HEADER DNA 30-APR-25 9URY TITLE CRYSTAL STRUCTURE OF ADE1304 DNA APTAMER (ADE1304B) BOUND TO ADENOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (38-MER); COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS ADENOSINE/ATP DNA APTAMER, ADENOSINE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR X.CHEN,Y.LUO,Y.REN,L.HUANG REVDAT 1 11-NOV-26 9URY 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. 2.33 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 9860 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 509 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 29.6400 - 3.6900 1.00 2474 137 0.1639 0.2103 REMARK 3 2 3.6900 - 2.9300 0.99 2283 137 0.1902 0.2219 REMARK 3 3 2.9300 - 2.5600 1.00 2314 120 0.3244 0.4034 REMARK 3 4 2.5600 - 2.3300 1.00 2280 115 0.3505 0.3755 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) : 0.346 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.657 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.52 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 : 0.010 1794 REMARK 3 ANGLE : 1.129 2766 REMARK 3 CHIRALITY : 0.060 310 REMARK 3 PLANARITY : 0.009 78 REMARK 3 DIHEDRAL : 33.427 864 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.8954 11.2808 -1.2655 REMARK 3 T TENSOR REMARK 3 T11: 0.3758 T22: 0.5900 REMARK 3 T33: 0.6242 T12: -0.0287 REMARK 3 T13: -0.0581 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 7.5621 L22: 0.8586 REMARK 3 L33: 5.5615 L12: 0.4546 REMARK 3 L13: 2.6072 L23: 2.2260 REMARK 3 S TENSOR REMARK 3 S11: -0.4946 S12: 0.0431 S13: 1.0896 REMARK 3 S21: -0.3547 S22: -0.1967 S23: 0.0425 REMARK 3 S31: -0.3477 S32: -0.4992 S33: 0.7432 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.8026 14.9306 6.5325 REMARK 3 T TENSOR REMARK 3 T11: 0.3567 T22: 0.4803 REMARK 3 T33: 0.5970 T12: 0.0009 REMARK 3 T13: -0.0681 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 3.0074 L22: 3.1687 REMARK 3 L33: 1.5879 L12: 2.7696 REMARK 3 L13: 1.7619 L23: 2.0011 REMARK 3 S TENSOR REMARK 3 S11: -0.4794 S12: -1.2661 S13: 0.9518 REMARK 3 S21: -0.0117 S22: 0.0210 S23: 0.1316 REMARK 3 S31: -0.2551 S32: -0.2840 S33: 0.3981 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.0234 7.8925 -6.9561 REMARK 3 T TENSOR REMARK 3 T11: 0.5067 T22: 0.8298 REMARK 3 T33: 0.6263 T12: -0.0943 REMARK 3 T13: -0.1240 T23: -0.0730 REMARK 3 L TENSOR REMARK 3 L11: 6.4413 L22: 5.2802 REMARK 3 L33: 2.5171 L12: 3.4541 REMARK 3 L13: 3.4696 L23: 2.2883 REMARK 3 S TENSOR REMARK 3 S11: -0.3561 S12: 0.8104 S13: -0.5043 REMARK 3 S21: -0.2715 S22: 0.3739 S23: -0.4022 REMARK 3 S31: -0.4763 S32: -0.0119 S33: -0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.5176 7.6106 -25.3092 REMARK 3 T TENSOR REMARK 3 T11: 0.4730 T22: 0.8481 REMARK 3 T33: 0.5908 T12: 0.2265 REMARK 3 T13: 0.0041 T23: 0.0167 REMARK 3 L TENSOR REMARK 3 L11: 3.7244 L22: 1.5184 REMARK 3 L33: 4.0797 L12: -1.8456 REMARK 3 L13: 3.9334 L23: -1.6386 REMARK 3 S TENSOR REMARK 3 S11: -0.8792 S12: -0.6771 S13: -0.2272 REMARK 3 S21: 0.6907 S22: 0.7625 S23: 0.2185 REMARK 3 S31: -0.9513 S32: -1.0733 S33: 0.0738 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 11 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1891 -2.5936 -18.6753 REMARK 3 T TENSOR REMARK 3 T11: 0.3890 T22: 0.2740 REMARK 3 T33: 0.4976 T12: 0.0666 REMARK 3 T13: 0.0179 T23: 0.0295 REMARK 3 L TENSOR REMARK 3 L11: 9.3210 L22: 1.2138 REMARK 3 L33: 3.2918 L12: -1.7816 REMARK 3 L13: -0.0909 L23: 0.5822 REMARK 3 S TENSOR REMARK 3 S11: -0.2484 S12: -0.4494 S13: 0.0854 REMARK 3 S21: 0.1894 S22: 0.2522 S23: -0.0233 REMARK 3 S31: -0.1154 S32: -0.3726 S33: 0.0507 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 31 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.1702 7.3654 -30.0134 REMARK 3 T TENSOR REMARK 3 T11: 0.6264 T22: 0.8140 REMARK 3 T33: 0.5079 T12: 0.1277 REMARK 3 T13: -0.0560 T23: 0.2164 REMARK 3 L TENSOR REMARK 3 L11: 8.8614 L22: 2.3910 REMARK 3 L33: 3.2048 L12: -0.0439 REMARK 3 L13: 1.1371 L23: 0.4263 REMARK 3 S TENSOR REMARK 3 S11: -0.2288 S12: 1.4737 S13: 0.1663 REMARK 3 S21: -0.3185 S22: -0.2848 S23: 0.1506 REMARK 3 S31: 0.2005 S32: 0.4119 S33: 0.5415 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 1 through 38 or REMARK 3 (resid 101 and (name C1" or name C2 or REMARK 3 name C2" or name C3" or name C4 or name REMARK 3 C4" or name C5 or name C5" or name C6 or REMARK 3 name C8 or name N1 or name N3 or name N6 REMARK 3 or name N7 or name N9 or name O2" or name REMARK 3 O3" or name O4" or name O5")))) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 1 through 38 or REMARK 3 (resid 101 and (name C1" or name C2 or REMARK 3 name C2" or name C3" or name C4 or name REMARK 3 C4" or name C5 or name C5" or name C6 or REMARK 3 name C8 or name N1 or name N3 or name N6 REMARK 3 or name N7 or name N9 or name O2" or name REMARK 3 O3" or name O4" or name O5")))) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9URY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 05-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300058551. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-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 : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 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 : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9919 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 48.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.79300 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 (%): 45.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM CHLORIDE DIHYDRATE, 0.05 REMARK 280 M HEPES SODIUM PH 7.5, 28% 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 21 21 2 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 88.90550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 12.00450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 88.90550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 12.00450 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -223.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 APPLY THE FOLLOWING TO CHAINS: A 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 -49.93400 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 -49.93400 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 APPLY THE FOLLOWING TO CHAINS: A 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 -49.93400 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 HOH B 206 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 209 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 O HOH A 213 O HOH A 215 2.03 REMARK 500 O HOH B 226 O HOH B 228 2.12 REMARK 500 OP2 DG A 21 O HOH A 201 2.13 REMARK 500 OP2 DG A 37 O HOH A 202 2.13 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 214 O HOH A 214 2575 1.53 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 DC B 7 O3' DC B 7 C3' -0.037 REMARK 500 DA B 16 O3' DA B 16 C3' -0.055 REMARK 500 DG B 17 O3' DG B 17 C3' -0.046 REMARK 500 DA A 16 O3' DA A 16 C3' -0.043 REMARK 500 DG A 17 O3' DG A 17 C3' -0.040 REMARK 500 DA A 24 O3' DA A 24 C3' -0.047 REMARK 500 DA A 25 O3' DA A 25 C3' -0.038 REMARK 500 DT A 35 O3' DT A 35 C3' -0.039 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 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT B 15 O4' - C1' - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 DA B 24 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG A 17 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG A 28 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 B 104 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC B 2 OP1 REMARK 620 2 DG A 29 OP1 76.0 REMARK 620 3 HOH A 208 O 118.0 153.3 REMARK 620 N 1 2 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 DC B 2 OP2 REMARK 620 2 DC A 7 O2 53.3 REMARK 620 3 DG A 8 O6 54.7 2.1 REMARK 620 4 DG A 29 OP2 53.7 5.5 4.0 REMARK 620 5 HOH A 206 O 54.2 2.6 1.0 3.1 REMARK 620 6 HOH A 212 O 51.3 3.4 3.5 3.6 2.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 105 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC B 13 OP2 REMARK 620 2 DG B 21 OP1 148.6 REMARK 620 3 HOH B 220 O 124.5 78.5 REMARK 620 4 HOH B 221 O 92.9 59.9 138.0 REMARK 620 5 HOH B 222 O 103.4 105.4 68.3 125.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT B 14 OP1 REMARK 620 2 DT B 20 OP2 80.8 REMARK 620 3 DA B 24 OP1 35.2 48.2 REMARK 620 4 HOH B 212 O 85.7 6.7 52.0 REMARK 620 5 HOH B 225 O 87.9 8.7 54.1 2.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 108 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 17 O6 REMARK 620 2 DT B 18 O4 117.4 REMARK 620 3 DG B 21 O6 81.6 141.3 REMARK 620 4 HOH B 203 O 64.5 78.6 138.5 REMARK 620 5 HOH B 203 O 119.4 57.1 144.8 55.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 106 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT B 20 OP1 REMARK 620 2 HOH B 213 O 69.4 REMARK 620 3 HOH B 222 O 78.3 71.8 REMARK 620 4 HOH B 224 O 88.9 132.1 61.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 107 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT B 27 O2 REMARK 620 2 DT B 30 O4 81.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 205 O REMARK 620 2 HOH B 211 O 74.0 REMARK 620 3 HOH B 216 O 87.1 161.0 REMARK 620 4 HOH B 229 O 86.9 72.5 104.9 REMARK 620 5 HOH B 230 O 142.8 134.7 61.5 82.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 109 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 223 O REMARK 620 2 HOH B 227 O 107.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 211 O REMARK 620 2 HOH A 216 O 75.2 REMARK 620 N 1 DBREF 9URY B 1 38 PDB 9URY 9URY 1 38 DBREF 9URY A 1 38 PDB 9URY 9URY 1 38 SEQRES 1 B 38 DA DC DG DA DC DA DC DG DG DA DG DG DC SEQRES 2 B 38 DT DT DA DG DT DT DT DG DC DT DA DA DA SEQRES 3 B 38 DT DG DG DT DC DA DT DG DT DC DG DT SEQRES 1 A 38 DA DC DG DA DC DA DC DG DG DA DG DG DC SEQRES 2 A 38 DT DT DA DG DT DT DT DG DC DT DA DA DA SEQRES 3 A 38 DT DG DG DT DC DA DT DG DT DC DG DT HET ADN B 101 32 HET CA B 102 1 HET CA B 103 1 HET CA B 104 1 HET CA B 105 1 HET NA B 106 1 HET NA B 107 1 HET NA B 108 1 HET NA B 109 1 HET ADN A 101 32 HET CA A 102 1 HET NA A 103 1 HETNAM ADN ADENOSINE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 3 ADN 2(C10 H13 N5 O4) FORMUL 4 CA 5(CA 2+) FORMUL 8 NA 5(NA 1+) FORMUL 15 HOH *46(H2 O) LINK OP1 DC B 2 CA CA B 104 1555 1555 1.96 LINK OP2 DC B 2 CA CA A 102 1555 1554 2.33 LINK OP2 DC B 13 CA CA B 105 1555 1555 2.47 LINK OP1 DT B 14 CA CA B 102 1555 2555 2.39 LINK O6 DG B 17 NA NA B 108 1555 1555 2.98 LINK O4 DT B 18 NA NA B 108 1555 1555 3.20 LINK OP2 DT B 20 CA CA B 102 1555 1555 2.65 LINK OP1 DT B 20 NA NA B 106 1555 1555 2.63 LINK OP1 DG B 21 CA CA B 105 1555 2555 2.44 LINK O6 DG B 21 NA NA B 108 1555 1555 2.68 LINK OP1 DA B 24 CA CA B 102 1555 2545 2.51 LINK O2 DT B 27 NA NA B 107 1555 1555 3.01 LINK O4 DT B 30 NA NA B 107 1555 1555 2.91 LINK CA CA B 102 O HOH B 212 1555 2555 2.26 LINK CA CA B 102 O HOH B 225 1555 2555 2.74 LINK CA CA B 103 O HOH B 205 1555 1555 2.56 LINK CA CA B 103 O HOH B 211 1555 1555 2.52 LINK CA CA B 103 O HOH B 216 1555 2545 2.32 LINK CA CA B 103 O HOH B 229 1555 1555 1.98 LINK CA CA B 103 O HOH B 230 1555 1555 2.34 LINK CA CA B 104 OP1 DG A 29 1556 1555 2.43 LINK CA CA B 104 O HOH A 208 1555 1554 2.12 LINK CA CA B 105 O HOH B 220 1555 1555 2.59 LINK CA CA B 105 O HOH B 221 1555 2555 3.20 LINK CA CA B 105 O HOH B 222 1555 1555 2.68 LINK NA NA B 106 O HOH B 213 1555 1555 2.16 LINK NA NA B 106 O HOH B 222 1555 2555 3.12 LINK NA NA B 106 O HOH B 224 1555 1555 2.23 LINK NA NA B 108 O HOH B 203 1555 1555 2.55 LINK NA NA B 108 O HOH B 203 1555 2555 2.64 LINK NA NA B 109 O HOH B 223 1555 1555 2.43 LINK NA NA B 109 O HOH B 227 1555 1555 2.29 LINK O2 DC A 7 CA CA A 102 1555 1555 2.55 LINK O6 DG A 8 CA CA A 102 1555 1555 2.15 LINK OP2 DG A 29 CA CA A 102 1555 1555 2.54 LINK CA CA A 102 O HOH A 206 1555 1555 2.19 LINK CA CA A 102 O HOH A 212 1555 1555 2.03 LINK NA NA A 103 O HOH A 211 1555 1555 2.74 LINK NA NA A 103 O HOH A 216 1555 1555 1.91 CRYST1 177.811 24.009 49.934 90.00 90.00 90.00 P 21 21 2 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 0.005624 0.000000 0.000000 0.00000 SCALE2 0.000000 0.041651 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020026 0.00000 MTRIX1 1 0.801216 0.597405 -0.034049 -8.47718 1 MTRIX2 1 -0.587407 0.774411 -0.235031 -21.01101 1 MTRIX3 1 -0.114041 0.208312 0.971391 -28.61300 1 CONECT 20 1599 CONECT 251 1600 CONECT 345 1603 CONECT 367 1603 CONECT 392 1601 CONECT 393 1597 CONECT 427 1603 CONECT 548 1602 CONECT 615 1602 CONECT 916 1637 CONECT 938 1637 CONECT 1361 1637 CONECT 1565 1566 1584 CONECT 1566 1565 1567 1585 1586 CONECT 1567 1566 1568 1569 1587 CONECT 1568 1567 1573 CONECT 1569 1567 1570 1571 1588 CONECT 1570 1569 1589 CONECT 1571 1569 1572 1573 1590 CONECT 1572 1571 1591 CONECT 1573 1568 1571 1574 1592 CONECT 1574 1573 1575 1583 CONECT 1575 1574 1576 1593 CONECT 1576 1575 1577 CONECT 1577 1576 1578 1583 CONECT 1578 1577 1579 1580 CONECT 1579 1578 1594 1595 CONECT 1580 1578 1581 CONECT 1581 1580 1582 1596 CONECT 1582 1581 1583 CONECT 1583 1574 1577 1582 CONECT 1584 1565 CONECT 1585 1566 CONECT 1586 1566 CONECT 1587 1567 CONECT 1588 1569 CONECT 1589 1570 CONECT 1590 1571 CONECT 1591 1572 CONECT 1592 1573 CONECT 1593 1575 CONECT 1594 1579 CONECT 1595 1579 CONECT 1596 1581 CONECT 1597 393 CONECT 1598 1643 1649 1667 1668 CONECT 1599 20 CONECT 1600 251 1658 1660 CONECT 1601 392 1651 1662 CONECT 1602 548 615 CONECT 1603 345 367 427 1641 CONECT 1604 1661 1665 CONECT 1605 1606 1624 CONECT 1606 1605 1607 1625 1626 CONECT 1607 1606 1608 1609 1627 CONECT 1608 1607 1613 CONECT 1609 1607 1610 1611 1628 CONECT 1610 1609 1629 CONECT 1611 1609 1612 1613 1630 CONECT 1612 1611 1631 CONECT 1613 1608 1611 1614 1632 CONECT 1614 1613 1615 1623 CONECT 1615 1614 1616 1633 CONECT 1616 1615 1617 CONECT 1617 1616 1618 1623 CONECT 1618 1617 1619 1620 CONECT 1619 1618 1634 1635 CONECT 1620 1618 1621 CONECT 1621 1620 1622 1636 CONECT 1622 1621 1623 CONECT 1623 1614 1617 1622 CONECT 1624 1605 CONECT 1625 1606 CONECT 1626 1606 CONECT 1627 1607 CONECT 1628 1609 CONECT 1629 1610 CONECT 1630 1611 CONECT 1631 1612 CONECT 1632 1613 CONECT 1633 1615 CONECT 1634 1619 CONECT 1635 1619 CONECT 1636 1621 CONECT 1637 916 938 1361 1674 CONECT 1637 1680 CONECT 1638 1679 1684 CONECT 1641 1603 CONECT 1643 1598 CONECT 1649 1598 CONECT 1651 1601 CONECT 1658 1600 CONECT 1660 1600 CONECT 1661 1604 CONECT 1662 1601 CONECT 1665 1604 CONECT 1667 1598 CONECT 1668 1598 CONECT 1674 1637 CONECT 1679 1638 CONECT 1680 1637 CONECT 1684 1638 MASTER 519 0 12 0 0 0 0 9 1656 2 102 6 END