HEADER HYDROLASE/DNA 27-JUN-16 5KN9 TITLE MUTY N-TERMINAL DOMAIN IN COMPLEX WITH DNA CONTAINING AN INTRAHELICAL TITLE 2 OXOG:A BASE-PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-229; COMPND 5 SYNONYM: OXOG:A-SPECIFIC ADENINE GLYCOSYLASE; COMPND 6 EC: 3.2.2.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3'); COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: MUTY; 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: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 10 ORGANISM_TAXID: 1422; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 14 ORGANISM_TAXID: 1422 KEYWDS ADENINE GLYCOSYLASE, OXOG, DNA REPAIR PROTEIN, INTRAHELICAL LESION KEYWDS 2 RECOGNITION, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.WANG,S.CHAKRAVARTHY,G.L.VERDINE REVDAT 6 27-SEP-23 5KN9 1 LINK REVDAT 5 04-DEC-19 5KN9 1 REMARK REVDAT 4 27-SEP-17 5KN9 1 REMARK REVDAT 3 05-APR-17 5KN9 1 JRNL REVDAT 2 22-FEB-17 5KN9 1 JRNL REVDAT 1 08-FEB-17 5KN9 0 JRNL AUTH L.WANG,S.CHAKRAVARTHY,G.L.VERDINE JRNL TITL STRUCTURAL BASIS FOR THE LESION-SCANNING MECHANISM OF THE JRNL TITL 2 MUTY DNA GLYCOSYLASE. JRNL REF J. BIOL. CHEM. V. 292 5007 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28130451 JRNL DOI 10.1074/JBC.M116.757039 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 23171 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1187 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 79.9471 - 3.8602 0.97 2750 179 0.1510 0.1788 REMARK 3 2 3.8602 - 3.0639 0.99 2778 143 0.1470 0.2253 REMARK 3 3 3.0639 - 2.6766 0.99 2753 156 0.1823 0.2705 REMARK 3 4 2.6766 - 2.4318 1.00 2748 128 0.1749 0.2676 REMARK 3 5 2.4318 - 2.2575 1.00 2747 149 0.1803 0.2578 REMARK 3 6 2.2575 - 2.1244 1.00 2751 155 0.1771 0.2447 REMARK 3 7 2.1244 - 2.0180 1.00 2733 136 0.2075 0.2666 REMARK 3 8 2.0180 - 1.9302 1.00 2724 141 0.2298 0.3053 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.700 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 : 0.008 2327 REMARK 3 ANGLE : 1.316 3251 REMARK 3 CHIRALITY : 0.043 348 REMARK 3 PLANARITY : 0.005 353 REMARK 3 DIHEDRAL : 19.335 897 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 8 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.3842 8.0023 -11.0229 REMARK 3 T TENSOR REMARK 3 T11: 0.1596 T22: 0.2186 REMARK 3 T33: 0.2870 T12: 0.0309 REMARK 3 T13: 0.0147 T23: -0.0143 REMARK 3 L TENSOR REMARK 3 L11: 6.9547 L22: 3.2406 REMARK 3 L33: 9.5543 L12: 3.4591 REMARK 3 L13: -2.6086 L23: -4.7914 REMARK 3 S TENSOR REMARK 3 S11: 0.1697 S12: 0.0957 S13: 0.3972 REMARK 3 S21: 0.3257 S22: 0.1100 S23: 0.8998 REMARK 3 S31: -0.4160 S32: -0.7928 S33: -0.2441 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 25 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.9083 7.0390 -31.3780 REMARK 3 T TENSOR REMARK 3 T11: 0.3672 T22: 0.2342 REMARK 3 T33: 0.1964 T12: -0.1331 REMARK 3 T13: -0.0200 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 1.1761 L22: 2.5213 REMARK 3 L33: 6.3080 L12: -0.2226 REMARK 3 L13: -0.0918 L23: -0.3291 REMARK 3 S TENSOR REMARK 3 S11: -0.2217 S12: 0.1854 S13: 0.1810 REMARK 3 S21: -0.6847 S22: 0.2116 S23: -0.1834 REMARK 3 S31: -0.5206 S32: 0.2610 S33: 0.0169 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4723 0.3772 -42.2879 REMARK 3 T TENSOR REMARK 3 T11: 0.8046 T22: 0.5849 REMARK 3 T33: 0.1693 T12: -0.3380 REMARK 3 T13: 0.1730 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 1.4647 L22: 1.5432 REMARK 3 L33: 2.6819 L12: -0.8040 REMARK 3 L13: 1.1041 L23: -1.7005 REMARK 3 S TENSOR REMARK 3 S11: -0.0822 S12: 0.4599 S13: 0.1165 REMARK 3 S21: -0.9675 S22: -0.0228 S23: -0.3944 REMARK 3 S31: 0.1548 S32: 0.4858 S33: 0.2586 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 89 THROUGH 105 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.0147 -7.1176 -39.7554 REMARK 3 T TENSOR REMARK 3 T11: 0.5729 T22: 0.3464 REMARK 3 T33: 0.1671 T12: -0.1578 REMARK 3 T13: 0.0379 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 7.6997 L22: 3.0446 REMARK 3 L33: 9.2337 L12: -0.1755 REMARK 3 L13: 6.7001 L23: 2.0520 REMARK 3 S TENSOR REMARK 3 S11: 0.1020 S12: 0.5179 S13: -0.1637 REMARK 3 S21: -0.6405 S22: 0.0216 S23: -0.2441 REMARK 3 S31: 0.2134 S32: 0.3445 S33: -0.2189 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 106 THROUGH 124 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.4743 -9.8620 -35.1166 REMARK 3 T TENSOR REMARK 3 T11: 0.4991 T22: 0.2687 REMARK 3 T33: 0.3026 T12: -0.1771 REMARK 3 T13: -0.0591 T23: -0.0235 REMARK 3 L TENSOR REMARK 3 L11: 5.3060 L22: 0.8587 REMARK 3 L33: 6.1375 L12: -1.9859 REMARK 3 L13: 1.4372 L23: -0.3687 REMARK 3 S TENSOR REMARK 3 S11: -0.1967 S12: 0.3232 S13: -0.7019 REMARK 3 S21: -0.2734 S22: -0.0109 S23: 0.3087 REMARK 3 S31: 0.3068 S32: -0.2895 S33: 0.1580 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 125 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.1227 -2.9198 -19.6700 REMARK 3 T TENSOR REMARK 3 T11: 0.1780 T22: 0.1740 REMARK 3 T33: 0.1805 T12: -0.0799 REMARK 3 T13: -0.0539 T23: 0.0384 REMARK 3 L TENSOR REMARK 3 L11: 0.8119 L22: 1.9511 REMARK 3 L33: 4.5096 L12: 0.4022 REMARK 3 L13: 1.3247 L23: 1.4273 REMARK 3 S TENSOR REMARK 3 S11: -0.0651 S12: -0.0477 S13: 0.0208 REMARK 3 S21: -0.2933 S22: 0.0566 S23: 0.1922 REMARK 3 S31: 0.0295 S32: -0.4252 S33: 0.0012 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.7763 -9.9924 -12.3505 REMARK 3 T TENSOR REMARK 3 T11: 0.2285 T22: 0.2105 REMARK 3 T33: 0.1621 T12: -0.1027 REMARK 3 T13: -0.0082 T23: 0.0282 REMARK 3 L TENSOR REMARK 3 L11: 4.3657 L22: 4.1814 REMARK 3 L33: 1.0547 L12: -2.4641 REMARK 3 L13: 0.4290 L23: 0.4897 REMARK 3 S TENSOR REMARK 3 S11: 0.0643 S12: -0.0036 S13: -0.3823 REMARK 3 S21: 0.0153 S22: 0.0087 S23: 0.4512 REMARK 3 S31: 0.4152 S32: -0.3129 S33: -0.0777 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 180 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.3518 3.9972 -18.1496 REMARK 3 T TENSOR REMARK 3 T11: 0.1855 T22: 0.1642 REMARK 3 T33: 0.2206 T12: -0.0631 REMARK 3 T13: -0.0431 T23: 0.0536 REMARK 3 L TENSOR REMARK 3 L11: 6.1522 L22: 4.4419 REMARK 3 L33: 3.9162 L12: 3.7378 REMARK 3 L13: 2.9997 L23: 2.4197 REMARK 3 S TENSOR REMARK 3 S11: -0.1323 S12: 0.0935 S13: 0.4752 REMARK 3 S21: -0.1033 S22: 0.0771 S23: 0.5493 REMARK 3 S31: -0.1048 S32: -0.2246 S33: 0.0527 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 197 THROUGH 210 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.4844 8.0714 -6.6452 REMARK 3 T TENSOR REMARK 3 T11: 0.2298 T22: 0.1282 REMARK 3 T33: 0.1783 T12: -0.0740 REMARK 3 T13: -0.0469 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 4.1337 L22: 7.1176 REMARK 3 L33: 6.5525 L12: -0.5724 REMARK 3 L13: -2.0908 L23: 1.2100 REMARK 3 S TENSOR REMARK 3 S11: -0.1525 S12: -0.0816 S13: 0.6273 REMARK 3 S21: -0.1407 S22: 0.0878 S23: -0.4756 REMARK 3 S31: -0.5611 S32: 0.4233 S33: 0.0726 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 211 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.8299 -1.0667 -2.3419 REMARK 3 T TENSOR REMARK 3 T11: 0.2382 T22: 0.1159 REMARK 3 T33: 0.1362 T12: -0.0446 REMARK 3 T13: -0.0317 T23: 0.0218 REMARK 3 L TENSOR REMARK 3 L11: 5.7579 L22: 8.0603 REMARK 3 L33: 4.6240 L12: -4.5419 REMARK 3 L13: -1.1840 L23: 1.3833 REMARK 3 S TENSOR REMARK 3 S11: -0.3183 S12: -0.3501 S13: -0.1017 REMARK 3 S21: 0.7494 S22: 0.2535 S23: -0.1612 REMARK 3 S31: 0.4154 S32: 0.1091 S33: 0.0313 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 3 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8715 -9.5652 -21.9416 REMARK 3 T TENSOR REMARK 3 T11: 0.2171 T22: 0.3230 REMARK 3 T33: 0.4315 T12: -0.0384 REMARK 3 T13: 0.0722 T23: -0.0755 REMARK 3 L TENSOR REMARK 3 L11: 4.7099 L22: 4.0790 REMARK 3 L33: 3.1553 L12: 3.5093 REMARK 3 L13: 0.3418 L23: -1.4018 REMARK 3 S TENSOR REMARK 3 S11: -0.1972 S12: 0.1328 S13: -0.1663 REMARK 3 S21: -0.4370 S22: 0.0548 S23: -0.7760 REMARK 3 S31: 0.2273 S32: 0.6523 S33: 0.0537 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 13 THROUGH 22 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.1363 -9.5780 -20.5985 REMARK 3 T TENSOR REMARK 3 T11: 0.2590 T22: 0.3177 REMARK 3 T33: 0.5091 T12: -0.1004 REMARK 3 T13: 0.0164 T23: 0.0259 REMARK 3 L TENSOR REMARK 3 L11: 5.0819 L22: 0.1855 REMARK 3 L33: 1.0947 L12: -0.7102 REMARK 3 L13: 0.0962 L23: -0.2603 REMARK 3 S TENSOR REMARK 3 S11: 0.1415 S12: -0.5411 S13: -0.2855 REMARK 3 S21: -0.4974 S22: -0.0682 S23: -0.9948 REMARK 3 S31: 0.0032 S32: 0.1570 S33: -0.1028 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 5KN9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222492. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-15 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23193 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 79.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 1RRQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 300 MM CA(OAC)2, 14% PEG 4000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 19.37950 REMARK 290 SMTRY3 2 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: 3670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ARG A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 ARG A 7 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 431 O HOH A 509 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 O3' DT D 22 O HOH A 507 1545 2.02 REMARK 500 O HOH A 507 O HOH D 119 1565 2.04 REMARK 500 O HOH A 404 O HOH A 439 1545 2.16 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 DT C 4 O4' - C1' - N1 ANGL. DEV. = 3.2 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 ASN A 182 75.34 -161.67 REMARK 500 VAL A 197 -52.87 -123.93 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 A 520 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A 521 DISTANCE = 7.97 ANGSTROMS REMARK 525 HOH C 219 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH C 220 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH C 221 DISTANCE = 7.30 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 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 118 O REMARK 620 2 SER A 118 OG 67.9 REMARK 620 3 VAL A 123 O 87.0 89.8 REMARK 620 4 HOH A 432 O 76.1 143.7 83.7 REMARK 620 5 HOH A 477 O 137.0 69.1 95.7 146.9 REMARK 620 6 HOH A 497 O 89.4 89.9 176.2 94.4 87.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 198 SG REMARK 620 2 SF4 A 301 S1 115.6 REMARK 620 3 SF4 A 301 S3 125.5 100.7 REMARK 620 4 SF4 A 301 S4 113.5 99.0 98.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 SF4 A 301 S2 117.2 REMARK 620 3 SF4 A 301 S3 115.9 100.8 REMARK 620 4 SF4 A 301 S4 122.9 98.0 98.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 SF4 A 301 S1 120.4 REMARK 620 3 SF4 A 301 S2 118.6 100.8 REMARK 620 4 SF4 A 301 S4 114.8 99.7 98.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 214 SG REMARK 620 2 SF4 A 301 S1 124.3 REMARK 620 3 SF4 A 301 S2 119.0 99.7 REMARK 620 4 SF4 A 301 S3 110.0 100.1 99.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 494 O REMARK 620 2 HOH A 515 O 83.4 REMARK 620 3 HOH C 204 O 75.5 151.6 REMARK 620 4 HOH C 209 O 75.8 92.3 100.6 REMARK 620 5 HOH C 218 O 152.4 72.1 131.7 92.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KN8 RELATED DB: PDB DBREF 5KN9 A 1 229 UNP P83847 MUTY_GEOSE 1 229 DBREF 5KN9 C 3 12 PDB 5KN9 5KN9 3 12 DBREF 5KN9 D 13 22 PDB 5KN9 5KN9 13 22 SEQADV 5KN9 GLY A -2 UNP P83847 EXPRESSION TAG SEQADV 5KN9 SER A -1 UNP P83847 EXPRESSION TAG SEQADV 5KN9 HIS A 0 UNP P83847 EXPRESSION TAG SEQADV 5KN9 TYR A 51 UNP P83847 VAL 51 CONFLICT SEQADV 5KN9 ASN A 144 UNP P83847 ASP 144 CONFLICT SEQADV 5KN9 CYS A 164 UNP P83847 PRO 164 CONFLICT SEQRES 1 A 232 GLY SER HIS MET THR ARG GLU THR GLU ARG PHE PRO ALA SEQRES 2 A 232 ARG GLU PHE GLN ARG ASP LEU LEU ASP TRP PHE ALA ARG SEQRES 3 A 232 GLU ARG ARG ASP LEU PRO TRP ARG LYS ASP ARG ASP PRO SEQRES 4 A 232 TYR LYS VAL TRP VAL SER GLU VAL MET LEU GLN GLN THR SEQRES 5 A 232 ARG TYR GLU THR VAL ILE PRO TYR PHE GLU GLN PHE ILE SEQRES 6 A 232 ASP ARG PHE PRO THR LEU GLU ALA LEU ALA ASP ALA ASP SEQRES 7 A 232 GLU ASP GLU VAL LEU LYS ALA TRP GLU GLY LEU GLY TYR SEQRES 8 A 232 TYR SER ARG VAL ARG ASN LEU HIS ALA ALA VAL LYS GLU SEQRES 9 A 232 VAL LYS THR ARG TYR GLY GLY LYS VAL PRO ASP ASP PRO SEQRES 10 A 232 ASP GLU PHE SER ARG LEU LYS GLY VAL GLY PRO TYR THR SEQRES 11 A 232 VAL GLY ALA VAL LEU SER LEU ALA TYR GLY VAL PRO GLU SEQRES 12 A 232 PRO ALA VAL ASN GLY ASN VAL MET ARG VAL LEU SER ARG SEQRES 13 A 232 LEU PHE LEU VAL THR ASP ASP ILE ALA LYS CYS SER THR SEQRES 14 A 232 ARG LYS ARG PHE GLU GLN ILE VAL ARG GLU ILE MET ALA SEQRES 15 A 232 TYR GLU ASN PRO GLY ALA PHE ASN GLU ALA LEU ILE GLU SEQRES 16 A 232 LEU GLY ALA LEU VAL CYS THR PRO ARG ARG PRO SER CYS SEQRES 17 A 232 LEU LEU CYS PRO VAL GLN ALA TYR CYS GLN ALA PHE ALA SEQRES 18 A 232 GLU GLY VAL ALA GLU GLU LEU PRO VAL LYS MET SEQRES 1 C 10 DA DT DC DC 8OG DG DT DG DC DT SEQRES 1 D 10 DA DG DC DA DC DA DG DG DA DT HET 8OG C 7 23 HET SF4 A 301 8 HET CA A 302 1 HET CA C 101 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM CA CALCIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 4 SF4 FE4 S4 FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *165(H2 O) HELIX 1 AA1 PRO A 9 ARG A 25 1 17 HELIX 2 AA2 LEU A 28 LYS A 32 5 5 HELIX 3 AA3 ASP A 35 THR A 49 1 15 HELIX 4 AA4 ARG A 50 PHE A 65 1 16 HELIX 5 AA5 THR A 67 ALA A 74 1 8 HELIX 6 AA6 ASP A 75 GLU A 84 1 10 HELIX 7 AA7 TYR A 88 GLY A 107 1 20 HELIX 8 AA8 ASP A 113 ARG A 119 1 7 HELIX 9 AA9 GLY A 124 GLY A 137 1 14 HELIX 10 AB1 ASN A 144 LEU A 156 1 13 HELIX 11 AB2 LYS A 163 MET A 178 1 16 HELIX 12 AB3 ASN A 182 VAL A 197 1 16 HELIX 13 AB4 SER A 204 CYS A 208 5 5 HELIX 14 AB5 VAL A 210 TYR A 213 5 4 HELIX 15 AB6 CYS A 214 GLY A 220 1 7 HELIX 16 AB7 VAL A 221 LEU A 225 5 5 LINK O3' DC C 6 P 8OG C 7 1555 1555 1.60 LINK O3' 8OG C 7 P DG C 8 1555 1555 1.60 LINK O SER A 118 CA CA A 302 1555 1555 2.28 LINK OG SER A 118 CA CA A 302 1555 1555 2.85 LINK O VAL A 123 CA CA A 302 1555 1555 2.48 LINK SG CYS A 198 FE2 SF4 A 301 1555 1555 2.37 LINK SG CYS A 205 FE1 SF4 A 301 1555 1555 2.35 LINK SG CYS A 208 FE3 SF4 A 301 1555 1555 2.34 LINK SG CYS A 214 FE4 SF4 A 301 1555 1555 2.39 LINK CA CA A 302 O HOH A 432 1555 1555 2.30 LINK CA CA A 302 O HOH A 477 1555 1555 2.46 LINK CA CA A 302 O HOH A 497 1555 1555 2.46 LINK O HOH A 494 CA CA C 101 1555 1555 2.57 LINK O HOH A 515 CA CA C 101 1555 1555 2.46 LINK CA CA C 101 O HOH C 204 1555 1555 2.56 LINK CA CA C 101 O HOH C 209 1555 1555 2.70 LINK CA CA C 101 O HOH C 218 1555 1555 2.46 CISPEP 1 LEU A 225 PRO A 226 0 3.37 SITE 1 AC1 5 ARG A 153 CYS A 198 CYS A 205 CYS A 208 SITE 2 AC1 5 CYS A 214 SITE 1 AC2 6 SER A 118 VAL A 123 HOH A 432 HOH A 477 SITE 2 AC2 6 HOH A 497 DA D 21 SITE 1 AC3 5 HOH A 494 HOH A 515 HOH C 204 HOH C 209 SITE 2 AC3 5 HOH C 218 CRYST1 49.878 38.759 82.960 90.00 105.66 90.00 P 1 21 1 2 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 0.020049 0.000000 0.005622 0.00000 SCALE2 0.000000 0.025800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012519 0.00000