PDB Short entry for 5CYS HEADER HYDROLASE/DNA 30-JUL-15 5CYS TITLE STRUCTURE OF THE ENZYME-PRODUCT COMPLEX RESULTING FROM TDG ACTION ON A TITLE 2 GCAC MISMATCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CORE DOMAIN; COMPND 5 SYNONYM: THYMINE-DNA GLYCOSYLASE,HTDG; COMPND 6 EC: 3.2.2.29; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (28-MER); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (28-MER); COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TDG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-DNA COMPLEX, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.POZHARSKI,S.S.MALIK,A.C.DROHAT REVDAT 4 06-MAR-24 5CYS 1 REMARK REVDAT 3 25-DEC-19 5CYS 1 REMARK REVDAT 2 20-SEP-17 5CYS 1 REMARK REVDAT 1 16-SEP-15 5CYS 0 JRNL AUTH S.S.MALIK,K.M.VARNEY,E.POZHARSKI,A.C.DROHAT JRNL TITL CHARACTERIZING THE ENZYME-PRODUCT COMPLEXES OF THYMINE DNA JRNL TITL 2 GLYCOSYLASE USING CRYSTALLOGRAPHY AND NMR JRNL REF NUCLEIC ACIDS RES. 2015 JRNL REFN ESSN 1362-4962 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 15396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 786 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.62 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.35 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2612 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2375 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2499 REMARK 3 BIN R VALUE (WORKING SET) : 0.2317 REMARK 3 BIN FREE R VALUE : 0.3637 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.33 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 113 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1532 REMARK 3 NUCLEIC ACID ATOMS : 1135 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.01600 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 2.06600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 4.45360 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.530 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.514 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.255 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.364 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.242 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2922 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4203 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 843 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 37 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 298 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2922 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 378 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 3125 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.04 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.96 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 23.17 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 16 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|109 - A|123 } REMARK 3 ORIGIN FOR THE GROUP (A): 26.2538 -16.8418 31.4392 REMARK 3 T TENSOR REMARK 3 T11: 1.1715 T22: 0.4869 REMARK 3 T33: 0.1428 T12: 0.1019 REMARK 3 T13: -0.1722 T23: 0.1040 REMARK 3 L TENSOR REMARK 3 L11: -1.3415 L22: 6.5397 REMARK 3 L33: 10.3429 L12: -8.2690 REMARK 3 L13: 11.6127 L23: -5.9134 REMARK 3 S TENSOR REMARK 3 S11: -0.0579 S12: 0.5602 S13: -0.0023 REMARK 3 S21: 0.1421 S22: -0.3247 S23: -0.9910 REMARK 3 S31: -0.0595 S32: 1.7014 S33: 0.3825 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|124 - A|170 } REMARK 3 ORIGIN FOR THE GROUP (A): 10.6717 -6.3548 29.3568 REMARK 3 T TENSOR REMARK 3 T11: 0.6524 T22: -0.0246 REMARK 3 T33: -0.0675 T12: -0.0494 REMARK 3 T13: -0.0865 T23: -0.0314 REMARK 3 L TENSOR REMARK 3 L11: 4.1535 L22: 5.7348 REMARK 3 L33: 3.2931 L12: -1.9804 REMARK 3 L13: 0.5740 L23: -1.6901 REMARK 3 S TENSOR REMARK 3 S11: -0.0431 S12: -0.2234 S13: -0.2036 REMARK 3 S21: 0.5783 S22: 0.0291 S23: 0.3479 REMARK 3 S31: 0.1780 S32: -0.0901 S33: 0.0140 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { A|171 - A|175 } REMARK 3 ORIGIN FOR THE GROUP (A): 7.5733 -5.1399 39.2763 REMARK 3 T TENSOR REMARK 3 T11: 0.6171 T22: 0.2861 REMARK 3 T33: -0.0993 T12: 0.1058 REMARK 3 T13: 0.0194 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 15.3481 L22: 11.1620 REMARK 3 L33: 12.4441 L12: -15.5563 REMARK 3 L13: -5.5480 L23: 8.4565 REMARK 3 S TENSOR REMARK 3 S11: -0.4439 S12: -1.0444 S13: -0.2220 REMARK 3 S21: 0.3106 S22: 0.1215 S23: 0.3631 REMARK 3 S31: 0.1784 S32: -0.1677 S33: 0.3224 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { A|176 - A|215 } REMARK 3 ORIGIN FOR THE GROUP (A): 14.3379 -8.8418 21.2167 REMARK 3 T TENSOR REMARK 3 T11: 0.5723 T22: -0.1652 REMARK 3 T33: -0.1540 T12: 0.0434 REMARK 3 T13: -0.0845 T23: -0.0375 REMARK 3 L TENSOR REMARK 3 L11: 4.6214 L22: 4.0615 REMARK 3 L33: 10.2929 L12: -0.3597 REMARK 3 L13: -1.1106 L23: -0.5818 REMARK 3 S TENSOR REMARK 3 S11: 0.0666 S12: 0.0395 S13: -0.5579 REMARK 3 S21: -0.4378 S22: -0.2600 S23: 0.5087 REMARK 3 S31: 0.0358 S32: 0.3431 S33: 0.1934 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { A|216 - A|235 } REMARK 3 ORIGIN FOR THE GROUP (A): 6.6464 -4.2467 16.4587 REMARK 3 T TENSOR REMARK 3 T11: 0.7136 T22: -0.0524 REMARK 3 T33: 0.0801 T12: 0.0017 REMARK 3 T13: -0.2201 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.2220 L22: 1.8043 REMARK 3 L33: 5.6398 L12: 1.9596 REMARK 3 L13: 2.8354 L23: 1.0897 REMARK 3 S TENSOR REMARK 3 S11: -0.2227 S12: 0.3931 S13: -0.1176 REMARK 3 S21: -0.8606 S22: 0.2016 S23: 0.4331 REMARK 3 S31: 0.3879 S32: -0.1178 S33: 0.0211 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: { A|236 - A|244 } REMARK 3 ORIGIN FOR THE GROUP (A): 13.3262 0.0572 9.0030 REMARK 3 T TENSOR REMARK 3 T11: 0.9849 T22: -0.0637 REMARK 3 T33: -0.2446 T12: 0.0132 REMARK 3 T13: -0.0562 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 9.8606 L22: 4.8685 REMARK 3 L33: 1.5242 L12: 8.3971 REMARK 3 L13: -1.7821 L23: -2.8069 REMARK 3 S TENSOR REMARK 3 S11: -0.4459 S12: 0.1738 S13: 0.6205 REMARK 3 S21: -0.4816 S22: -0.0334 S23: -0.2872 REMARK 3 S31: 0.1497 S32: 0.3197 S33: 0.4794 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: { A|245 - A|277 } REMARK 3 ORIGIN FOR THE GROUP (A): 9.5008 4.6479 16.3099 REMARK 3 T TENSOR REMARK 3 T11: 0.8358 T22: -0.0281 REMARK 3 T33: -0.0102 T12: 0.0660 REMARK 3 T13: -0.2226 T23: -0.0189 REMARK 3 L TENSOR REMARK 3 L11: 0.7154 L22: 3.4040 REMARK 3 L33: 3.8509 L12: 0.7103 REMARK 3 L13: -1.5632 L23: -0.9019 REMARK 3 S TENSOR REMARK 3 S11: -0.1261 S12: 0.1200 S13: 0.3026 REMARK 3 S21: -1.3189 S22: -0.0427 S23: 0.3996 REMARK 3 S31: -0.0233 S32: 0.3760 S33: 0.1688 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: { A|278 - A|293 } REMARK 3 ORIGIN FOR THE GROUP (A): 10.8256 9.0346 30.0810 REMARK 3 T TENSOR REMARK 3 T11: 0.8874 T22: 0.0493 REMARK 3 T33: 0.0653 T12: 0.0963 REMARK 3 T13: -0.1803 T23: -0.0718 REMARK 3 L TENSOR REMARK 3 L11: 3.8108 L22: 6.1523 REMARK 3 L33: 0.4873 L12: -0.6966 REMARK 3 L13: -1.1100 L23: 0.4022 REMARK 3 S TENSOR REMARK 3 S11: -0.2043 S12: 0.2561 S13: 0.8740 REMARK 3 S21: 0.5988 S22: 0.0836 S23: 0.5948 REMARK 3 S31: -0.0052 S32: -0.2472 S33: 0.1207 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: { A|294 - A|305 } REMARK 3 ORIGIN FOR THE GROUP (A): -7.5796 3.9505 23.3033 REMARK 3 T TENSOR REMARK 3 T11: 0.7085 T22: 0.2428 REMARK 3 T33: 0.6144 T12: 0.2039 REMARK 3 T13: -0.2890 T23: -0.0260 REMARK 3 L TENSOR REMARK 3 L11: 8.4824 L22: 0.0000 REMARK 3 L33: 2.5989 L12: -2.1361 REMARK 3 L13: -0.2368 L23: 0.4192 REMARK 3 S TENSOR REMARK 3 S11: -0.1643 S12: -0.0093 S13: 0.3315 REMARK 3 S21: 0.1201 S22: -0.1378 S23: 0.5908 REMARK 3 S31: 0.1822 S32: -0.6157 S33: 0.3020 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: { C|1 - C|7 } REMARK 3 ORIGIN FOR THE GROUP (A): 28.5431 13.1424 3.5989 REMARK 3 T TENSOR REMARK 3 T11: 1.3710 T22: 0.7218 REMARK 3 T33: -0.2616 T12: -0.2050 REMARK 3 T13: 0.0219 T23: 0.2556 REMARK 3 L TENSOR REMARK 3 L11: 5.5009 L22: 17.8289 REMARK 3 L33: 15.0915 L12: 3.3292 REMARK 3 L13: -3.5005 L23: -5.1317 REMARK 3 S TENSOR REMARK 3 S11: 0.1780 S12: 0.0360 S13: -0.4277 REMARK 3 S21: 0.2003 S22: 0.4776 S23: 1.5135 REMARK 3 S31: 0.2395 S32: -0.9665 S33: -0.6557 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: { C|8 - C|11 } REMARK 3 ORIGIN FOR THE GROUP (A): 33.1341 8.8871 21.6148 REMARK 3 T TENSOR REMARK 3 T11: 1.0206 T22: 0.6227 REMARK 3 T33: -0.1221 T12: -0.0844 REMARK 3 T13: -0.0754 T23: 0.1912 REMARK 3 L TENSOR REMARK 3 L11: 11.5601 L22: 0.0004 REMARK 3 L33: 7.0887 L12: 2.2685 REMARK 3 L13: -2.9259 L23: -0.5446 REMARK 3 S TENSOR REMARK 3 S11: 0.1241 S12: 0.0414 S13: 0.4252 REMARK 3 S21: 0.0538 S22: 0.1617 S23: -0.8954 REMARK 3 S31: 0.4739 S32: 0.9304 S33: -0.2858 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: { C|12 - C|17 } REMARK 3 ORIGIN FOR THE GROUP (A): 25.3975 3.3333 39.4485 REMARK 3 T TENSOR REMARK 3 T11: 0.7310 T22: 0.0349 REMARK 3 T33: -0.2566 T12: 0.0178 REMARK 3 T13: -0.4442 T23: 0.0503 REMARK 3 L TENSOR REMARK 3 L11: 3.5646 L22: 12.8508 REMARK 3 L33: 9.0721 L12: -6.3138 REMARK 3 L13: -5.6673 L23: 8.6895 REMARK 3 S TENSOR REMARK 3 S11: 0.1025 S12: -0.7532 S13: -0.0500 REMARK 3 S21: 0.5877 S22: -0.2338 S23: 0.1996 REMARK 3 S31: 0.0599 S32: 0.2627 S33: 0.1314 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: { C|18 - C|28 } REMARK 3 ORIGIN FOR THE GROUP (A): 35.8491 -5.7413 63.5815 REMARK 3 T TENSOR REMARK 3 T11: 1.1185 T22: 0.0223 REMARK 3 T33: -0.1278 T12: -0.0466 REMARK 3 T13: -0.4353 T23: 0.0485 REMARK 3 L TENSOR REMARK 3 L11: 2.1501 L22: 9.9716 REMARK 3 L33: 24.2262 L12: -0.0897 REMARK 3 L13: -2.0438 L23: -2.6646 REMARK 3 S TENSOR REMARK 3 S11: 0.2254 S12: -0.1375 S13: -0.0800 REMARK 3 S21: 0.7408 S22: 0.1174 S23: 0.0410 REMARK 3 S31: -0.8831 S32: 0.4451 S33: -0.3428 REMARK 3 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: { D|1 - D|13 } REMARK 3 ORIGIN FOR THE GROUP (A): 36.0353 -3.9970 60.5969 REMARK 3 T TENSOR REMARK 3 T11: 1.3165 T22: 0.0681 REMARK 3 T33: -0.2302 T12: -0.0188 REMARK 3 T13: -0.2844 T23: -0.0326 REMARK 3 L TENSOR REMARK 3 L11: 4.4526 L22: 9.5466 REMARK 3 L33: 1.5095 L12: 2.1082 REMARK 3 L13: 1.4580 L23: -3.6558 REMARK 3 S TENSOR REMARK 3 S11: 0.3492 S12: -0.2829 S13: 0.1105 REMARK 3 S21: 0.0066 S22: -0.0768 S23: -0.1927 REMARK 3 S31: -0.2733 S32: 0.5076 S33: -0.2723 REMARK 3 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: { D|14 - D|24 } REMARK 3 ORIGIN FOR THE GROUP (A): 28.3172 7.1413 22.0429 REMARK 3 T TENSOR REMARK 3 T11: 0.8181 T22: 0.1377 REMARK 3 T33: -0.2558 T12: -0.1474 REMARK 3 T13: -0.1027 T23: 0.0587 REMARK 3 L TENSOR REMARK 3 L11: 9.7287 L22: 7.1240 REMARK 3 L33: 10.2768 L12: 1.0027 REMARK 3 L13: -2.4583 L23: -1.6318 REMARK 3 S TENSOR REMARK 3 S11: -0.2579 S12: 0.1579 S13: 0.6320 REMARK 3 S21: -0.9280 S22: 0.2607 S23: -0.2981 REMARK 3 S31: -0.8548 S32: 1.2155 S33: -0.0028 REMARK 3 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: { D|25 - D|28 } REMARK 3 ORIGIN FOR THE GROUP (A): 32.2774 11.3876 -2.0984 REMARK 3 T TENSOR REMARK 3 T11: 1.3204 T22: 0.6301 REMARK 3 T33: -0.1870 T12: -0.0028 REMARK 3 T13: -0.0191 T23: 0.1965 REMARK 3 L TENSOR REMARK 3 L11: 5.6290 L22: 16.3643 REMARK 3 L33: 6.9878 L12: 4.1121 REMARK 3 L13: 1.5811 L23: 4.5160 REMARK 3 S TENSOR REMARK 3 S11: 0.1768 S12: 0.3338 S13: -1.3625 REMARK 3 S21: -0.0540 S22: 0.4275 S23: 0.1825 REMARK 3 S31: 0.2439 S32: 0.7342 S33: -0.6043 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5CYS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212232. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28357 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 : AIMLESS 0.5.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15396 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 32.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.04600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.2M AMMONIUM ACETATE, REMARK 280 0.1M SODIUM ACETATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 48.94350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.90200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.94350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.90200 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: 4950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 105 REMARK 465 SER A 106 REMARK 465 HIS A 107 REMARK 465 MET A 108 REMARK 465 MET A 306 REMARK 465 ASP A 307 REMARK 465 VAL A 308 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 161 CD CE NZ REMARK 470 GLU A 170 CG CD OE1 OE2 REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 LYS A 246 CG CD CE NZ REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 291 CE NZ REMARK 470 ILE A 302 CG1 CG2 CD1 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 DC D 8 O3' DC D 8 C3' -0.044 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 DG C 3 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG C 14 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 24 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC D 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT D 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA D 16 C3' - O3' - P ANGL. DEV. = 19.9 DEGREES REMARK 500 DC D 26 O4' - C1' - N1 ANGL. DEV. = 2.2 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 PHE A 111 35.80 -95.88 REMARK 500 ASN A 112 60.53 13.68 REMARK 500 LYS A 300 20.48 -74.33 REMARK 500 ARG A 304 28.52 -79.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues DA D REMARK 800 16 through DG D 18 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XEG RELATED DB: PDB REMARK 900 RELATED ID: 4Z3A RELATED DB: PDB REMARK 900 RELATED ID: 4Z47 RELATED DB: PDB REMARK 900 RELATED ID: 4Z7B RELATED DB: PDB REMARK 900 RELATED ID: 4Z7Z RELATED DB: PDB DBREF 5CYS A 111 308 UNP Q13569 TDG_HUMAN 111 308 DBREF 5CYS C 1 28 PDB 5CYS 5CYS 1 28 DBREF 5CYS D 1 28 PDB 5CYS 5CYS 1 28 SEQADV 5CYS GLY A 105 UNP Q13569 EXPRESSION TAG SEQADV 5CYS SER A 106 UNP Q13569 EXPRESSION TAG SEQADV 5CYS HIS A 107 UNP Q13569 EXPRESSION TAG SEQADV 5CYS MET A 108 UNP Q13569 EXPRESSION TAG SEQADV 5CYS ALA A 109 UNP Q13569 EXPRESSION TAG SEQADV 5CYS SER A 110 UNP Q13569 EXPRESSION TAG SEQRES 1 A 204 GLY SER HIS MET ALA SER PHE ASN GLY VAL SER GLU ALA SEQRES 2 A 204 GLU LEU LEU THR LYS THR LEU PRO ASP ILE LEU THR PHE SEQRES 3 A 204 ASN LEU ASP ILE VAL ILE ILE GLY ILE ASN PRO GLY LEU SEQRES 4 A 204 MET ALA ALA TYR LYS GLY HIS HIS TYR PRO GLY PRO GLY SEQRES 5 A 204 ASN HIS PHE TRP LYS CYS LEU PHE MET SER GLY LEU SER SEQRES 6 A 204 GLU VAL GLN LEU ASN HIS MET ASP ASP HIS THR LEU PRO SEQRES 7 A 204 GLY LYS TYR GLY ILE GLY PHE THR ASN MET VAL GLU ARG SEQRES 8 A 204 THR THR PRO GLY SER LYS ASP LEU SER SER LYS GLU PHE SEQRES 9 A 204 ARG GLU GLY GLY ARG ILE LEU VAL GLN LYS LEU GLN LYS SEQRES 10 A 204 TYR GLN PRO ARG ILE ALA VAL PHE ASN GLY LYS CYS ILE SEQRES 11 A 204 TYR GLU ILE PHE SER LYS GLU VAL PHE GLY VAL LYS VAL SEQRES 12 A 204 LYS ASN LEU GLU PHE GLY LEU GLN PRO HIS LYS ILE PRO SEQRES 13 A 204 ASP THR GLU THR LEU CYS TYR VAL MET PRO SER SER SER SEQRES 14 A 204 ALA ARG CYS ALA GLN PHE PRO ARG ALA GLN ASP LYS VAL SEQRES 15 A 204 HIS TYR TYR ILE LYS LEU LYS ASP LEU ARG ASP GLN LEU SEQRES 16 A 204 LYS GLY ILE GLU ARG ASN MET ASP VAL SEQRES 1 C 28 DC DA DG DC DT DC DT DG DT DA DC DG DT SEQRES 2 C 28 DG DA DG DC DG DA DT DG DG DA DC DA DG SEQRES 3 C 28 DC DT SEQRES 1 D 28 DA DG DC DT DG DT DC DC DA DT DC DG DC SEQRES 2 D 28 DT DC DA ORP DG DT DA DC DA DG DA DG DC SEQRES 3 D 28 DT DG HET ORP D 17 12 HET ACY A 401 4 HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM ACY ACETIC ACID FORMUL 3 ORP C5 H11 O7 P FORMUL 4 ACY C2 H4 O2 FORMUL 5 HOH *207(H2 O) HELIX 1 AA1 SER A 115 LEU A 120 1 6 HELIX 2 AA2 GLY A 142 GLY A 149 1 8 HELIX 3 AA3 HIS A 158 SER A 166 1 9 HELIX 4 AA4 ASN A 174 HIS A 179 5 6 HELIX 5 AA5 THR A 180 GLY A 186 1 7 HELIX 6 AA6 SER A 204 GLN A 223 1 20 HELIX 7 AA7 GLY A 231 GLY A 244 1 14 HELIX 8 AA8 LYS A 285 GLU A 303 1 19 SHEET 1 AA1 5 ILE A 187 ASN A 191 0 SHEET 2 AA1 5 ILE A 134 GLY A 138 1 N GLY A 138 O THR A 190 SHEET 3 AA1 5 ILE A 226 ASN A 230 1 O VAL A 228 N ILE A 137 SHEET 4 AA1 5 LEU A 265 MET A 269 1 O LEU A 265 N ALA A 227 SHEET 5 AA1 5 GLY A 253 LYS A 258 -1 N GLY A 253 O VAL A 268 LINK O3' DA D 16 P ORP D 17 1555 1555 1.54 LINK O3 ORP D 17 P DG D 18 1555 1555 1.62 SITE 1 AC1 9 GLY A 138 ILE A 139 ASN A 140 TYR A 152 SITE 2 AC1 9 ASN A 191 HOH A 505 HOH A 509 HOH A 540 SITE 3 AC1 9 ORP D 17 SITE 1 AC2 22 ASN A 140 PRO A 141 ASN A 157 THR A 197 SITE 2 AC2 22 SER A 200 SER A 271 SER A 273 ALA A 274 SITE 3 AC2 22 ARG A 275 CYS A 276 ALA A 277 GLN A 278 SITE 4 AC2 22 ACY A 401 DA C 10 DC C 11 DG C 12 SITE 5 AC2 22 DT C 13 DG C 14 DC D 15 DT D 19 SITE 6 AC2 22 HOH D 102 HOH D 124 CRYST1 97.887 53.804 81.245 90.00 96.07 90.00 C 1 2 1 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 0.010216 0.000000 0.001086 0.00000 SCALE2 0.000000 0.018586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012378 0.00000