HEADER DNA 30-APR-25 9URU TITLE CRYSTAL STRUCTURE OF ADE1304 DNA APTAMER (1304B9) BOUND TO ADENOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (44-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS DNA APTAMER, ADENOSINE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR X.CHEN,Y.LUO,Y.REN,L.HUANG REVDAT 1 04-NOV-26 9URU 0 JRNL AUTH X.CHEN,Y.LUO,Y.REN,L.HUANG JRNL TITL CRYSTAL STRUCTURE OF ADENOSINE AND ATP-BINDING DNA APTAMER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.1_5286:) 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17687 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1768 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 38.9800 - 3.7200 1.00 1379 154 0.1691 0.1840 REMARK 3 2 3.7100 - 2.9500 1.00 1265 141 0.1721 0.1831 REMARK 3 3 2.9500 - 2.5800 1.00 1250 139 0.2511 0.2781 REMARK 3 4 2.5800 - 2.3400 1.00 1223 135 0.2685 0.2972 REMARK 3 5 2.3400 - 2.1700 1.00 1218 134 0.2721 0.3083 REMARK 3 6 2.1700 - 2.0400 1.00 1224 136 0.2836 0.3388 REMARK 3 7 2.0400 - 1.9400 1.00 1204 133 0.2833 0.2910 REMARK 3 8 1.9400 - 1.8600 1.00 1202 134 0.2906 0.3349 REMARK 3 9 1.8600 - 1.7900 1.00 1199 134 0.2905 0.4122 REMARK 3 10 1.7900 - 1.7200 1.00 1178 130 0.2866 0.3086 REMARK 3 11 1.7200 - 1.6700 1.00 1188 133 0.2677 0.2973 REMARK 3 12 1.6700 - 1.6200 1.00 1214 135 0.2932 0.3030 REMARK 3 13 1.6200 - 1.5800 1.00 1175 130 0.3277 0.3451 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.014 1035 REMARK 3 ANGLE : 1.657 1596 REMARK 3 CHIRALITY : 0.076 179 REMARK 3 PLANARITY : 0.015 45 REMARK 3 DIHEDRAL : 32.458 502 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -2 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.1563 -1.7744 -10.4379 REMARK 3 T TENSOR REMARK 3 T11: 0.3131 T22: 0.2858 REMARK 3 T33: 0.3352 T12: -0.0057 REMARK 3 T13: 0.0471 T23: 0.0403 REMARK 3 L TENSOR REMARK 3 L11: 0.3433 L22: 6.5661 REMARK 3 L33: 0.8879 L12: -1.4235 REMARK 3 L13: 0.4965 L23: 0.2959 REMARK 3 S TENSOR REMARK 3 S11: 0.0285 S12: 0.2460 S13: 0.0514 REMARK 3 S21: 0.1997 S22: -0.1655 S23: -0.2624 REMARK 3 S31: 0.0696 S32: 0.0135 S33: 0.1558 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 13 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2519 20.2448 -11.2681 REMARK 3 T TENSOR REMARK 3 T11: 0.3227 T22: 0.2419 REMARK 3 T33: 0.2828 T12: 0.0398 REMARK 3 T13: 0.0136 T23: 0.0452 REMARK 3 L TENSOR REMARK 3 L11: 4.7265 L22: 6.5505 REMARK 3 L33: 1.7315 L12: -5.8155 REMARK 3 L13: 3.2333 L23: -2.8207 REMARK 3 S TENSOR REMARK 3 S11: -0.1227 S12: 0.2167 S13: 0.4440 REMARK 3 S21: 0.2363 S22: -0.1513 S23: -0.4324 REMARK 3 S31: -0.3122 S32: -0.0832 S33: 0.2127 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 33 THROUGH 41 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9457 -10.9367 -10.2883 REMARK 3 T TENSOR REMARK 3 T11: 0.3895 T22: 0.2527 REMARK 3 T33: 0.1991 T12: 0.0032 REMARK 3 T13: 0.0472 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 6.0483 L22: 7.4694 REMARK 3 L33: 3.7624 L12: -2.7249 REMARK 3 L13: 2.1947 L23: 0.6719 REMARK 3 S TENSOR REMARK 3 S11: -0.0581 S12: 0.0572 S13: 0.2374 REMARK 3 S21: -0.1518 S22: -0.1009 S23: -0.5939 REMARK 3 S31: 0.1097 S32: 0.1709 S33: 0.1738 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 9URU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 03-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300058977. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-23 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97861 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17744 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 38.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 36.40 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 3.08900 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM CHLORIDE DIHYDRATE, 0.05 REMARK 280 M HEPES SODIUM PH 7.5, 30% V/V POLYETHYLENE GLYCOL 400, 0.002 M REMARK 280 SPERMINE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.17333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.58667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 81.17333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.58667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 81.17333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 40.58667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 81.17333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 40.58667 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -217.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A 105 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 206 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 212 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 261 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 319 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 328 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H1 DG A 21 O HOH A 205 1.37 REMARK 500 NA NA A 108 O HOH A 293 1.54 REMARK 500 O HOH A 323 O HOH A 326 1.66 REMARK 500 O4 DT A 23 O HOH A 201 1.68 REMARK 500 O HOH A 295 O HOH A 313 1.69 REMARK 500 OP1 DC A 5 O HOH A 202 1.71 REMARK 500 OP2 DC A 22 O HOH A 203 1.96 REMARK 500 O4 DT A 15 O HOH A 204 2.00 REMARK 500 O HOH A 325 O HOH A 327 2.05 REMARK 500 O HOH A 259 O HOH A 326 2.08 REMARK 500 O HOH A 245 O HOH A 293 2.08 REMARK 500 N1 DG A 21 O HOH A 205 2.12 REMARK 500 O3' DG A 21 O HOH A 203 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 202 O HOH A 295 8555 1.77 REMARK 500 O HOH A 263 O HOH A 324 7554 1.90 REMARK 500 O HOH A 246 O HOH A 286 1565 1.96 REMARK 500 O HOH A 210 O HOH A 214 10654 2.03 REMARK 500 O HOH A 294 O HOH A 304 4555 2.08 REMARK 500 O HOH A 246 O HOH A 273 1565 2.13 REMARK 500 O HOH A 312 O HOH A 318 10554 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 DT A -2 O3' DT A -2 C3' -0.040 REMARK 500 DG A -1 O3' DG A -1 C3' -0.061 REMARK 500 DG A 9 O3' DG A 9 C3' -0.037 REMARK 500 DT A 19 O3' DT A 19 C3' -0.049 REMARK 500 DC A 22 O3' DC A 22 C3' -0.042 REMARK 500 DA A 25 N9 DA A 25 C4 -0.036 REMARK 500 DT A 33 O3' DT A 33 C3' -0.038 REMARK 500 DC A 36 O3' DC A 36 C3' -0.036 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 3 O5' - P - OP1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 4 O3' - P - OP2 ANGL. DEV. = 8.0 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG A 17 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA A 25 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG A 28 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT A 30 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 32 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES 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 CA A 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A -1 OP1 REMARK 620 2 DT A 19 OP2 89.9 REMARK 620 3 DT A 20 OP2 87.5 2.9 REMARK 620 4 HOH A 232 O 87.5 3.1 3.5 REMARK 620 5 HOH A 246 O 88.7 2.5 4.0 1.2 REMARK 620 6 HOH A 273 O 87.5 2.5 2.3 1.3 2.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 108 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 0 OP1 REMARK 620 2 DG A 21 O6 105.3 REMARK 620 3 HOH A 205 O 105.2 2.4 REMARK 620 4 HOH A 245 O 105.9 1.8 4.1 REMARK 620 5 HOH A 254 O 104.3 1.1 3.0 2.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 4 OP2 REMARK 620 2 DG A 29 OP1 61.4 REMARK 620 3 HOH A 223 O 63.5 4.0 REMARK 620 4 HOH A 281 O 70.8 9.5 7.6 REMARK 620 5 HOH A 301 O 62.6 8.1 4.8 10.8 REMARK 620 6 HOH A 310 O 69.7 14.0 10.0 10.4 7.7 REMARK 620 7 HOH A 315 O 68.5 9.0 5.4 5.0 6.4 6.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 104 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 4 OP1 REMARK 620 2 DC A 7 O2 80.8 REMARK 620 3 DG A 8 O6 73.3 7.7 REMARK 620 4 DG A 29 OP2 75.4 11.7 8.8 REMARK 620 5 HOH A 292 O 81.5 3.6 8.4 9.2 REMARK 620 6 HOH A 307 O 75.8 10.5 7.9 1.1 8.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 105 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 32 OP2 REMARK 620 2 DA A 32 OP2 0.0 REMARK 620 3 HOH A 271 O 68.8 68.8 REMARK 620 4 HOH A 271 O 80.9 80.9 129.5 REMARK 620 5 HOH A 294 O 83.7 83.7 128.3 84.8 REMARK 620 6 HOH A 294 O 150.1 150.1 84.8 128.3 103.2 REMARK 620 7 HOH A 304 O 99.8 99.8 66.4 161.5 76.9 55.1 REMARK 620 8 HOH A 304 O 127.9 127.9 161.5 66.4 55.1 76.9 99.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 106 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 230 O REMARK 620 2 HOH A 302 O 86.7 REMARK 620 3 HOH A 305 O 165.1 81.6 REMARK 620 4 HOH A 328 O 106.3 161.0 83.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 107 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 235 O REMARK 620 2 HOH A 287 O 62.7 REMARK 620 N 1 DBREF 9URU A -2 41 PDB 9URU 9URU -2 41 SEQRES 1 A 44 DT DG DT DA DC DG DA DC DA DC DG DG DA SEQRES 2 A 44 DG DG DC DT DT DA DG DT DT DT DG DC DT SEQRES 3 A 44 DA DA DA DT DG DG DT DC DA DT DG DT DC SEQRES 4 A 44 DG DT DA DC DA HET ADN A 101 32 HET CA A 102 1 HET CA A 103 1 HET CA A 104 1 HET NA A 105 1 HET NA A 106 1 HET NA A 107 1 HET NA A 108 1 HETNAM ADN ADENOSINE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 2 ADN C10 H13 N5 O4 FORMUL 3 CA 3(CA 2+) FORMUL 6 NA 4(NA 1+) FORMUL 10 HOH *131(H2 O) LINK OP1 DG A -1 CA CA A 103 1555 1545 2.60 LINK OP1 DT A 0 NA NA A 108 1555 1545 2.42 LINK OP2 DA A 4 CA CA A 102 1555 8555 2.20 LINK OP1 DA A 4 CA CA A 104 1555 8555 2.37 LINK O2 DC A 7 CA CA A 104 1555 1555 2.29 LINK O6 DG A 8 CA CA A 104 1555 1555 2.29 LINK OP2 DT A 19 CA CA A 103 1555 1555 2.54 LINK OP2 DT A 20 CA CA A 103 1555 1555 2.39 LINK O6 DG A 21 NA NA A 108 1555 1555 2.06 LINK OP1 DG A 29 CA CA A 102 1555 1555 2.29 LINK OP2 DG A 29 CA CA A 104 1555 1555 2.29 LINK OP2 DA A 32 NA NA A 105 1555 1555 2.10 LINK OP2 DA A 32 NA NA A 105 1555 4555 2.10 LINK CA CA A 102 O HOH A 223 1555 8555 2.61 LINK CA CA A 102 O HOH A 281 1555 1555 2.30 LINK CA CA A 102 O HOH A 301 1555 8555 2.51 LINK CA CA A 102 O HOH A 310 1555 8555 2.30 LINK CA CA A 102 O HOH A 315 1555 1555 2.26 LINK CA CA A 103 O HOH A 232 1555 1565 2.19 LINK CA CA A 103 O HOH A 246 1555 1555 3.04 LINK CA CA A 103 O HOH A 273 1555 1565 2.12 LINK CA CA A 104 O HOH A 292 1555 1555 2.34 LINK CA CA A 104 O HOH A 307 1555 1555 2.27 LINK NA NA A 105 O HOH A 271 1555 1555 3.06 LINK NA NA A 105 O HOH A 271 1555 4555 3.06 LINK NA NA A 105 O HOH A 294 1555 1555 2.42 LINK NA NA A 105 O HOH A 294 1555 4555 2.42 LINK NA NA A 105 O HOH A 304 1555 1555 2.02 LINK NA NA A 105 O HOH A 304 1555 4555 2.02 LINK NA NA A 106 O HOH A 230 1555 1545 2.12 LINK NA NA A 106 O HOH A 302 1555 4545 2.31 LINK NA NA A 106 O HOH A 305 1555 4545 2.24 LINK NA NA A 106 O HOH A 328 1555 4555 2.17 LINK NA NA A 107 O HOH A 235 1555 1555 2.51 LINK NA NA A 107 O HOH A 287 1555 1545 2.53 LINK NA NA A 108 O HOH A 205 1555 1555 2.28 LINK NA NA A 108 O HOH A 245 1555 1555 2.34 LINK NA NA A 108 O HOH A 254 1555 1565 1.90 CRYST1 58.600 58.600 121.760 90.00 90.00 120.00 P 62 2 2 12 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 0.017065 0.009852 0.000000 0.00000 SCALE2 0.000000 0.019705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008213 0.00000 CONECT 298 1439 CONECT 331 1439 CONECT 672 1438 CONECT 704 1438 CONECT 750 1443 CONECT 991 1437 CONECT 992 1439 CONECT 1087 1440 CONECT 1405 1406 1424 CONECT 1406 1405 1407 1425 1426 CONECT 1407 1406 1408 1409 1427 CONECT 1408 1407 1413 CONECT 1409 1407 1410 1411 1428 CONECT 1410 1409 1429 CONECT 1411 1409 1412 1413 1430 CONECT 1412 1411 1431 CONECT 1413 1408 1411 1414 1432 CONECT 1414 1413 1415 1423 CONECT 1415 1414 1416 1433 CONECT 1416 1415 1417 CONECT 1417 1416 1418 1423 CONECT 1418 1417 1419 1420 CONECT 1419 1418 1434 1435 CONECT 1420 1418 1421 CONECT 1421 1420 1422 1436 CONECT 1422 1421 1423 CONECT 1423 1414 1417 1422 CONECT 1424 1405 CONECT 1425 1406 CONECT 1426 1406 CONECT 1427 1407 CONECT 1428 1409 CONECT 1429 1410 CONECT 1430 1411 CONECT 1431 1412 CONECT 1432 1413 CONECT 1433 1415 CONECT 1434 1419 CONECT 1435 1419 CONECT 1436 1421 CONECT 1437 991 1524 1558 CONECT 1438 672 704 1489 CONECT 1439 298 331 992 1535 CONECT 1439 1550 CONECT 1440 1087 1514 1537 1547 CONECT 1442 1478 CONECT 1443 750 1448 1488 CONECT 1448 1443 CONECT 1478 1442 CONECT 1488 1443 CONECT 1489 1438 CONECT 1514 1440 CONECT 1524 1437 CONECT 1535 1439 CONECT 1537 1440 CONECT 1547 1440 CONECT 1550 1439 CONECT 1558 1437 MASTER 484 0 8 0 0 0 0 6 1061 1 58 4 END