24 REMARK 500 LEU A 510 56.08 -90.74 REMARK 500 TRP A 519 91.75 -65.31 REMARK 500 SER A 520 -158.71 -78.47 REMARK 500 SER A 520 -160.44 -74.00 REMARK 500 PHE A 521 68.30 -119.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 88 -28.18 REMARK 500 LYS A 127 18.88 REMARK 500 LYS A 127 18.86 REMARK 500 MET A 168 -22.03 REMARK 500 MET A 168 -22.07 REMARK 500 LEU A 259 -11.09 REMARK 500 LEU A 259 -11.22 REMARK 500 LYS A 298 -16.82 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 A1166 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A1167 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A1168 DISTANCE = 7.08 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 287 OD2 REMARK 620 2 GLU A 514 OE2 79.3 REMARK 620 3 U2F A 601 O2B 159.0 121.3 REMARK 620 4 U2F A 601 O2A 93.5 172.4 66.1 REMARK 620 5 HOH A 705 O 85.3 82.7 93.0 99.4 REMARK 620 6 HOH A 765 O 83.8 77.9 103.3 98.9 159.2 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 U2F 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UQN RELATED DB: PDB REMARK 900 RELATED ID: 5UQL RELATED DB: PDB REMARK 900 RELATED ID: 5UQM RELATED DB: PDB REMARK 900 RELATED ID: 5UQT RELATED DB: PDB DBREF 5UQK A 1 544 UNP P16154 TOXA_CLODI 1 544 SEQADV 5UQK PRO A 545 UNP P16154 EXPRESSION TAG SEQADV 5UQK HIS A 546 UNP P16154 EXPRESSION TAG SEQADV 5UQK ALA A 547 UNP P16154 EXPRESSION TAG SEQADV 5UQK GLY A 548 UNP P16154 EXPRESSION TAG SEQADV 5UQK LEU A 549 UNP P16154 EXPRESSION TAG SEQADV 5UQK ARG A 550 UNP P16154 EXPRESSION TAG SEQADV 5UQK GLY A 551 UNP P16154 EXPRESSION TAG SEQADV 5UQK SER A 552 UNP P16154 EXPRESSION TAG SEQADV 5UQK HIS A 553 UNP P16154 EXPRESSION TAG SEQADV 5UQK HIS A 554 UNP P16154 EXPRESSION TAG SEQADV 5UQK HIS A 555 UNP P16154 EXPRESSION TAG SEQADV 5UQK HIS A 556 UNP P16154 EXPRESSION TAG SEQADV 5UQK HIS A 557 UNP P16154 EXPRESSION TAG SEQADV 5UQK HIS A 558 UNP P16154 EXPRESSION TAG SEQRES 1 A 558 MET SER LEU ILE SER LYS GLU GLU LEU ILE LYS LEU ALA SEQRES 2 A 558 TYR SER ILE ARG PRO ARG GLU ASN GLU TYR LYS THR ILE SEQRES 3 A 558 LEU THR ASN LEU ASP GLU TYR ASN LYS LEU THR THR ASN SEQRES 4 A 558 ASN ASN GLU ASN LYS TYR LEU GLN LEU LYS LYS LEU ASN SEQRES 5 A 558 GLU SER ILE ASP VAL PHE MET ASN LYS TYR LYS THR SER SEQRES 6 A 558 SER ARG ASN ARG ALA LEU SER ASN LEU LYS LYS ASP ILE SEQRES 7 A 558 LEU LYS GLU VAL ILE LEU ILE LYS ASN SER ASN THR SER SEQRES 8 A 558 PRO VAL GLU LYS ASN LEU HIS PHE VAL TRP ILE GLY GLY SEQRES 9 A 558 GLU VAL SER ASP ILE ALA LEU GLU TYR ILE LYS GLN TRP SEQRES 10 A 558 ALA ASP ILE ASN ALA GLU TYR ASN ILE LYS LEU TRP TYR SEQRES 11 A 558 ASP SER GLU ALA PHE LEU VAL ASN THR LEU LYS LYS ALA SEQRES 12 A 558 ILE VAL GLU SER SER THR THR GLU ALA LEU GLN LEU LEU SEQRES 13 A 558 GLU GLU GLU ILE GLN ASN PRO GLN PHE ASP ASN MET LYS SEQRES 14 A 558 PHE TYR LYS LYS ARG MET GLU PHE ILE TYR ASP ARG GLN SEQRES 15 A 558 LYS ARG PHE ILE ASN TYR TYR LYS SER GLN ILE ASN LYS SEQRES 16 A 558 PRO THR VAL PRO THR ILE ASP ASP ILE ILE LYS SER HIS SEQRES 17 A 558 LEU VAL SER GLU TYR ASN ARG ASP GLU THR VAL LEU GLU SEQRES 18 A 558 SER TYR ARG THR ASN SER LEU ARG LYS ILE ASN SER ASN SEQRES 19 A 558 HIS GLY ILE ASP ILE ARG ALA ASN SER LEU PHE THR GLU SEQRES 20 A 558 GLN GLU LEU LEU ASN ILE TYR SER GLN GLU LEU LEU ASN SEQRES 21 A 558 ARG GLY ASN LEU ALA ALA ALA SER ASP ILE VAL ARG LEU SEQRES 22 A 558 LEU ALA LEU LYS ASN PHE GLY GLY VAL TYR LEU ASP VAL SEQRES 23 A 558 ASP MET LEU PRO GLY ILE HIS SER ASP LEU PHE LYS THR SEQRES 24 A 558 ILE SER ARG PRO SER SER ILE GLY LEU ASP ARG TRP GLU SEQRES 25 A 558 MET ILE LYS LEU GLU ALA ILE MET LYS TYR LYS LYS TYR SEQRES 26 A 558 ILE ASN ASN TYR THR SER GLU ASN PHE ASP LYS LEU ASP SEQRES 27 A 558 GLN GLN LEU LYS ASP ASN PHE LYS LEU ILE ILE GLU SER SEQRES 28 A 558 LYS SER GLU LYS SER GLU ILE PHE SER LYS LEU GLU ASN SEQRES 29 A 558 LEU ASN VAL SER ASP LEU GLU ILE LYS ILE ALA PHE ALA SEQRES 30 A 558 LEU GLY SER VAL ILE ASN GLN ALA LEU ILE SER LYS GLN SEQRES 31 A 558 GLY SER TYR LEU THR ASN LEU VAL ILE GLU GLN VAL LYS SEQRES 32 A 558 ASN ARG TYR GLN PHE LEU ASN GLN HIS LEU ASN PRO ALA SEQRES 33 A 558 ILE GLU SER ASP ASN ASN PHE THR ASP THR THR LYS ILE SEQRES 34 A 558 PHE HIS ASP SER LEU PHE ASN SER ALA THR ALA GLU ASN SEQRES 35 A 558 SER MET PHE LEU THR LYS ILE ALA PRO TYR LEU GLN VAL SEQRES 36 A 558 GLY PHE MET PRO GLU ALA ARG SER THR ILE SER LEU SER SEQRES 37 A 558 GLY PRO GLY ALA TYR ALA SER ALA TYR TYR ASP PHE ILE SEQRES 38 A 558 ASN LEU GLN GLU ASN THR ILE GLU LYS THR LEU LYS ALA SEQRES 39 A 558 SER ASP LEU ILE GLU PHE LYS PHE PRO GLU ASN ASN LEU SEQRES 40 A 558 SER GLN LEU THR GLU GLN GLU ILE ASN SER LEU TRP SER SEQRES 41 A 558 PHE ASP GLN ALA SER ALA LYS TYR GLN PHE GLU LYS TYR SEQRES 42 A 558 VAL ARG ASP TYR THR GLY GLY SER LEU SER GLU PRO HIS SEQRES 43 A 558 ALA GLY LEU ARG GLY SER HIS HIS HIS HIS HIS HIS HET U2F A 601 57 HET MN A 602 1 HETNAM U2F URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE HETNAM MN MANGANESE (II) ION FORMUL 2 U2F C15 H23 F N2 O16 P2 FORMUL 3 MN MN 2+ FORMUL 4 HOH *468(H2 O) HELIX 1 AA1 SER A 5 ALA A 13 1 9 HELIX 2 AA2 GLU A 20 LYS A 35 1 16 HELIX 3 AA3 ASN A 40 TYR A 62 1 23 HELIX 4 AA4 ARG A 67 ASN A 89 1 23 HELIX 5 AA5 SER A 107 ASN A 121 1 15 HELIX 6 AA6 LEU A 136 LEU A 156 1 21 HELIX 7 AA7 ASP A 166 ILE A 193 1 28 HELIX 8 AA8 THR A 200 TYR A 213 1 14 HELIX 9 AA9 ASP A 216 SER A 233 1 18 HELIX 10 AB1 ARG A 240 ASN A 242 5 3 HELIX 11 AB2 GLU A 247 LEU A 259 1 13 HELIX 12 AB3 ASN A 263 GLY A 280 1 18 HELIX 13 AB4 SER A 294 LYS A 298 5 5 HELIX 14 AB5 GLY A 307 LYS A 324 1 18 HELIX 15 AB6 SER A 331 LYS A 336 1 6 HELIX 16 AB7 ASP A 338 SER A 351 1 14 HELIX 17 AB8 GLU A 354 ILE A 358 5 5 HELIX 18 AB9 SER A 392 GLU A 418 1 27 HELIX 19 AC1 ASN A 422 ASN A 436 1 15 HELIX 20 AC2 ASN A 442 ALA A 450 1 9 HELIX 21 AC3 PRO A 451 VAL A 455 5 5 HELIX 22 AC4 ARG A 462 LEU A 467 5 6 HELIX 23 AC5 GLY A 469 LEU A 483 1 15 HELIX 24 AC6 LYS A 493 LYS A 501 5 9 HELIX 25 AC7 PRO A 503 LEU A 507 5 5 HELIX 26 AC8 THR A 511 LEU A 518 1 8 HELIX 27 AC9 ASP A 522 THR A 538 1 17 SHEET 1 AA1 2 SER A 91 PRO A 92 0 SHEET 2 AA1 2 ASN A 366 VAL A 367 -1 O VAL A 367 N SER A 91 SHEET 1 AA2 6 GLY A 236 ASP A 238 0 SHEET 2 AA2 6 ASN A 125 TYR A 130 1 N LEU A 128 O ILE A 237 SHEET 3 AA2 6 ASN A 96 VAL A 100 1 N PHE A 99 O TRP A 129 SHEET 4 AA2 6 GLY A 281 LEU A 284 1 O VAL A 282 N HIS A 98 SHEET 5 AA2 6 SER A 380 SER A 388 -1 O SER A 388 N GLY A 281 SHEET 6 AA2 6 LYS A 373 ALA A 377 -1 N ALA A 377 O SER A 380 LINK OD2 ASP A 287 MN MN A 602 1555 1555 2.26 LINK OE2 GLU A 514 MN MN A 602 1555 1555 2.17 LINK O2B U2F A 601 MN MN A 602 1555 1555 2.33 LINK O2A U2F A 601 MN MN A 602 1555 1555 2.36 LINK MN MN A 602 O HOH A 705 1555 1555 2.22 LINK MN MN A 602 O HOH A 765 1555 1555 2.16 SITE 1 AC1 22 VAL A 100 TRP A 101 ILE A 102 ASN A 138 SITE 2 AC1 22 LEU A 264 ALA A 265 SER A 268 ASP A 269 SITE 3 AC1 22 ARG A 272 TYR A 283 ASP A 285 VAL A 286 SITE 4 AC1 22 ASP A 287 ASN A 383 GLN A 384 THR A 464 SITE 5 AC1 22 SER A 517 MN A 602 HOH A 710 HOH A 722 SITE 6 AC1 22 HOH A 899 HOH A 909 SITE 1 AC2 7 ASP A 287 GLU A 514 SER A 517 U2F A 601 SITE 2 AC2 7 HOH A 705 HOH A 710 HOH A 765 CRYST1 142.810 142.810 66.074 90.00 90.00 120.00 P 65 6 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 0.007002 0.004043 0.000000 0.00000 SCALE2 0.000000 0.008086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015135 0.00000