HEADER HYDROLASE/DNA/RNA 28-MAR-18 6CVT TITLE HUMAN APRATAXIN (APTX) V263G BOUND TO RNA-DNA, AMP AND ZN PRODUCT TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: APRATAXIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: APRATAXIN CATALYTIC DOMAIN; COMPND 5 SYNONYM: FORKHEAD-ASSOCIATED DOMAIN HISTIDINE TRIAD-LIKE PROTEIN,FHA- COMPND 6 HIT; COMPND 7 EC: 3.1.11.7,3.1.12.2; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA/RNA (5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'); COMPND 12 CHAIN: D, G; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'); COMPND 16 CHAIN: E, H; COMPND 17 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: APTX, AXA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_TAXID: 9606 KEYWDS PROTEIN-DNA COMPLEX, DNA REPAIR, 5'-DNA END PROCESSING, HISTIDINE KEYWDS 2 TRIAD DOMAIN, HIT DOMAIN, ZINC-FINGER, 5'-DNA END RECOGNITION, KEYWDS 3 HYDROLASE, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SCHELLENBERG,P.S.TUMBALE,R.S.WILLIAMS REVDAT 5 04-OCT-23 6CVT 1 REMARK REVDAT 4 18-DEC-19 6CVT 1 REMARK REVDAT 3 06-NOV-19 6CVT 1 REMARK REVDAT 2 25-JUL-18 6CVT 1 JRNL REVDAT 1 04-JUL-18 6CVT 0 JRNL AUTH P.TUMBALE,M.J.SCHELLENBERG,G.A.MUELLER,E.FAIRWEATHER, JRNL AUTH 2 M.WATSON,J.N.LITTLE,J.KRAHN,I.WADDELL,R.E.LONDON, JRNL AUTH 3 R.S.WILLIAMS JRNL TITL MECHANISM OF APTX NICKED DNA SENSING AND PLEIOTROPIC JRNL TITL 2 INACTIVATION IN NEURODEGENERATIVE DISEASE. JRNL REF EMBO J. V. 37 2018 JRNL REFN ESSN 1460-2075 JRNL PMID 29934293 JRNL DOI 10.15252/EMBJ.201798875 REMARK 2 REMARK 2 RESOLUTION. 2.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 11635 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 556 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 38.9647 - 4.6667 0.99 3176 163 0.2219 0.2476 REMARK 3 2 4.6667 - 3.7050 1.00 3026 155 0.2393 0.2880 REMARK 3 3 3.7050 - 3.2369 0.91 2791 116 0.2806 0.3349 REMARK 3 4 3.2369 - 2.9411 0.71 2086 122 0.3072 0.3815 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.35 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 : 0.011 3978 REMARK 3 ANGLE : 1.435 5561 REMARK 3 CHIRALITY : 0.041 603 REMARK 3 PLANARITY : 0.005 548 REMARK 3 DIHEDRAL : 20.634 1542 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 164:206 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.1527 -28.5829 -12.3152 REMARK 3 T TENSOR REMARK 3 T11: 0.2814 T22: 0.2236 REMARK 3 T33: 0.3647 T12: 0.0278 REMARK 3 T13: 0.0294 T23: 0.0766 REMARK 3 L TENSOR REMARK 3 L11: 0.0293 L22: 0.0206 REMARK 3 L33: 0.0906 L12: -0.0269 REMARK 3 L13: 0.0048 L23: 0.0073 REMARK 3 S TENSOR REMARK 3 S11: -0.0864 S12: -0.0162 S13: -0.0433 REMARK 3 S21: 0.2271 S22: -0.1845 S23: -0.0349 REMARK 3 S31: -0.3785 S32: -0.1214 S33: -0.0062 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 207:217 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.3447 -21.1764 -4.2353 REMARK 3 T TENSOR REMARK 3 T11: 0.9629 T22: 0.5785 REMARK 3 T33: 0.3932 T12: 0.1517 REMARK 3 T13: -0.2894 T23: -0.1392 REMARK 3 L TENSOR REMARK 3 L11: 0.0031 L22: -0.0009 REMARK 3 L33: 0.0018 L12: -0.0021 REMARK 3 L13: 0.0031 L23: -0.0018 REMARK 3 S TENSOR REMARK 3 S11: -0.0211 S12: -0.0244 S13: 0.0876 REMARK 3 S21: 0.0055 S22: 0.0010 S23: 0.0124 REMARK 3 S31: -0.0457 S32: -0.0393 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 218:300 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5771 -26.0530 -18.3725 REMARK 3 T TENSOR REMARK 3 T11: 0.1358 T22: 0.2236 REMARK 3 T33: 0.1362 T12: 0.1533 REMARK 3 T13: -0.3072 T23: 0.0676 REMARK 3 L TENSOR REMARK 3 L11: 0.1223 L22: 0.1464 REMARK 3 L33: 0.0526 L12: -0.0967 REMARK 3 L13: 0.0424 L23: 0.0069 REMARK 3 S TENSOR REMARK 3 S11: -0.1811 S12: -0.0184 S13: -0.0941 REMARK 3 S21: 0.2546 S22: 0.0583 S23: 0.0247 REMARK 3 S31: 0.0369 S32: 0.2288 S33: -0.1368 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 301:340 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.6609 -17.7647 -31.3800 REMARK 3 T TENSOR REMARK 3 T11: 0.4849 T22: 0.3697 REMARK 3 T33: 0.3867 T12: -0.1340 REMARK 3 T13: -0.1232 T23: -0.0161 REMARK 3 L TENSOR REMARK 3 L11: 0.0502 L22: 0.0397 REMARK 3 L33: 0.0301 L12: -0.0261 REMARK 3 L13: -0.0338 L23: 0.0035 REMARK 3 S TENSOR REMARK 3 S11: -0.1210 S12: 0.1306 S13: -0.1540 REMARK 3 S21: -0.0655 S22: -0.0725 S23: -0.0934 REMARK 3 S31: -0.0458 S32: 0.1220 S33: -0.0002 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN D AND RESID 1:10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1574 -6.7715 -28.8564 REMARK 3 T TENSOR REMARK 3 T11: 0.3134 T22: 0.4183 REMARK 3 T33: 0.4941 T12: 0.0600 REMARK 3 T13: -0.1033 T23: 0.1150 REMARK 3 L TENSOR REMARK 3 L11: 0.0208 L22: 0.0015 REMARK 3 L33: 0.0100 L12: -0.0090 REMARK 3 L13: -0.0175 L23: 0.0011 REMARK 3 S TENSOR REMARK 3 S11: 0.2813 S12: -0.2826 S13: -0.2119 REMARK 3 S21: 0.0194 S22: 0.2607 S23: -0.0046 REMARK 3 S31: 0.1908 S32: 0.1001 S33: 0.0003 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN E AND RESID 1:10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.8503 -6.2434 -28.6630 REMARK 3 T TENSOR REMARK 3 T11: 0.6122 T22: 0.3811 REMARK 3 T33: 0.3871 T12: -0.1478 REMARK 3 T13: -0.0980 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: -0.0041 L22: 0.0229 REMARK 3 L33: 0.0058 L12: -0.0084 REMARK 3 L13: -0.0092 L23: -0.0063 REMARK 3 S TENSOR REMARK 3 S11: 0.0961 S12: -0.1171 S13: 0.1633 REMARK 3 S21: -0.1258 S22: 0.2145 S23: 0.0818 REMARK 3 S31: -0.0235 S32: 0.1216 S33: 0.0006 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN B AND RESID 164:206 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7722 8.9755 -16.0935 REMARK 3 T TENSOR REMARK 3 T11: 0.2215 T22: 0.2291 REMARK 3 T33: 0.8056 T12: 0.3615 REMARK 3 T13: -0.5778 T23: -0.1271 REMARK 3 L TENSOR REMARK 3 L11: 0.0453 L22: 0.0378 REMARK 3 L33: 0.0104 L12: -0.0443 REMARK 3 L13: 0.0110 L23: -0.0124 REMARK 3 S TENSOR REMARK 3 S11: 0.0039 S12: 0.0685 S13: -0.0099 REMARK 3 S21: -0.0705 S22: -0.1148 S23: 0.2168 REMARK 3 S31: -0.0731 S32: -0.0722 S33: -0.0648 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN B AND RESID 207:220 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.5933 18.3587 -27.0566 REMARK 3 T TENSOR REMARK 3 T11: 1.5072 T22: 1.4583 REMARK 3 T33: 1.1106 T12: 0.2139 REMARK 3 T13: 0.0262 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.0004 L22: 0.0001 REMARK 3 L33: 0.0033 L12: 0.0007 REMARK 3 L13: -0.0020 L23: 0.0025 REMARK 3 S TENSOR REMARK 3 S11: -0.0428 S12: 0.0094 S13: 0.0652 REMARK 3 S21: -0.0419 S22: -0.0997 S23: -0.0941 REMARK 3 S31: -0.0235 S32: 0.0641 S33: 0.0001 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN B AND RESID 221:265 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1316 19.8618 -13.7040 REMARK 3 T TENSOR REMARK 3 T11: 0.4837 T22: 0.4163 REMARK 3 T33: 0.7915 T12: 0.5578 REMARK 3 T13: -0.5859 T23: -0.1340 REMARK 3 L TENSOR REMARK 3 L11: 0.0042 L22: 0.0463 REMARK 3 L33: 0.0161 L12: -0.0152 REMARK 3 L13: 0.0099 L23: -0.0267 REMARK 3 S TENSOR REMARK 3 S11: 0.0026 S12: 0.0296 S13: -0.0033 REMARK 3 S21: -0.1306 S22: -0.1490 S23: 0.1195 REMARK 3 S31: -0.0803 S32: 0.1304 S33: 0.0173 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN B AND ( RESID 266:339 OR RESID 401:401 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.8227 20.1217 -3.3442 REMARK 3 T TENSOR REMARK 3 T11: 0.4200 T22: 0.5340 REMARK 3 T33: 0.7018 T12: 0.2887 REMARK 3 T13: -0.2566 T23: 0.0821 REMARK 3 L TENSOR REMARK 3 L11: 0.2383 L22: 0.1613 REMARK 3 L33: 0.2696 L12: 0.1670 REMARK 3 L13: 0.0664 L23: 0.1159 REMARK 3 S TENSOR REMARK 3 S11: -0.3571 S12: 0.1438 S13: 0.4673 REMARK 3 S21: 0.2660 S22: -0.0031 S23: -0.4113 REMARK 3 S31: -0.3303 S32: 0.2451 S33: -0.0195 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN G AND RESID 1:10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.5645 -0.3339 1.7367 REMARK 3 T TENSOR REMARK 3 T11: 0.6639 T22: 0.4701 REMARK 3 T33: 0.4361 T12: 0.2908 REMARK 3 T13: -0.0888 T23: -0.0152 REMARK 3 L TENSOR REMARK 3 L11: 0.0609 L22: 0.1515 REMARK 3 L33: 0.1540 L12: 0.0504 REMARK 3 L13: 0.0168 L23: -0.1263 REMARK 3 S TENSOR REMARK 3 S11: 0.2502 S12: 0.0182 S13: 0.0774 REMARK 3 S21: -0.1578 S22: 0.0996 S23: 0.2284 REMARK 3 S31: -0.0026 S32: 0.0754 S33: 0.0487 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: ( CHAIN H AND RESID 1:10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.3649 -0.0230 1.2138 REMARK 3 T TENSOR REMARK 3 T11: 0.8189 T22: 0.7470 REMARK 3 T33: 0.5583 T12: 0.2013 REMARK 3 T13: -0.0740 T23: -0.0133 REMARK 3 L TENSOR REMARK 3 L11: -0.0051 L22: 0.0082 REMARK 3 L33: 0.0180 L12: 0.0020 REMARK 3 L13: 0.0025 L23: -0.0117 REMARK 3 S TENSOR REMARK 3 S11: 0.0366 S12: -0.2930 S13: 0.2024 REMARK 3 S21: -0.1948 S22: 0.1151 S23: -0.0902 REMARK 3 S31: 0.0579 S32: 0.0331 S33: 0.0004 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 6CVT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000233586. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12827 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.940 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.40600 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: PHENIX REMARK 200 STARTING MODEL: 4NDH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 20% W/V POLYETHYLENE REMARK 280 GLYCOL 3350, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.36350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.56550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.36350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.56550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E 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 350 REMARK 350 BIOMOLECULE: 2 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: 2600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, G, H 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 161 REMARK 465 SER A 162 REMARK 465 HIS A 163 REMARK 465 THR A 341 REMARK 465 GLN A 342 REMARK 465 GLY B 161 REMARK 465 SER B 162 REMARK 465 TRP B 340 REMARK 465 THR B 341 REMARK 465 GLN B 342 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 HIS A 166 -56.15 51.17 REMARK 500 LYS A 243 32.71 -85.83 REMARK 500 HIS A 258 162.34 82.46 REMARK 500 GLU A 321 -73.59 -96.89 REMARK 500 GLN A 323 15.04 80.94 REMARK 500 GLN B 187 -30.70 -130.88 REMARK 500 ALA B 217 -175.89 52.87 REMARK 500 HIS B 220 -9.81 60.34 REMARK 500 HIS B 258 117.48 78.24 REMARK 500 GLU B 321 -77.37 -95.93 REMARK 500 GLN B 323 0.00 87.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 319 SG REMARK 620 2 CYS A 322 SG 101.2 REMARK 620 3 HIS A 335 NE2 86.3 82.2 REMARK 620 4 HIS A 339 NE2 124.9 127.9 119.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 319 SG REMARK 620 2 CYS B 322 SG 110.2 REMARK 620 3 HIS B 335 NE2 112.5 106.2 REMARK 620 4 HIS B 339 NE2 124.3 115.9 83.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NDF RELATED DB: PDB REMARK 900 4NDF CONTAINS WILDTYE APTX COMPLEXED WITH THE SAME DNA DBREF 6CVT A 165 342 UNP Q7Z2E3 APTX_HUMAN 179 356 DBREF 6CVT D 1 10 PDB 6CVT 6CVT 1 10 DBREF 6CVT E 1 10 PDB 6CVT 6CVT 1 10 DBREF 6CVT B 165 342 UNP Q7Z2E3 APTX_HUMAN 179 356 DBREF 6CVT G 1 10 PDB 6CVT 6CVT 1 10 DBREF 6CVT H 1 10 PDB 6CVT 6CVT 1 10 SEQADV 6CVT GLY A 161 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVT SER A 162 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVT HIS A 163 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVT MET A 164 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVT GLY A 263 UNP Q7Z2E3 VAL 277 ENGINEERED MUTATION SEQADV 6CVT GLY B 161 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVT SER B 162 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVT HIS B 163 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVT MET B 164 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVT GLY B 263 UNP Q7Z2E3 VAL 277 ENGINEERED MUTATION SEQRES 1 A 182 GLY SER HIS MET GLY HIS TRP SER GLN GLY LEU LYS ILE SEQRES 2 A 182 SER MET GLN ASP PRO LYS MET GLN VAL TYR LYS ASP GLU SEQRES 3 A 182 GLN VAL VAL VAL ILE LYS ASP LYS TYR PRO LYS ALA ARG SEQRES 4 A 182 TYR HIS TRP LEU VAL LEU PRO TRP THR SER ILE SER SER SEQRES 5 A 182 LEU LYS ALA VAL ALA ARG GLU HIS LEU GLU LEU LEU LYS SEQRES 6 A 182 HIS MET HIS THR VAL GLY GLU LYS VAL ILE VAL ASP PHE SEQRES 7 A 182 ALA GLY SER SER LYS LEU ARG PHE ARG LEU GLY TYR HIS SEQRES 8 A 182 ALA ILE PRO SER MET SER HIS VAL HIS LEU HIS GLY ILE SEQRES 9 A 182 SER GLN ASP PHE ASP SER PRO CYS LEU LYS ASN LYS LYS SEQRES 10 A 182 HIS TRP ASN SER PHE ASN THR GLU TYR PHE LEU GLU SER SEQRES 11 A 182 GLN ALA VAL ILE GLU MET VAL GLN GLU ALA GLY ARG VAL SEQRES 12 A 182 THR VAL ARG ASP GLY MET PRO GLU LEU LEU LYS LEU PRO SEQRES 13 A 182 LEU ARG CYS HIS GLU CYS GLN GLN LEU LEU PRO SER ILE SEQRES 14 A 182 PRO GLN LEU LYS GLU HIS LEU ARG LYS HIS TRP THR GLN SEQRES 1 D 10 G DT DT DA DT DG DA DT DT DC SEQRES 1 E 10 DG DA DA DT DC DA DT DA DA DC SEQRES 1 B 182 GLY SER HIS MET GLY HIS TRP SER GLN GLY LEU LYS ILE SEQRES 2 B 182 SER MET GLN ASP PRO LYS MET GLN VAL TYR LYS ASP GLU SEQRES 3 B 182 GLN VAL VAL VAL ILE LYS ASP LYS TYR PRO LYS ALA ARG SEQRES 4 B 182 TYR HIS TRP LEU VAL LEU PRO TRP THR SER ILE SER SER SEQRES 5 B 182 LEU LYS ALA VAL ALA ARG GLU HIS LEU GLU LEU LEU LYS SEQRES 6 B 182 HIS MET HIS THR VAL GLY GLU LYS VAL ILE VAL ASP PHE SEQRES 7 B 182 ALA GLY SER SER LYS LEU ARG PHE ARG LEU GLY TYR HIS SEQRES 8 B 182 ALA ILE PRO SER MET SER HIS VAL HIS LEU HIS GLY ILE SEQRES 9 B 182 SER GLN ASP PHE ASP SER PRO CYS LEU LYS ASN LYS LYS SEQRES 10 B 182 HIS TRP ASN SER PHE ASN THR GLU TYR PHE LEU GLU SER SEQRES 11 B 182 GLN ALA VAL ILE GLU MET VAL GLN GLU ALA GLY ARG VAL SEQRES 12 B 182 THR VAL ARG ASP GLY MET PRO GLU LEU LEU LYS LEU PRO SEQRES 13 B 182 LEU ARG CYS HIS GLU CYS GLN GLN LEU LEU PRO SER ILE SEQRES 14 B 182 PRO GLN LEU LYS GLU HIS LEU ARG LYS HIS TRP THR GLN SEQRES 1 G 10 G DT DT DA DT DG DA DT DT DC SEQRES 1 H 10 DG DA DA DT DC DA DT DA DA DC HET ZN A 401 1 HET AMP A 402 23 HET ZN B 401 1 HET AMP B 402 23 HETNAM ZN ZINC ION HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 7 ZN 2(ZN 2+) FORMUL 8 AMP 2(C10 H14 N5 O7 P) FORMUL 11 HOH *11(H2 O) HELIX 1 AA1 HIS A 166 SER A 168 5 3 HELIX 2 AA2 GLN A 169 ASP A 177 1 9 HELIX 3 AA3 SER A 212 VAL A 216 5 5 HELIX 4 AA4 ALA A 217 GLU A 219 5 3 HELIX 5 AA5 HIS A 220 GLY A 240 1 21 HELIX 6 AA6 ASN A 275 THR A 284 1 10 HELIX 7 AA7 SER A 290 GLY A 301 1 12 HELIX 8 AA8 GLY A 308 LEU A 313 1 6 HELIX 9 AA9 SER A 328 LYS A 338 1 11 HELIX 10 AB1 GLY B 165 SER B 168 5 4 HELIX 11 AB2 GLN B 169 MET B 175 1 7 HELIX 12 AB3 HIS B 220 GLY B 240 1 21 HELIX 13 AB4 ASN B 275 THR B 284 1 10 HELIX 14 AB5 SER B 290 GLY B 301 1 12 HELIX 15 AB6 GLY B 308 LYS B 314 1 7 HELIX 16 AB7 SER B 328 LYS B 338 1 11 SHEET 1 AA1 6 GLN A 181 LYS A 184 0 SHEET 2 AA1 6 VAL A 188 LYS A 192 -1 O VAL A 190 N VAL A 182 SHEET 3 AA1 6 HIS A 201 PRO A 206 -1 O LEU A 203 N ILE A 191 SHEET 4 AA1 6 LEU A 261 SER A 265 -1 O LEU A 261 N VAL A 204 SHEET 5 AA1 6 PHE A 246 HIS A 251 -1 N ARG A 247 O ILE A 264 SHEET 6 AA1 6 PHE A 287 GLU A 289 -1 O LEU A 288 N TYR A 250 SHEET 1 AA2 6 GLN B 181 LYS B 184 0 SHEET 2 AA2 6 VAL B 188 LYS B 192 -1 O VAL B 190 N TYR B 183 SHEET 3 AA2 6 HIS B 201 PRO B 206 -1 O LEU B 203 N ILE B 191 SHEET 4 AA2 6 LEU B 261 SER B 265 -1 O LEU B 261 N VAL B 204 SHEET 5 AA2 6 PHE B 246 HIS B 251 -1 N ARG B 247 O ILE B 264 SHEET 6 AA2 6 PHE B 287 GLU B 289 -1 O LEU B 288 N TYR B 250 SHEET 1 AA3 2 LEU B 317 ARG B 318 0 SHEET 2 AA3 2 LEU B 325 LEU B 326 -1 O LEU B 326 N LEU B 317 LINK SG CYS A 319 ZN ZN A 401 1555 1555 2.40 LINK SG CYS A 322 ZN ZN A 401 1555 1555 2.30 LINK NE2 HIS A 335 ZN ZN A 401 1555 1555 2.09 LINK NE2 HIS A 339 ZN ZN A 401 1555 1555 2.20 LINK SG CYS B 319 ZN ZN B 401 1555 1555 2.11 LINK SG CYS B 322 ZN ZN B 401 1555 1555 2.03 LINK NE2 HIS B 335 ZN ZN B 401 1555 1555 2.07 LINK NE2 HIS B 339 ZN ZN B 401 1555 1555 2.51 SITE 1 AC1 4 CYS A 319 CYS A 322 HIS A 335 HIS A 339 SITE 1 AC2 15 LEU A 171 SER A 174 ASP A 193 LYS A 194 SITE 2 AC2 15 TYR A 195 LYS A 197 LEU A 203 HIS A 251 SITE 3 AC2 15 PRO A 254 SER A 255 MET A 256 HIS A 260 SITE 4 AC2 15 HIS A 262 HOH A 501 G D 1 SITE 1 AC3 4 CYS B 319 CYS B 322 HIS B 335 HIS B 339 SITE 1 AC4 15 LEU B 171 SER B 174 ASP B 193 LYS B 194 SITE 2 AC4 15 TYR B 195 LYS B 197 LEU B 203 HIS B 251 SITE 3 AC4 15 PRO B 254 SER B 255 MET B 256 HIS B 260 SITE 4 AC4 15 HIS B 262 HOH B 501 G G 1 CRYST1 40.727 113.131 124.500 90.00 90.00 90.00 P 21 21 21 8 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 0.024554 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008032 0.00000