HEADER DNA BINDING PROTEIN/RNA/DNA 26-OCT-13 4NDG TITLE HUMAN APRATAXIN (APTX) BOUND TO RNA-DNA AND ZN - ADENOSINE VANADATE TITLE 2 TRANSITION STATE MIMIC COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: APRATAXIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: FORKHEAD-ASSOCIATED DOMAIN HISTIDINE TRIAD-LIKE PROTEIN, COMPND 5 FHA-HIT; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'; COMPND 9 CHAIN: D, G; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'; COMPND 13 CHAIN: E, H; COMPND 14 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 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, DNA REPAIR, 5'-DNA END PROCESSING, HISTIDINE KEYWDS 2 TRIAD DOMAIN, HIT DOMAIN, ZINC FINGER, 5'-DNA END RECOGNITION, DNA KEYWDS 3 BINDING PROTEIN-RNA-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SCHELLENBERG,P.S.TUMBALE,R.S.WILLIAMS REVDAT 4 20-SEP-23 4NDG 1 REMARK SEQADV LINK REVDAT 3 05-FEB-14 4NDG 1 JRNL REVDAT 2 15-JAN-14 4NDG 1 JRNL REVDAT 1 18-DEC-13 4NDG 0 JRNL AUTH P.TUMBALE,J.S.WILLIAMS,M.J.SCHELLENBERG,T.A.KUNKEL, JRNL AUTH 2 R.S.WILLIAMS JRNL TITL APRATAXIN RESOLVES ADENYLATED RNA-DNA JUNCTIONS TO MAINTAIN JRNL TITL 2 GENOME INTEGRITY. JRNL REF NATURE V. 506 111 2013 JRNL REFN ISSN 0028-0836 JRNL PMID 24362567 JRNL DOI 10.1038/NATURE12824 REMARK 2 REMARK 2 RESOLUTION. 2.54 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) : 2.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 19503 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1002 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 39.0679 - 4.8574 0.97 2744 159 0.1717 0.2141 REMARK 3 2 4.8574 - 3.8565 0.99 2695 147 0.1784 0.2294 REMARK 3 3 3.8565 - 3.3693 0.99 2620 142 0.2155 0.2837 REMARK 3 4 3.3693 - 3.0614 0.98 2645 129 0.2184 0.2726 REMARK 3 5 3.0614 - 2.8421 1.00 2622 150 0.2882 0.3541 REMARK 3 6 2.8421 - 2.6745 1.00 2594 157 0.3140 0.3337 REMARK 3 7 2.6745 - 2.5410 0.98 2581 118 0.3442 0.4316 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) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.55 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 : 0.015 4000 REMARK 3 ANGLE : 1.223 5585 REMARK 3 CHIRALITY : 0.048 606 REMARK 3 PLANARITY : 0.007 553 REMARK 3 DIHEDRAL : 20.484 1532 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 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9355 -28.6671 -12.9645 REMARK 3 T TENSOR REMARK 3 T11: 0.6834 T22: 0.4151 REMARK 3 T33: 0.4656 T12: -0.0433 REMARK 3 T13: -0.0102 T23: 0.1306 REMARK 3 L TENSOR REMARK 3 L11: 5.0898 L22: 4.5717 REMARK 3 L33: 5.6213 L12: -2.2505 REMARK 3 L13: 1.0503 L23: -2.5831 REMARK 3 S TENSOR REMARK 3 S11: -0.2459 S12: -0.4711 S13: -0.6895 REMARK 3 S21: 1.3096 S22: 0.2305 S23: 0.5123 REMARK 3 S31: 0.3484 S32: -0.3035 S33: -0.0063 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 207 THROUGH 217 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.4014 -21.3060 -4.1782 REMARK 3 T TENSOR REMARK 3 T11: 1.7963 T22: 0.7610 REMARK 3 T33: 0.5223 T12: 0.1475 REMARK 3 T13: -0.1066 T23: 0.1148 REMARK 3 L TENSOR REMARK 3 L11: 9.0590 L22: 4.4908 REMARK 3 L33: 7.6537 L12: 2.9007 REMARK 3 L13: -7.1995 L23: -4.9235 REMARK 3 S TENSOR REMARK 3 S11: 0.3883 S12: -0.2000 S13: 1.1440 REMARK 3 S21: 1.7009 S22: 0.4947 S23: 0.0736 REMARK 3 S31: -1.9365 S32: -0.3888 S33: -0.6074 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 218 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7793 -26.0082 -18.3620 REMARK 3 T TENSOR REMARK 3 T11: 0.6447 T22: 0.5458 REMARK 3 T33: 0.4140 T12: 0.0679 REMARK 3 T13: -0.0831 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 6.3100 L22: 6.2665 REMARK 3 L33: 8.2792 L12: -0.3625 REMARK 3 L13: 3.1059 L23: -0.4257 REMARK 3 S TENSOR REMARK 3 S11: -0.2148 S12: 0.2910 S13: -0.2323 REMARK 3 S21: 0.4668 S22: 0.2292 S23: -0.5465 REMARK 3 S31: 0.2247 S32: 0.9253 S33: -0.0778 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 301 THROUGH 340 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5859 -17.5668 -31.6528 REMARK 3 T TENSOR REMARK 3 T11: 0.9651 T22: 0.9004 REMARK 3 T33: 0.5834 T12: -0.2886 REMARK 3 T13: 0.0227 T23: 0.1383 REMARK 3 L TENSOR REMARK 3 L11: 2.8566 L22: 8.8513 REMARK 3 L33: 5.6575 L12: -2.7969 REMARK 3 L13: 0.6190 L23: -1.7838 REMARK 3 S TENSOR REMARK 3 S11: -0.3827 S12: 1.0120 S13: 0.3380 REMARK 3 S21: -1.1238 S22: 0.0574 S23: -0.5889 REMARK 3 S31: -0.7232 S32: 1.7550 S33: 0.3357 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.0358 -6.8902 -29.0292 REMARK 3 T TENSOR REMARK 3 T11: 1.0876 T22: 0.5962 REMARK 3 T33: 0.5017 T12: -0.0675 REMARK 3 T13: -0.1979 T23: 0.0404 REMARK 3 L TENSOR REMARK 3 L11: 4.3739 L22: 9.0614 REMARK 3 L33: 4.8860 L12: -1.1110 REMARK 3 L13: -0.7484 L23: -5.0885 REMARK 3 S TENSOR REMARK 3 S11: 0.0809 S12: 0.4845 S13: 0.1762 REMARK 3 S21: -0.8814 S22: 0.6229 S23: 0.4645 REMARK 3 S31: -0.5498 S32: -0.5459 S33: -0.7570 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.8548 -6.1317 -28.8061 REMARK 3 T TENSOR REMARK 3 T11: 1.2119 T22: 0.5343 REMARK 3 T33: 0.5369 T12: -0.1448 REMARK 3 T13: -0.1946 T23: 0.1004 REMARK 3 L TENSOR REMARK 3 L11: 4.2702 L22: 1.6256 REMARK 3 L33: 6.7163 L12: -2.4555 REMARK 3 L13: -2.4450 L23: 2.2639 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: 0.2499 S13: 0.4638 REMARK 3 S21: -0.6544 S22: 0.3827 S23: 0.1166 REMARK 3 S31: 0.1725 S32: 0.4710 S33: -0.2776 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 164 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.9849 8.9778 -15.8088 REMARK 3 T TENSOR REMARK 3 T11: 1.1650 T22: 0.7827 REMARK 3 T33: 1.2538 T12: 0.3808 REMARK 3 T13: -0.8524 T23: -0.5482 REMARK 3 L TENSOR REMARK 3 L11: 0.3127 L22: 4.0631 REMARK 3 L33: 0.6006 L12: -0.9045 REMARK 3 L13: 0.1073 L23: -1.1101 REMARK 3 S TENSOR REMARK 3 S11: 1.6525 S12: 1.0003 S13: -0.9882 REMARK 3 S21: -2.5907 S22: -0.4548 S23: 2.8870 REMARK 3 S31: 0.8888 S32: -0.2155 S33: 1.1223 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 207 THROUGH 217 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2174 16.3287 -25.7886 REMARK 3 T TENSOR REMARK 3 T11: 1.8155 T22: 2.4571 REMARK 3 T33: 0.8691 T12: 0.7763 REMARK 3 T13: -0.5084 T23: 0.0671 REMARK 3 L TENSOR REMARK 3 L11: 6.6337 L22: 3.7010 REMARK 3 L33: 6.3598 L12: 1.0390 REMARK 3 L13: 5.1066 L23: 3.1001 REMARK 3 S TENSOR REMARK 3 S11: 0.0451 S12: 1.8181 S13: -0.0898 REMARK 3 S21: -1.9379 S22: -0.5985 S23: 0.0929 REMARK 3 S31: 0.6493 S32: 3.4069 S33: 1.2251 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 218 THROUGH 275 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3898 19.0411 -12.1237 REMARK 3 T TENSOR REMARK 3 T11: 0.7455 T22: 0.6794 REMARK 3 T33: 1.1127 T12: 0.4743 REMARK 3 T13: -0.4928 T23: -0.2997 REMARK 3 L TENSOR REMARK 3 L11: 4.3517 L22: 4.8381 REMARK 3 L33: 1.3695 L12: -1.4461 REMARK 3 L13: 1.6175 L23: -1.9863 REMARK 3 S TENSOR REMARK 3 S11: 0.5455 S12: 0.1555 S13: 0.5197 REMARK 3 S21: -2.1342 S22: -0.8726 S23: 1.6390 REMARK 3 S31: -0.0486 S32: -0.0577 S33: 0.0438 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 276 THROUGH 340 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.9637 21.6587 -3.9872 REMARK 3 T TENSOR REMARK 3 T11: 0.5679 T22: 0.5765 REMARK 3 T33: 0.9686 T12: 0.1144 REMARK 3 T13: -0.1191 T23: -0.0621 REMARK 3 L TENSOR REMARK 3 L11: 7.3209 L22: 9.4159 REMARK 3 L33: 2.9188 L12: -3.8482 REMARK 3 L13: 3.1992 L23: -2.2381 REMARK 3 S TENSOR REMARK 3 S11: -0.1561 S12: 0.0885 S13: 1.4818 REMARK 3 S21: 0.6416 S22: -0.6004 S23: -0.7443 REMARK 3 S31: -1.1200 S32: 0.5304 S33: 0.5366 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'G' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.3795 0.2253 1.4662 REMARK 3 T TENSOR REMARK 3 T11: 1.0820 T22: 0.9128 REMARK 3 T33: 0.5808 T12: 0.3860 REMARK 3 T13: -0.0714 T23: -0.1389 REMARK 3 L TENSOR REMARK 3 L11: 5.9870 L22: 5.7865 REMARK 3 L33: 7.1125 L12: -1.3915 REMARK 3 L13: 3.3800 L23: -2.3633 REMARK 3 S TENSOR REMARK 3 S11: 0.9961 S12: -0.7945 S13: -0.5894 REMARK 3 S21: 0.3154 S22: 0.1219 S23: 0.5469 REMARK 3 S31: 1.0068 S32: 0.8213 S33: -0.9167 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.2522 0.3284 0.9365 REMARK 3 T TENSOR REMARK 3 T11: 1.0664 T22: 1.0195 REMARK 3 T33: 0.5011 T12: 0.2027 REMARK 3 T13: -0.0363 T23: 0.0076 REMARK 3 L TENSOR REMARK 3 L11: 1.9657 L22: 4.3156 REMARK 3 L33: 9.5090 L12: -1.4068 REMARK 3 L13: -2.2978 L23: 6.1967 REMARK 3 S TENSOR REMARK 3 S11: 0.2661 S12: -0.8377 S13: -0.0560 REMARK 3 S21: 0.0551 S22: 0.3009 S23: 0.0671 REMARK 3 S31: 0.7190 S32: 0.5928 S33: -0.4558 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 4NDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083063. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : ROSENBAUM-ROCK DOUBLE-CRYSTAL REMARK 200 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 : 19635 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.541 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.58200 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 1.8.2_1309 REMARK 200 STARTING MODEL: PDB ENTRY 4NDH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM FORMATE, 20% W/V REMARK 280 PEG3350, PH 7.5, 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 20.13800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.32900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.32900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.13800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.29000 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: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 GLN A 342 REMARK 465 GLY B 161 REMARK 465 SER B 162 REMARK 465 HIS B 163 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 ALA A 215 57.27 -92.20 REMARK 500 ALA A 239 23.81 -149.38 REMARK 500 HIS A 258 117.75 79.61 REMARK 500 GLU A 321 -62.03 -100.41 REMARK 500 SER B 211 -83.36 -103.59 REMARK 500 ALA B 239 23.53 -150.89 REMARK 500 HIS B 258 118.67 79.45 REMARK 500 GLU B 321 -65.72 -108.71 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 V5A A 401 V REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 260 NE2 REMARK 620 2 V5A A 401 O5' 83.5 REMARK 620 3 V5A A 401 OV2 89.7 117.6 REMARK 620 4 V5A A 401 OV1 92.8 121.1 121.1 REMARK 620 5 G D 1 OP3 168.5 91.3 83.6 98.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 319 SG REMARK 620 2 CYS A 322 SG 110.5 REMARK 620 3 HIS A 335 NE2 102.5 93.7 REMARK 620 4 HIS A 339 NE2 112.2 127.5 105.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 V5A B 401 V REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 260 NE2 REMARK 620 2 V5A B 401 O5' 94.2 REMARK 620 3 V5A B 401 OV2 86.9 117.3 REMARK 620 4 V5A B 401 OV1 88.7 120.3 122.5 REMARK 620 5 G G 1 OP3 170.2 89.6 83.3 97.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 319 SG REMARK 620 2 CYS B 322 SG 114.4 REMARK 620 3 HIS B 335 NE2 111.1 89.8 REMARK 620 4 HIS B 339 NE2 102.2 131.0 106.6 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 V5A A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE V5A B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SZQ RELATED DB: PDB REMARK 900 RELATED ID: 4NDF RELATED DB: PDB REMARK 900 RELATED ID: 4NDH RELATED DB: PDB REMARK 900 RELATED ID: 4NDI RELATED DB: PDB DBREF 4NDG A 165 342 UNP Q7Z2E3 APTX_HUMAN 179 356 DBREF 4NDG B 165 342 UNP Q7Z2E3 APTX_HUMAN 179 356 DBREF 4NDG D 1 10 PDB 4NDG 4NDG 1 10 DBREF 4NDG G 1 10 PDB 4NDG 4NDG 1 10 DBREF 4NDG E 1 10 PDB 4NDG 4NDG 1 10 DBREF 4NDG H 1 10 PDB 4NDG 4NDG 1 10 SEQADV 4NDG GLY A 161 UNP Q7Z2E3 EXPRESSION TAG SEQADV 4NDG SER A 162 UNP Q7Z2E3 EXPRESSION TAG SEQADV 4NDG HIS A 163 UNP Q7Z2E3 EXPRESSION TAG SEQADV 4NDG MET A 164 UNP Q7Z2E3 EXPRESSION TAG SEQADV 4NDG GLY B 161 UNP Q7Z2E3 EXPRESSION TAG SEQADV 4NDG SER B 162 UNP Q7Z2E3 EXPRESSION TAG SEQADV 4NDG HIS B 163 UNP Q7Z2E3 EXPRESSION TAG SEQADV 4NDG MET B 164 UNP Q7Z2E3 EXPRESSION TAG 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 VAL 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 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 VAL 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 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 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 V5A A 401 22 HET ZN A 402 1 HET V5A B 401 22 HET ZN B 402 1 HETNAM V5A ADENOSINE-5'-VANADATE HETNAM ZN ZINC ION FORMUL 7 V5A 2(C10 H13 N5 O6 V) FORMUL 8 ZN 2(ZN 2+) FORMUL 11 HOH *25(H2 O) HELIX 1 1 HIS A 166 SER A 168 5 3 HELIX 2 2 GLN A 169 ASP A 177 1 9 HELIX 3 3 SER A 212 VAL A 216 5 5 HELIX 4 4 ALA A 217 GLU A 219 5 3 HELIX 5 5 HIS A 220 GLY A 240 1 21 HELIX 6 6 ASN A 275 THR A 284 1 10 HELIX 7 7 SER A 290 GLY A 301 1 12 HELIX 8 8 GLY A 308 LEU A 313 1 6 HELIX 9 9 SER A 328 LYS A 338 1 11 HELIX 10 10 GLY B 165 SER B 168 5 4 HELIX 11 11 GLN B 169 ASP B 177 1 9 HELIX 12 12 ALA B 217 GLU B 219 5 3 HELIX 13 13 HIS B 220 GLY B 240 1 21 HELIX 14 14 ASN B 275 THR B 284 1 10 HELIX 15 15 SER B 290 GLY B 301 1 12 HELIX 16 16 GLY B 308 LYS B 314 1 7 HELIX 17 17 SER B 328 LYS B 338 1 11 SHEET 1 A 6 GLN A 181 LYS A 184 0 SHEET 2 A 6 VAL A 188 LYS A 192 -1 O VAL A 190 N TYR A 183 SHEET 3 A 6 HIS A 201 PRO A 206 -1 O LEU A 203 N ILE A 191 SHEET 4 A 6 LEU A 261 SER A 265 -1 O VAL A 263 N TRP A 202 SHEET 5 A 6 PHE A 246 HIS A 251 -1 N GLY A 249 O HIS A 262 SHEET 6 A 6 PHE A 287 GLU A 289 -1 O LEU A 288 N TYR A 250 SHEET 1 B 6 GLN B 181 LYS B 184 0 SHEET 2 B 6 VAL B 188 LYS B 192 -1 O VAL B 190 N TYR B 183 SHEET 3 B 6 HIS B 201 PRO B 206 -1 O LEU B 205 N VAL B 189 SHEET 4 B 6 LEU B 261 SER B 265 -1 O VAL B 263 N TRP B 202 SHEET 5 B 6 PHE B 246 HIS B 251 -1 N ARG B 247 O ILE B 264 SHEET 6 B 6 PHE B 287 GLU B 289 -1 O LEU B 288 N TYR B 250 LINK NE2 HIS A 260 V V5A A 401 1555 1555 2.14 LINK SG CYS A 319 ZN ZN A 402 1555 1555 2.41 LINK SG CYS A 322 ZN ZN A 402 1555 1555 2.10 LINK NE2 HIS A 335 ZN ZN A 402 1555 1555 1.98 LINK NE2 HIS A 339 ZN ZN A 402 1555 1555 2.07 LINK V V5A A 401 OP3 G D 1 1555 1555 2.02 LINK NE2 HIS B 260 V V5A B 401 1555 1555 2.10 LINK SG CYS B 319 ZN ZN B 402 1555 1555 2.19 LINK SG CYS B 322 ZN ZN B 402 1555 1555 1.93 LINK NE2 HIS B 335 ZN ZN B 402 1555 1555 1.94 LINK NE2 HIS B 339 ZN ZN B 402 1555 1555 2.12 LINK V V5A B 401 OP3 G G 1 1555 1555 1.99 SITE 1 AC1 14 LEU A 171 SER A 174 ASP A 193 LYS A 194 SITE 2 AC1 14 TYR A 195 LYS A 197 LEU A 203 HIS A 251 SITE 3 AC1 14 SER A 255 MET A 256 HIS A 260 HIS A 262 SITE 4 AC1 14 HOH A 501 G D 1 SITE 1 AC2 4 CYS A 319 CYS A 322 HIS A 335 HIS A 339 SITE 1 AC3 14 LEU B 171 SER B 174 ILE B 191 LYS B 192 SITE 2 AC3 14 ASP B 193 LYS B 194 LYS B 197 LEU B 203 SITE 3 AC3 14 HIS B 251 SER B 255 MET B 256 HIS B 260 SITE 4 AC3 14 HIS B 262 G G 1 SITE 1 AC4 4 CYS B 319 CYS B 322 HIS B 335 HIS B 339 CRYST1 40.276 114.580 124.658 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 0.024829 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008022 0.00000