HEADER HYDROLASE/DNA 08-APR-15 4Z7Z TITLE STRUCTURE OF THE ENZYME-PRODUCT COMPLEX RESULTING FROM TDG ACTION ON A TITLE 2 GT MISMATCH IN THE PRESENCE OF EXCESS BASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 111-308; 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 6 27-SEP-23 4Z7Z 1 REMARK REVDAT 5 25-DEC-19 4Z7Z 1 REMARK REVDAT 4 13-SEP-17 4Z7Z 1 JRNL REMARK REVDAT 3 11-NOV-15 4Z7Z 1 JRNL REVDAT 2 30-SEP-15 4Z7Z 1 JRNL REVDAT 1 16-SEP-15 4Z7Z 0 JRNL AUTH S.S.MALIK,C.T.COEY,K.M.VARNEY,E.POZHARSKI,A.C.DROHAT JRNL TITL THYMINE DNA GLYCOSYLASE EXHIBITS NEGLIGIBLE AFFINITY FOR JRNL TITL 2 NUCLEOBASES THAT IT REMOVES FROM DNA. JRNL REF NUCLEIC ACIDS RES. V. 43 9541 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26358812 JRNL DOI 10.1093/NAR/GKV890 REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 34036 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1660 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.89 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.07 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2781 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE : 0.2667 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.66 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 167 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1535 REMARK 3 NUCLEIC ACID ATOMS : 1135 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -13.58600 REMARK 3 B22 (A**2) : 2.01910 REMARK 3 B33 (A**2) : 11.56690 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.86570 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.441 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.139 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.134 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.128 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.127 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 : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2927 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4202 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 857 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 36 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 297 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2927 ; 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 : 376 ; 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 : 3189 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.99 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.35 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 21.74 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 18 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|111 - A|117 } REMARK 3 ORIGIN FOR THE GROUP (A): 26.7746 -16.7768 35.0298 REMARK 3 T TENSOR REMARK 3 T11: 0.4198 T22: 0.5243 REMARK 3 T33: 0.1483 T12: 0.1015 REMARK 3 T13: 0.0355 T23: 0.2035 REMARK 3 L TENSOR REMARK 3 L11: 11.4354 L22: 1.6755 REMARK 3 L33: 22.9657 L12: 0.3822 REMARK 3 L13: -8.4001 L23: 5.3758 REMARK 3 S TENSOR REMARK 3 S11: 0.2000 S12: 0.2855 S13: 0.1396 REMARK 3 S21: 0.0769 S22: 0.1157 S23: -0.4454 REMARK 3 S31: 0.2787 S32: 0.3439 S33: -0.3157 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|118 - A|144 } REMARK 3 ORIGIN FOR THE GROUP (A): 11.5015 -11.2291 25.1003 REMARK 3 T TENSOR REMARK 3 T11: 0.3883 T22: 0.0913 REMARK 3 T33: 0.1058 T12: -0.0445 REMARK 3 T13: 0.0404 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 4.4486 L22: 4.1929 REMARK 3 L33: 5.5224 L12: -1.3052 REMARK 3 L13: 1.8164 L23: -2.3175 REMARK 3 S TENSOR REMARK 3 S11: 0.0874 S12: -0.1633 S13: -0.3293 REMARK 3 S21: 0.2029 S22: -0.1238 S23: 0.3602 REMARK 3 S31: 0.5443 S32: 0.1073 S33: 0.0364 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { A|145 - A|162 } REMARK 3 ORIGIN FOR THE GROUP (A): 13.9079 -6.3040 33.8523 REMARK 3 T TENSOR REMARK 3 T11: 0.4984 T22: 0.1337 REMARK 3 T33: 0.0684 T12: 0.0203 REMARK 3 T13: -0.0004 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 2.3590 L22: 4.1977 REMARK 3 L33: 3.6266 L12: -1.4538 REMARK 3 L13: -1.1496 L23: -1.2670 REMARK 3 S TENSOR REMARK 3 S11: -0.2041 S12: -0.3039 S13: -0.1194 REMARK 3 S21: 1.2120 S22: 0.0565 S23: 0.0267 REMARK 3 S31: 0.2146 S32: 0.1727 S33: 0.1475 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { A|163 - A|190 } REMARK 3 ORIGIN FOR THE GROUP (A): 3.1478 -5.1456 34.1539 REMARK 3 T TENSOR REMARK 3 T11: 0.4028 T22: 0.1567 REMARK 3 T33: 0.1916 T12: -0.0463 REMARK 3 T13: 0.2090 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 2.0879 L22: 4.4368 REMARK 3 L33: 7.3797 L12: 0.4707 REMARK 3 L13: 0.6561 L23: 1.7826 REMARK 3 S TENSOR REMARK 3 S11: -0.0504 S12: -0.3341 S13: 0.0073 REMARK 3 S21: 1.2054 S22: -0.0015 S23: 0.7418 REMARK 3 S31: 0.2515 S32: -0.5019 S33: 0.0519 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { A|191 - A|200 } REMARK 3 ORIGIN FOR THE GROUP (A): 20.3378 -10.0596 20.9139 REMARK 3 T TENSOR REMARK 3 T11: 0.5039 T22: 0.3450 REMARK 3 T33: 0.0478 T12: 0.0093 REMARK 3 T13: 0.0517 T23: 0.0326 REMARK 3 L TENSOR REMARK 3 L11: 7.7083 L22: 6.7809 REMARK 3 L33: 6.8796 L12: -2.4489 REMARK 3 L13: -0.9329 L23: -4.7548 REMARK 3 S TENSOR REMARK 3 S11: -0.0451 S12: 0.0440 S13: -0.0816 REMARK 3 S21: 0.0713 S22: -0.2972 S23: -0.0523 REMARK 3 S31: -0.2411 S32: 0.9826 S33: 0.3423 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: { A|201 - A|216 } REMARK 3 ORIGIN FOR THE GROUP (A): 18.1610 -7.9513 12.9642 REMARK 3 T TENSOR REMARK 3 T11: 0.4816 T22: 0.2817 REMARK 3 T33: 0.0235 T12: 0.0131 REMARK 3 T13: 0.0709 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 10.3975 L22: 4.6817 REMARK 3 L33: 4.2434 L12: 2.1676 REMARK 3 L13: -0.4678 L23: -1.4359 REMARK 3 S TENSOR REMARK 3 S11: 0.2524 S12: 0.0854 S13: -0.0991 REMARK 3 S21: -0.3341 S22: -0.4627 S23: -0.1009 REMARK 3 S31: 0.2377 S32: 0.7638 S33: 0.2103 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: { A|217 - A|233 } REMARK 3 ORIGIN FOR THE GROUP (A): 4.4817 -4.9482 17.1027 REMARK 3 T TENSOR REMARK 3 T11: 0.3276 T22: 0.1468 REMARK 3 T33: 0.1727 T12: -0.0304 REMARK 3 T13: -0.0412 T23: -0.0400 REMARK 3 L TENSOR REMARK 3 L11: 4.5940 L22: 4.2277 REMARK 3 L33: 2.9480 L12: 0.4843 REMARK 3 L13: 0.9180 L23: -0.4900 REMARK 3 S TENSOR REMARK 3 S11: -0.1556 S12: 0.1603 S13: -0.1800 REMARK 3 S21: -0.5129 S22: 0.0319 S23: 0.5332 REMARK 3 S31: 0.1460 S32: -0.2881 S33: 0.1237 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: { A|234 - A|247 } REMARK 3 ORIGIN FOR THE GROUP (A): 13.2617 1.9406 9.7446 REMARK 3 T TENSOR REMARK 3 T11: 0.4709 T22: 0.1665 REMARK 3 T33: 0.0246 T12: -0.0255 REMARK 3 T13: 0.0408 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 6.1019 L22: 3.5625 REMARK 3 L33: 3.6686 L12: 1.0496 REMARK 3 L13: 0.2785 L23: 1.3761 REMARK 3 S TENSOR REMARK 3 S11: -0.0723 S12: 0.3999 S13: 0.1888 REMARK 3 S21: -0.5831 S22: -0.0079 S23: -0.0099 REMARK 3 S31: -0.3593 S32: 0.4092 S33: 0.0802 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: { A|248 - A|257 } REMARK 3 ORIGIN FOR THE GROUP (A): 9.4239 9.6862 13.6228 REMARK 3 T TENSOR REMARK 3 T11: -0.0032 T22: 0.1892 REMARK 3 T33: 0.2586 T12: 0.0926 REMARK 3 T13: -0.0238 T23: 0.0661 REMARK 3 L TENSOR REMARK 3 L11: 7.2692 L22: 0.0000 REMARK 3 L33: 5.1266 L12: -4.9248 REMARK 3 L13: -0.9356 L23: -4.3277 REMARK 3 S TENSOR REMARK 3 S11: 0.0361 S12: 0.2096 S13: 0.4613 REMARK 3 S21: -1.1769 S22: -0.1144 S23: 0.0405 REMARK 3 S31: -0.3084 S32: 0.0981 S33: 0.0783 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: { A|258 - A|267 } REMARK 3 ORIGIN FOR THE GROUP (A): 0.4713 -0.3995 12.3809 REMARK 3 T TENSOR REMARK 3 T11: 0.3574 T22: 0.1637 REMARK 3 T33: 0.1906 T12: -0.0794 REMARK 3 T13: -0.1003 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 3.2446 L22: 5.1171 REMARK 3 L33: 8.7514 L12: 1.6955 REMARK 3 L13: 0.4096 L23: 3.7381 REMARK 3 S TENSOR REMARK 3 S11: -0.0402 S12: 0.3194 S13: -0.0619 REMARK 3 S21: -0.3385 S22: 0.0188 S23: 0.5412 REMARK 3 S31: 0.2386 S32: -0.3995 S33: 0.0214 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: { A|268 - A|280 } REMARK 3 ORIGIN FOR THE GROUP (A): 17.4140 5.8420 27.0717 REMARK 3 T TENSOR REMARK 3 T11: 0.3088 T22: 0.1242 REMARK 3 T33: 0.0706 T12: 0.0133 REMARK 3 T13: -0.0088 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 1.9777 L22: 2.1944 REMARK 3 L33: 5.3265 L12: 0.2895 REMARK 3 L13: 3.4050 L23: 0.8586 REMARK 3 S TENSOR REMARK 3 S11: -0.0757 S12: 0.0259 S13: 0.2620 REMARK 3 S21: 0.2739 S22: -0.0853 S23: 0.1537 REMARK 3 S31: -0.0906 S32: 0.3363 S33: 0.1610 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: { A|281 - A|303 } REMARK 3 ORIGIN FOR THE GROUP (A): 1.4210 6.9707 27.1247 REMARK 3 T TENSOR REMARK 3 T11: 0.2689 T22: 0.1009 REMARK 3 T33: 0.1870 T12: 0.0707 REMARK 3 T13: 0.0664 T23: -0.0598 REMARK 3 L TENSOR REMARK 3 L11: 6.3860 L22: 1.7838 REMARK 3 L33: 4.1880 L12: 0.7865 REMARK 3 L13: 1.8507 L23: 0.3085 REMARK 3 S TENSOR REMARK 3 S11: -0.1299 S12: -0.3102 S13: 0.2788 REMARK 3 S21: 0.3877 S22: -0.0764 S23: 0.6636 REMARK 3 S31: -0.2993 S32: -0.6425 S33: 0.2063 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: { C|1 - C|4 } REMARK 3 ORIGIN FOR THE GROUP (A): 25.3317 17.7771 0.1219 REMARK 3 T TENSOR REMARK 3 T11: 0.8124 T22: 0.5368 REMARK 3 T33: 0.0425 T12: -0.0025 REMARK 3 T13: 0.1761 T23: 0.1536 REMARK 3 L TENSOR REMARK 3 L11: 9.0894 L22: 4.5977 REMARK 3 L33: 3.7566 L12: -2.4560 REMARK 3 L13: -1.9858 L23: -1.2868 REMARK 3 S TENSOR REMARK 3 S11: 0.3958 S12: -0.3854 S13: 0.2903 REMARK 3 S21: -0.0503 S22: -0.0872 S23: 1.3394 REMARK 3 S31: -0.0131 S32: -0.4977 S33: -0.3086 REMARK 3 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: { C|5 - C|8 } REMARK 3 ORIGIN FOR THE GROUP (A): 29.0259 6.5756 9.9875 REMARK 3 T TENSOR REMARK 3 T11: 0.6093 T22: 0.7123 REMARK 3 T33: 0.0221 T12: -0.0749 REMARK 3 T13: 0.0935 T23: 0.1029 REMARK 3 L TENSOR REMARK 3 L11: 8.4070 L22: 11.4540 REMARK 3 L33: 8.6392 L12: 3.9627 REMARK 3 L13: 4.3945 L23: 5.1790 REMARK 3 S TENSOR REMARK 3 S11: 0.0560 S12: 0.5655 S13: -1.2290 REMARK 3 S21: -0.1037 S22: 0.3760 S23: -0.0096 REMARK 3 S31: 0.4138 S32: 0.4243 S33: -0.4321 REMARK 3 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: { C|9 - C|17 } REMARK 3 ORIGIN FOR THE GROUP (A): 26.5149 5.5970 34.5797 REMARK 3 T TENSOR REMARK 3 T11: 0.3165 T22: 0.2898 REMARK 3 T33: 0.0018 T12: 0.0048 REMARK 3 T13: -0.1406 T23: 0.0248 REMARK 3 L TENSOR REMARK 3 L11: 6.3953 L22: 5.4870 REMARK 3 L33: 9.9490 L12: -0.8739 REMARK 3 L13: -0.0737 L23: -0.2922 REMARK 3 S TENSOR REMARK 3 S11: 0.2975 S12: -0.2368 S13: 0.0857 REMARK 3 S21: 0.3752 S22: -0.2726 S23: -0.1892 REMARK 3 S31: -0.2673 S32: 0.8782 S33: -0.0249 REMARK 3 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: { C|18 - C|28 } REMARK 3 ORIGIN FOR THE GROUP (A): 33.6836 -5.7518 64.2077 REMARK 3 T TENSOR REMARK 3 T11: 0.6225 T22: 0.2226 REMARK 3 T33: 0.2070 T12: 0.0375 REMARK 3 T13: -0.2068 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 1.5506 L22: 8.7114 REMARK 3 L33: 13.3361 L12: 0.3436 REMARK 3 L13: 0.9666 L23: -3.3458 REMARK 3 S TENSOR REMARK 3 S11: 0.2298 S12: -0.0593 S13: 0.0085 REMARK 3 S21: 0.6376 S22: -0.1254 S23: -0.2389 REMARK 3 S31: -1.0663 S32: 0.4397 S33: -0.1045 REMARK 3 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: { D|1 - D|15 } REMARK 3 ORIGIN FOR THE GROUP (A): 33.5574 -3.4218 58.0817 REMARK 3 T TENSOR REMARK 3 T11: 0.5325 T22: 0.1065 REMARK 3 T33: 0.1431 T12: 0.0100 REMARK 3 T13: -0.1143 T23: -0.0006 REMARK 3 L TENSOR REMARK 3 L11: 3.2148 L22: 5.3731 REMARK 3 L33: 7.2099 L12: 0.2092 REMARK 3 L13: -0.2458 L23: -2.7787 REMARK 3 S TENSOR REMARK 3 S11: 0.3844 S12: 0.1112 S13: 0.1023 REMARK 3 S21: 0.7912 S22: -0.2271 S23: -0.3050 REMARK 3 S31: -0.6452 S32: 0.5292 S33: -0.1573 REMARK 3 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: { D|16 - D|28 } REMARK 3 ORIGIN FOR THE GROUP (A): 27.3302 9.3570 12.3343 REMARK 3 T TENSOR REMARK 3 T11: 0.5961 T22: 0.4758 REMARK 3 T33: 0.1418 T12: -0.0936 REMARK 3 T13: -0.0369 T23: 0.1423 REMARK 3 L TENSOR REMARK 3 L11: 2.2250 L22: 3.2518 REMARK 3 L33: 12.7148 L12: 2.1227 REMARK 3 L13: -5.3832 L23: -4.2148 REMARK 3 S TENSOR REMARK 3 S11: 0.0939 S12: 0.1700 S13: 0.2280 REMARK 3 S21: -0.7057 S22: -0.1229 S23: -0.0698 REMARK 3 S31: -0.0804 S32: 0.9724 S33: 0.0289 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4Z7Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-14 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 : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34165 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 39.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.05700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.400 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: 4FNC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 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 45.36450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.73000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.36450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.73000 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: 5100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 ALA A 109 REMARK 465 SER A 110 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 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 248 CG CD CE NZ REMARK 470 ASN A 249 CG OD1 ND2 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' -0.037 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. = 2.6 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC C 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 28 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT D 4 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC D 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC D 21 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 ASN A 249 64.40 -107.54 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 EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 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: 5CYS RELATED DB: PDB DBREF 4Z7Z A 111 308 UNP Q13569 TDG_HUMAN 111 308 DBREF 4Z7Z C 1 28 PDB 4Z7Z 4Z7Z 1 28 DBREF 4Z7Z D 1 28 PDB 4Z7Z 4Z7Z 1 28 SEQADV 4Z7Z GLY A 105 UNP Q13569 EXPRESSION TAG SEQADV 4Z7Z SER A 106 UNP Q13569 EXPRESSION TAG SEQADV 4Z7Z HIS A 107 UNP Q13569 EXPRESSION TAG SEQADV 4Z7Z MET A 108 UNP Q13569 EXPRESSION TAG SEQADV 4Z7Z ALA A 109 UNP Q13569 EXPRESSION TAG SEQADV 4Z7Z 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 EDO A 401 4 HET ACY A 402 4 HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM ACY ACETIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ORP C5 H11 O7 P FORMUL 4 EDO C2 H6 O2 FORMUL 5 ACY C2 H4 O2 FORMUL 6 HOH *205(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 GLY A 199 LEU A 203 5 5 HELIX 7 AA7 SER A 204 GLN A 223 1 20 HELIX 8 AA8 GLY A 231 PHE A 243 1 13 HELIX 9 AA9 ARG A 281 ASN A 305 1 25 SHEET 1 AA1 5 ILE A 187 ASN A 191 0 SHEET 2 AA1 5 ILE A 134 GLY A 138 1 N ILE A 136 O GLY A 188 SHEET 3 AA1 5 ILE A 226 ASN A 230 1 O VAL A 228 N VAL A 135 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 LEU A 254 -1 N GLY A 253 O VAL A 268 LINK O3' DA D 16 P ORP D 17 1555 1555 1.61 LINK O3 ORP D 17 P DG D 18 1555 1555 1.57 SITE 1 AC1 4 ASN A 131 LEU A 132 GLN A 223 ARG A 225 SITE 1 AC2 9 GLY A 138 ILE A 139 ASN A 140 TYR A 152 SITE 2 AC2 9 ASN A 191 HOH A 503 HOH A 504 HOH A 547 SITE 3 AC2 9 ORP D 17 SITE 1 AC3 23 ASN A 140 ASN A 157 SER A 200 SER A 271 SITE 2 AC3 23 SER A 273 ALA A 274 ARG A 275 CYS A 276 SITE 3 AC3 23 ALA A 277 GLN A 278 ACY A 402 HOH A 533 SITE 4 AC3 23 HOH A 572 DA C 10 DC C 11 DG C 12 SITE 5 AC3 23 DT C 13 DG C 14 DC D 15 DT D 19 SITE 6 AC3 23 HOH D 108 HOH D 110 HOH D 129 CRYST1 90.729 53.460 82.033 90.00 95.54 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 0.011022 0.000000 0.001069 0.00000 SCALE2 0.000000 0.018706 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012247 0.00000