PDB Short entry for 4Z3A HEADER HYDROLASE/DNA 31-MAR-15 4Z3A TITLE ACETATE-FREE STRUCTURE OF THE ENZYME-PRODUCT COMPLEX RESULTING FROM TITLE 2 TDG ACTION ON A GU MISMATCH 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 4Z3A 1 REMARK REVDAT 5 25-DEC-19 4Z3A 1 REMARK REVDAT 4 13-SEP-17 4Z3A 1 JRNL REMARK REVDAT 3 11-NOV-15 4Z3A 1 JRNL REVDAT 2 30-SEP-15 4Z3A 1 JRNL REVDAT 1 16-SEP-15 4Z3A 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. 1.72 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 42189 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1732 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.87 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) : 2760 REMARK 3 BIN R VALUE (WORKING SET) : 0.2627 REMARK 3 BIN FREE R VALUE : 0.2567 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.02 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 146 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1550 REMARK 3 NUCLEIC ACID ATOMS : 1147 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 185 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.61530 REMARK 3 B22 (A**2) : -0.05590 REMARK 3 B33 (A**2) : 10.67110 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.03590 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.357 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.113 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.107 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.106 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.103 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 : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2949 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4229 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 861 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 34 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 297 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2949 ; 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 : 3136 ; 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) : 3.31 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 21.40 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|105 - A|116 } REMARK 3 ORIGIN FOR THE GROUP (A): 28.6568 -12.4548 37.0737 REMARK 3 T TENSOR REMARK 3 T11: 0.4579 T22: 0.1910 REMARK 3 T33: 0.2329 T12: 0.0305 REMARK 3 T13: -0.0390 T23: 0.1141 REMARK 3 L TENSOR REMARK 3 L11: 9.5868 L22: 3.4374 REMARK 3 L33: 9.6659 L12: 3.5335 REMARK 3 L13: 3.7274 L23: 9.4204 REMARK 3 S TENSOR REMARK 3 S11: 0.0213 S12: 0.4206 S13: 0.9440 REMARK 3 S21: -0.2345 S22: 0.2831 S23: -0.1405 REMARK 3 S31: -0.7212 S32: 0.5797 S33: -0.3044 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|117 - A|142 } REMARK 3 ORIGIN FOR THE GROUP (A): 11.8307 -11.4054 24.3755 REMARK 3 T TENSOR REMARK 3 T11: 0.2578 T22: 0.0728 REMARK 3 T33: 0.2062 T12: -0.0312 REMARK 3 T13: -0.0192 T23: -0.0418 REMARK 3 L TENSOR REMARK 3 L11: 3.7934 L22: 2.7974 REMARK 3 L33: 4.0453 L12: -0.0988 REMARK 3 L13: 1.5269 L23: -0.4402 REMARK 3 S TENSOR REMARK 3 S11: 0.2635 S12: 0.1214 S13: -0.4288 REMARK 3 S21: 0.0926 S22: -0.2224 S23: 0.3649 REMARK 3 S31: 0.4843 S32: 0.0646 S33: -0.0411 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { A|143 - A|169 } REMARK 3 ORIGIN FOR THE GROUP (A): 13.1978 -4.5254 34.0760 REMARK 3 T TENSOR REMARK 3 T11: 0.2523 T22: 0.0435 REMARK 3 T33: 0.1092 T12: -0.0212 REMARK 3 T13: 0.0011 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 3.7940 L22: 5.7949 REMARK 3 L33: 2.6263 L12: -2.4354 REMARK 3 L13: 0.7074 L23: -0.9943 REMARK 3 S TENSOR REMARK 3 S11: -0.1499 S12: -0.1899 S13: -0.0239 REMARK 3 S21: 0.6854 S22: 0.0259 S23: 0.2829 REMARK 3 S31: 0.0816 S32: 0.0139 S33: 0.1240 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { A|170 - A|176 } REMARK 3 ORIGIN FOR THE GROUP (A): 6.9640 -5.8110 39.4347 REMARK 3 T TENSOR REMARK 3 T11: 0.3624 T22: 0.1528 REMARK 3 T33: 0.1890 T12: -0.0229 REMARK 3 T13: 0.0959 T23: 0.0551 REMARK 3 L TENSOR REMARK 3 L11: 13.5469 L22: 6.3907 REMARK 3 L33: 8.8057 L12: -1.9185 REMARK 3 L13: -0.9909 L23: 2.7809 REMARK 3 S TENSOR REMARK 3 S11: -0.2350 S12: -0.6457 S13: -0.3133 REMARK 3 S21: 0.3691 S22: 0.1603 S23: 0.5712 REMARK 3 S31: 0.4606 S32: -0.2039 S33: 0.0747 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { A|177 - A|198 } REMARK 3 ORIGIN FOR THE GROUP (A): 9.5899 -9.4531 26.9492 REMARK 3 T TENSOR REMARK 3 T11: 0.2853 T22: 0.0936 REMARK 3 T33: 0.2281 T12: -0.0483 REMARK 3 T13: 0.0202 T23: -0.0396 REMARK 3 L TENSOR REMARK 3 L11: 3.4249 L22: 2.9928 REMARK 3 L33: 5.2321 L12: -0.4663 REMARK 3 L13: -1.0411 L23: -0.7462 REMARK 3 S TENSOR REMARK 3 S11: -0.0529 S12: 0.0218 S13: -0.1898 REMARK 3 S21: 0.2667 S22: -0.1335 S23: 0.5352 REMARK 3 S31: 0.4251 S32: -0.1890 S33: 0.1864 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: { A|199 - A|216 } REMARK 3 ORIGIN FOR THE GROUP (A): 19.4153 -7.3952 12.9549 REMARK 3 T TENSOR REMARK 3 T11: 0.3034 T22: 0.2203 REMARK 3 T33: 0.0192 T12: 0.0476 REMARK 3 T13: -0.0141 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 10.8689 L22: 6.7444 REMARK 3 L33: 4.4930 L12: 4.3669 REMARK 3 L13: 0.7970 L23: -0.5581 REMARK 3 S TENSOR REMARK 3 S11: 0.1768 S12: 0.0600 S13: -0.3450 REMARK 3 S21: -0.4480 S22: -0.4067 S23: -0.3091 REMARK 3 S31: 0.4901 S32: 0.7733 S33: 0.2299 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: { A|217 - A|269 } REMARK 3 ORIGIN FOR THE GROUP (A): 7.5010 0.5603 13.9443 REMARK 3 T TENSOR REMARK 3 T11: 0.2269 T22: 0.1060 REMARK 3 T33: 0.1243 T12: -0.0022 REMARK 3 T13: -0.1406 T23: -0.0483 REMARK 3 L TENSOR REMARK 3 L11: 1.8872 L22: 5.5736 REMARK 3 L33: 3.3207 L12: -1.4484 REMARK 3 L13: 0.2280 L23: -0.3341 REMARK 3 S TENSOR REMARK 3 S11: 0.0447 S12: 0.2654 S13: -0.0303 REMARK 3 S21: -0.5813 S22: -0.2292 S23: 0.4998 REMARK 3 S31: -0.0208 S32: -0.1588 S33: 0.1845 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: { A|270 - A|300 } REMARK 3 ORIGIN FOR THE GROUP (A): 8.6485 6.8646 28.3123 REMARK 3 T TENSOR REMARK 3 T11: 0.1483 T22: -0.0031 REMARK 3 T33: 0.1234 T12: 0.0353 REMARK 3 T13: -0.0366 T23: -0.0667 REMARK 3 L TENSOR REMARK 3 L11: 3.6692 L22: 1.8399 REMARK 3 L33: 2.7277 L12: -1.7355 REMARK 3 L13: 1.3728 L23: -0.8636 REMARK 3 S TENSOR REMARK 3 S11: -0.1505 S12: -0.1318 S13: -0.0676 REMARK 3 S21: 0.2428 S22: -0.0340 S23: 0.3877 REMARK 3 S31: -0.2658 S32: -0.2412 S33: 0.1845 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: { C|1 - C|16 } REMARK 3 ORIGIN FOR THE GROUP (A): 28.1257 9.2292 19.4267 REMARK 3 T TENSOR REMARK 3 T11: 0.3864 T22: 0.3451 REMARK 3 T33: 0.1496 T12: -0.1541 REMARK 3 T13: -0.0701 T23: 0.1407 REMARK 3 L TENSOR REMARK 3 L11: 3.3620 L22: 3.4266 REMARK 3 L33: 14.5585 L12: 1.3770 REMARK 3 L13: -2.9488 L23: -4.1232 REMARK 3 S TENSOR REMARK 3 S11: -0.3050 S12: 0.8210 S13: 0.3500 REMARK 3 S21: -0.7167 S22: 0.1943 S23: -0.2702 REMARK 3 S31: 0.2595 S32: 0.4740 S33: 0.1107 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: { C|17 - C|28 } REMARK 3 ORIGIN FOR THE GROUP (A): 35.5904 -5.7162 62.1753 REMARK 3 T TENSOR REMARK 3 T11: 0.4783 T22: 0.1646 REMARK 3 T33: 0.1803 T12: -0.0190 REMARK 3 T13: -0.2304 T23: 0.0243 REMARK 3 L TENSOR REMARK 3 L11: 1.1975 L22: 4.4745 REMARK 3 L33: 15.0205 L12: 0.2974 REMARK 3 L13: 3.0794 L23: -2.8056 REMARK 3 S TENSOR REMARK 3 S11: 0.2534 S12: -0.1284 S13: -0.0933 REMARK 3 S21: 0.7695 S22: -0.1634 S23: -0.3104 REMARK 3 S31: -0.9310 S32: 0.4086 S33: -0.0900 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: { D|1 - D|15 } REMARK 3 ORIGIN FOR THE GROUP (A): 35.7086 -3.4182 57.5504 REMARK 3 T TENSOR REMARK 3 T11: 0.4899 T22: 0.1176 REMARK 3 T33: 0.2172 T12: -0.0179 REMARK 3 T13: -0.1579 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 2.2761 L22: 3.5270 REMARK 3 L33: 8.1248 L12: 0.2478 REMARK 3 L13: 0.1455 L23: -2.4809 REMARK 3 S TENSOR REMARK 3 S11: 0.2606 S12: 0.0462 S13: 0.0731 REMARK 3 S21: 0.8483 S22: -0.0945 S23: -0.2829 REMARK 3 S31: -0.8591 S32: 0.5135 S33: -0.1660 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: { D|16 - D|28 } REMARK 3 ORIGIN FOR THE GROUP (A): 28.6634 9.2171 12.2948 REMARK 3 T TENSOR REMARK 3 T11: 0.5966 T22: 0.4593 REMARK 3 T33: 0.1876 T12: -0.0875 REMARK 3 T13: 0.0353 T23: 0.1632 REMARK 3 L TENSOR REMARK 3 L11: 1.9870 L22: 0.0958 REMARK 3 L33: 11.0460 L12: 1.7257 REMARK 3 L13: -3.1768 L23: -2.3664 REMARK 3 S TENSOR REMARK 3 S11: 0.1624 S12: 0.3417 S13: 0.2071 REMARK 3 S21: -0.9689 S22: -0.1581 S23: 0.0580 REMARK 3 S31: -0.2930 S32: 1.2237 S33: -0.0043 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4Z3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208472. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-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 : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI 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 : 43547 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 32.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.63 REMARK 200 R MERGE FOR SHELL (I) : 0.04400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.570 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 (%): 52.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE, 20% PEG 3350, REMARK 280 PH 6.0, VAPOR DIFFUSION, SITTING DROP, 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 47.57900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.78250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.57900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.78250 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: 6140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 ILE A 302 REMARK 465 GLU A 303 REMARK 465 ARG A 304 REMARK 465 ASN A 305 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 MET A 108 CG SD CE REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 ASN A 249 CG OD1 ND2 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 DG C 16 O3' DG C 16 C3' -0.041 REMARK 500 DC D 8 O3' DC D 8 C3' -0.051 REMARK 500 DA D 16 O3' AAB D 17 P -0.118 REMARK 500 DT D 19 O3' DT D 19 C3' -0.041 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. = 2.1 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT C 28 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC D 13 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC D 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA D 16 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 DG D 23 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT D 27 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XEG 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 REMARK 900 RELATED ID: 5CYS RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 MICROHETEROGENEITY AT RESIDUES 17 IN CHAIN D, THIS STRUCTURE REMARK 999 CONTAINS BOTH ANOMERIC FORMS OF THE ABASIC NUCLEOTIDE, ORP AND AAB REMARK 999 AT 0.5 OCCUPANCY. DBREF 4Z3A A 111 308 UNP Q13569 TDG_HUMAN 111 308 DBREF 4Z3A C 1 28 PDB 4Z3A 4Z3A 1 28 DBREF 4Z3A D 1 28 PDB 4Z3A 4Z3A 1 28 SEQADV 4Z3A GLY A 105 UNP Q13569 EXPRESSION TAG SEQADV 4Z3A SER A 106 UNP Q13569 EXPRESSION TAG SEQADV 4Z3A HIS A 107 UNP Q13569 EXPRESSION TAG SEQADV 4Z3A MET A 108 UNP Q13569 EXPRESSION TAG SEQADV 4Z3A ALA A 109 UNP Q13569 EXPRESSION TAG SEQADV 4Z3A 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 AAB D 17 12 HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM AAB 2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE HETSYN AAB ABASIC DEOXYRIBOSE FORMUL 3 ORP C5 H11 O7 P FORMUL 3 AAB C5 H11 O7 P FORMUL 4 HOH *185(H2 O) HELIX 1 AA1 HIS A 107 ASN A 112 5 6 HELIX 2 AA2 SER A 115 THR A 121 1 7 HELIX 3 AA3 GLY A 142 GLY A 149 1 8 HELIX 4 AA4 HIS A 158 SER A 166 1 9 HELIX 5 AA5 ASN A 174 HIS A 179 5 6 HELIX 6 AA6 THR A 180 GLY A 186 1 7 HELIX 7 AA7 GLY A 199 LEU A 203 5 5 HELIX 8 AA8 SER A 204 GLN A 223 1 20 HELIX 9 AA9 GLY A 231 PHE A 243 1 13 HELIX 10 AB1 ARG A 281 LYS A 300 1 20 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 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 AORP D 17 1555 1555 1.59 LINK O3' DA D 16 P BAAB D 17 1555 1555 1.49 LINK O3 AORP D 17 P DG D 18 1555 1555 1.60 LINK O3'BAAB D 17 P DG D 18 1555 1555 1.64 CRYST1 95.158 53.565 81.390 90.00 95.06 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 0.010509 0.000000 0.000930 0.00000 SCALE2 0.000000 0.018669 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012335 0.00000