HEADER TOXIN/DNA 21-AUG-22 8E5D TITLE CRYSTAL STRUCTURE OF DOUBLE-STRANDED DNA DEAMINASE TOXIN DDDA IN TITLE 2 COMPLEX WITH DNA WITH THE TARGET CYTOSINE PARKED IN THE MAJOR GROOVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE-STRANDED DNA DEAMINASE TOXIN A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DDDA,CYTIDINE DEAMINASE,CD; COMPND 5 EC: 3.5.4.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3'); COMPND 14 CHAIN: B; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA CENOCEPACIA; SOURCE 3 ORGANISM_TAXID: 95486; SOURCE 4 GENE: DDDA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS TOXIN, DNA BINDING, DEAMINASE, TOXIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.YIN,K.SHI,H.AIHARA REVDAT 6 18-SEP-24 8E5D 1 AUTHOR REVDAT 5 25-OCT-23 8E5D 1 REMARK REVDAT 4 30-AUG-23 8E5D 1 JRNL REVDAT 3 02-AUG-23 8E5D 1 JRNL REVDAT 2 19-JUL-23 8E5D 1 JRNL REVDAT 1 24-MAY-23 8E5D 0 JRNL AUTH L.YIN,K.SHI,H.AIHARA JRNL TITL STRUCTURAL BASIS OF SEQUENCE-SPECIFIC CYTOSINE DEAMINATION JRNL TITL 2 BY DOUBLE-STRANDED DNA DEAMINASE TOXIN DDDA. JRNL REF NAT.STRUCT.MOL.BIOL. V. 30 1153 2023 JRNL REFN ESSN 1545-9985 JRNL PMID 37460895 JRNL DOI 10.1038/S41594-023-01034-3 REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 76.4 REMARK 3 NUMBER OF REFLECTIONS : 13172 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 677 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 44.7700 - 5.1600 0.96 1735 84 0.1561 0.1788 REMARK 3 2 5.1500 - 4.0900 0.99 1651 84 0.1445 0.1673 REMARK 3 3 4.0900 - 3.5800 0.98 1605 94 0.1856 0.2265 REMARK 3 4 3.5800 - 3.2500 1.00 1633 82 0.2130 0.2764 REMARK 3 5 3.2500 - 3.0200 1.00 1633 84 0.2483 0.2641 REMARK 3 6 3.0200 - 2.8400 0.97 1544 92 0.2912 0.3154 REMARK 3 7 2.8400 - 2.7000 0.75 1208 62 0.2926 0.2920 REMARK 3 8 2.7000 - 2.5800 0.43 690 46 0.2996 0.3373 REMARK 3 9 2.5800 - 2.4800 0.30 471 28 0.3050 0.3711 REMARK 3 10 2.4800 - 2.3900 0.21 325 21 0.3942 0.4224 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.22 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : 0.047 258 REMARK 3 PLANARITY : 0.005 220 REMARK 3 DIHEDRAL : 25.812 639 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1290 THROUGH 1300 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2852 0.1992 -5.1203 REMARK 3 T TENSOR REMARK 3 T11: 0.2412 T22: 0.5058 REMARK 3 T33: 0.5063 T12: -0.0624 REMARK 3 T13: -0.1259 T23: -0.3150 REMARK 3 L TENSOR REMARK 3 L11: 1.1243 L22: 2.5758 REMARK 3 L33: 2.3064 L12: 1.6702 REMARK 3 L13: 0.4717 L23: 1.1481 REMARK 3 S TENSOR REMARK 3 S11: -0.4291 S12: -0.1772 S13: 0.5827 REMARK 3 S21: -0.2992 S22: 0.1568 S23: 0.3001 REMARK 3 S31: -0.3552 S32: -0.1817 S33: 0.3260 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1301 THROUGH 1311 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4475 -17.7766 3.1458 REMARK 3 T TENSOR REMARK 3 T11: 0.6220 T22: 0.6967 REMARK 3 T33: 0.2654 T12: 0.2629 REMARK 3 T13: 0.0936 T23: -0.1445 REMARK 3 L TENSOR REMARK 3 L11: 0.6845 L22: 0.0645 REMARK 3 L33: 1.8001 L12: -0.0326 REMARK 3 L13: -0.6651 L23: -0.2385 REMARK 3 S TENSOR REMARK 3 S11: -0.2594 S12: -0.3541 S13: -0.0178 REMARK 3 S21: 0.4217 S22: 0.0042 S23: 0.0547 REMARK 3 S31: 0.3982 S32: 0.0450 S33: -0.1572 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1312 THROUGH 1330 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.9269 -7.4808 -3.1965 REMARK 3 T TENSOR REMARK 3 T11: 0.1707 T22: 0.5111 REMARK 3 T33: 0.4601 T12: 0.0498 REMARK 3 T13: 0.0410 T23: -0.2392 REMARK 3 L TENSOR REMARK 3 L11: 4.6544 L22: 2.0784 REMARK 3 L33: 3.2947 L12: 0.7263 REMARK 3 L13: -0.0297 L23: 1.9428 REMARK 3 S TENSOR REMARK 3 S11: -0.3612 S12: -0.3678 S13: 0.6968 REMARK 3 S21: 0.1244 S22: -0.1682 S23: 0.6095 REMARK 3 S31: 0.0018 S32: -0.1633 S33: 0.0073 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1331 THROUGH 1366 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.7407 -17.3382 -10.4999 REMARK 3 T TENSOR REMARK 3 T11: 0.1291 T22: 0.3988 REMARK 3 T33: 0.3912 T12: 0.0673 REMARK 3 T13: 0.0916 T23: -0.1389 REMARK 3 L TENSOR REMARK 3 L11: 3.3769 L22: 1.7395 REMARK 3 L33: 1.6767 L12: 0.2420 REMARK 3 L13: -0.1063 L23: 0.9572 REMARK 3 S TENSOR REMARK 3 S11: -0.2414 S12: -0.2415 S13: 0.3069 REMARK 3 S21: 0.1419 S22: 0.0270 S23: 0.2242 REMARK 3 S31: 0.0839 S32: 0.0972 S33: 0.2022 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1367 THROUGH 1383 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.2394 -19.7125 -12.6242 REMARK 3 T TENSOR REMARK 3 T11: 0.1796 T22: 0.3833 REMARK 3 T33: 0.3325 T12: -0.0056 REMARK 3 T13: 0.0622 T23: -0.1063 REMARK 3 L TENSOR REMARK 3 L11: 5.0890 L22: 6.4025 REMARK 3 L33: 6.0979 L12: -0.7812 REMARK 3 L13: -1.5193 L23: 3.9842 REMARK 3 S TENSOR REMARK 3 S11: -0.3251 S12: -0.1473 S13: 0.1617 REMARK 3 S21: 0.1768 S22: 0.2367 S23: 0.2060 REMARK 3 S31: 0.2894 S32: 0.4538 S33: -0.0111 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1384 THROUGH 1393 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0792 -9.4064 -15.8804 REMARK 3 T TENSOR REMARK 3 T11: 0.1698 T22: 0.2688 REMARK 3 T33: 0.3447 T12: 0.0747 REMARK 3 T13: -0.0596 T23: -0.1866 REMARK 3 L TENSOR REMARK 3 L11: 5.2974 L22: 3.8127 REMARK 3 L33: 5.8586 L12: 4.1812 REMARK 3 L13: 4.2836 L23: 3.5117 REMARK 3 S TENSOR REMARK 3 S11: -0.3317 S12: -0.3893 S13: 1.1615 REMARK 3 S21: -0.3882 S22: -0.3105 S23: 0.6426 REMARK 3 S31: -0.6501 S32: -0.4536 S33: 0.9508 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1394 THROUGH 1403 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.8742 -18.9514 -7.7110 REMARK 3 T TENSOR REMARK 3 T11: 0.1579 T22: 0.4390 REMARK 3 T33: 0.2049 T12: 0.0972 REMARK 3 T13: 0.0022 T23: -0.1017 REMARK 3 L TENSOR REMARK 3 L11: 7.1880 L22: 2.0919 REMARK 3 L33: 1.2462 L12: -2.0723 REMARK 3 L13: -1.2324 L23: -0.8882 REMARK 3 S TENSOR REMARK 3 S11: -0.2962 S12: -0.5703 S13: 0.2044 REMARK 3 S21: 0.5252 S22: 0.4831 S23: -0.0468 REMARK 3 S31: 0.2100 S32: 0.5411 S33: -0.0398 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1404 THROUGH 1413 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8426 -12.7680 -13.9532 REMARK 3 T TENSOR REMARK 3 T11: 0.1895 T22: 0.4743 REMARK 3 T33: 0.3515 T12: -0.0222 REMARK 3 T13: 0.0369 T23: -0.0714 REMARK 3 L TENSOR REMARK 3 L11: 5.9910 L22: 6.0303 REMARK 3 L33: 5.5970 L12: -4.6965 REMARK 3 L13: 4.8264 L23: -2.7197 REMARK 3 S TENSOR REMARK 3 S11: -0.3276 S12: 0.1832 S13: 0.9413 REMARK 3 S21: -0.3079 S22: 0.0614 S23: -0.8825 REMARK 3 S31: 0.2116 S32: 0.2202 S33: 0.2402 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1414 THROUGH 1425 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.6683 -25.2553 -21.4943 REMARK 3 T TENSOR REMARK 3 T11: 0.2000 T22: 0.3875 REMARK 3 T33: 0.3618 T12: 0.0435 REMARK 3 T13: -0.0324 T23: -0.1569 REMARK 3 L TENSOR REMARK 3 L11: 8.2375 L22: 7.0419 REMARK 3 L33: 7.2551 L12: 5.1560 REMARK 3 L13: -3.7794 L23: -4.7170 REMARK 3 S TENSOR REMARK 3 S11: -0.3100 S12: -0.3120 S13: -0.4165 REMARK 3 S21: -1.1105 S22: -0.7024 S23: 0.4360 REMARK 3 S31: 0.6055 S32: 0.4584 S33: 0.8517 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.2836 -32.8443 -17.9004 REMARK 3 T TENSOR REMARK 3 T11: 0.4761 T22: 0.5011 REMARK 3 T33: 0.3696 T12: 0.0662 REMARK 3 T13: 0.0599 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 4.8064 L22: 2.7496 REMARK 3 L33: 1.5191 L12: 0.9641 REMARK 3 L13: -0.3889 L23: 1.8751 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: -0.6074 S13: -0.9086 REMARK 3 S21: 0.7928 S22: -0.2158 S23: -0.1318 REMARK 3 S31: 0.8074 S32: 0.3801 S33: 0.2270 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.1946 -35.4224 -15.3617 REMARK 3 T TENSOR REMARK 3 T11: 0.8795 T22: 0.6042 REMARK 3 T33: 0.4439 T12: -0.0424 REMARK 3 T13: 0.2825 T23: 0.1197 REMARK 3 L TENSOR REMARK 3 L11: 5.2691 L22: 1.5760 REMARK 3 L33: 3.6750 L12: -0.0394 REMARK 3 L13: -1.2310 L23: -0.5520 REMARK 3 S TENSOR REMARK 3 S11: -0.1362 S12: -0.4288 S13: -0.8019 REMARK 3 S21: 0.4940 S22: 0.4209 S23: 0.5014 REMARK 3 S31: 1.3817 S32: -0.5007 S33: 0.8235 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 8E5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13177 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 REMARK 200 RESOLUTION RANGE LOW (A) : 47.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.13900 REMARK 200 R SYM FOR SHELL (I) : 1.13900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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: 6U08 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM DIHYDROGEN PHOSPHATE, 20 REMARK 280 % POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.23250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.23250 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, 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 HIS A 1426 REMARK 465 HIS A 1427 REMARK 465 HIS A 1428 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 DT C 12 O4' - C1' - N1 ANGL. DEV. = 1.9 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 PRO A1422 -169.22 -79.58 REMARK 500 HIS A1424 72.26 -116.71 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 ZN A1501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1345 ND1 REMARK 620 2 CYS A1373 SG 113.0 REMARK 620 3 CYS A1376 SG 108.1 109.2 REMARK 620 4 PO4 A1503 O1 99.8 99.1 127.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A1381 O REMARK 620 2 THR A1382 O 81.9 REMARK 620 3 LEU A1384 O 87.3 81.8 REMARK 620 4 ASN A1415 O 108.7 169.4 97.4 REMARK 620 5 ASN A1415 OD1 74.6 118.7 149.4 66.6 REMARK 620 6 ASN A1417 O 147.9 84.0 119.1 87.2 87.3 REMARK 620 N 1 2 3 4 5 DBREF 8E5D A 1290 1422 UNP P0DUH5 DDDA_BURC1 1290 1422 DBREF 8E5D C 1 14 PDB 8E5D 8E5D 1 14 DBREF 8E5D B 1 14 PDB 8E5D 8E5D 1 14 SEQADV 8E5D ALA A 1347 UNP P0DUH5 GLU 1347 ENGINEERED MUTATION SEQADV 8E5D HIS A 1423 UNP P0DUH5 EXPRESSION TAG SEQADV 8E5D HIS A 1424 UNP P0DUH5 EXPRESSION TAG SEQADV 8E5D HIS A 1425 UNP P0DUH5 EXPRESSION TAG SEQADV 8E5D HIS A 1426 UNP P0DUH5 EXPRESSION TAG SEQADV 8E5D HIS A 1427 UNP P0DUH5 EXPRESSION TAG SEQADV 8E5D HIS A 1428 UNP P0DUH5 EXPRESSION TAG SEQRES 1 A 139 GLY SER TYR ALA LEU GLY PRO TYR GLN ILE SER ALA PRO SEQRES 2 A 139 GLN LEU PRO ALA TYR ASN GLY GLN THR VAL GLY THR PHE SEQRES 3 A 139 TYR TYR VAL ASN ASP ALA GLY GLY LEU GLU SER LYS VAL SEQRES 4 A 139 PHE SER SER GLY GLY PRO THR PRO TYR PRO ASN TYR ALA SEQRES 5 A 139 ASN ALA GLY HIS VAL ALA GLY GLN SER ALA LEU PHE MET SEQRES 6 A 139 ARG ASP ASN GLY ILE SER GLU GLY LEU VAL PHE HIS ASN SEQRES 7 A 139 ASN PRO GLU GLY THR CYS GLY PHE CYS VAL ASN MET THR SEQRES 8 A 139 GLU THR LEU LEU PRO GLU ASN ALA LYS MET THR VAL VAL SEQRES 9 A 139 PRO PRO GLU GLY ALA ILE PRO VAL LYS ARG GLY ALA THR SEQRES 10 A 139 GLY GLU THR LYS VAL PHE THR GLY ASN SER ASN SER PRO SEQRES 11 A 139 LYS SER PRO HIS HIS HIS HIS HIS HIS SEQRES 1 C 14 DG DT DA DC DC DG DG DA DC DG DT DT DG SEQRES 2 C 14 DC SEQRES 1 B 14 DG DC DA DA DC DG DT DC DC DG DG DT DA SEQRES 2 B 14 DC HET ZN A1501 1 HET MG A1502 1 HET PO4 A1503 5 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 4 ZN ZN 2+ FORMUL 5 MG MG 2+ FORMUL 6 PO4 O4 P 3- FORMUL 7 HOH *12(H2 O) HELIX 1 AA1 HIS A 1345 GLY A 1358 1 14 HELIX 2 AA2 CYS A 1373 LEU A 1384 1 12 SHEET 1 AA1 2 SER A1291 LEU A1294 0 SHEET 2 AA1 2 TYR A1297 SER A1300 -1 O TYR A1297 N LEU A1294 SHEET 1 AA2 5 LEU A1324 SER A1330 0 SHEET 2 AA2 5 VAL A1312 VAL A1318 -1 N TYR A1317 O GLU A1325 SHEET 3 AA2 5 GLU A1361 HIS A1366 -1 O LEU A1363 N TYR A1316 SHEET 4 AA2 5 LYS A1389 VAL A1393 1 O VAL A1393 N VAL A1364 SHEET 5 AA2 5 LYS A1410 THR A1413 -1 O LYS A1410 N VAL A1392 LINK ND1 HIS A1345 ZN ZN A1501 1555 1555 2.00 LINK SG CYS A1373 ZN ZN A1501 1555 1555 2.34 LINK SG CYS A1376 ZN ZN A1501 1555 1555 2.23 LINK O GLU A1381 MG MG A1502 1555 1555 2.50 LINK O THR A1382 MG MG A1502 1555 1555 2.41 LINK O LEU A1384 MG MG A1502 1555 1555 2.40 LINK O ASN A1415 MG MG A1502 1555 1555 2.38 LINK OD1 ASN A1415 MG MG A1502 1555 1555 2.37 LINK O ASN A1417 MG MG A1502 1555 1555 2.25 LINK ZN ZN A1501 O1 PO4 A1503 1555 1555 1.94 CRYST1 31.699 94.611 138.465 90.00 90.00 90.00 P 2 2 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 0.031547 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010570 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007222 0.00000