HEADER DNA/RNA 29-JUL-14 4U6K TITLE CRYSTAL STRUCTURE OF DNA/RNA DUPLEX CONTAINING 2'-4'-BNA-NC COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3'); COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*(NCU)P*(NTT)P*CP*TP*TP*CP*TP*(NTT)P*(NCU))-3'); COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS DNA/RNA DUPLEX, ANTISENSE, BRIDGED NUCLEIC ACID, DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,Y.NOMURA,Y.KITAHARA,S.OBIKA,H.TORIGOE REVDAT 3 06-JUL-22 4U6K 1 JRNL REVDAT 2 29-JAN-20 4U6K 1 REMARK REVDAT 1 19-AUG-15 4U6K 0 JRNL AUTH J.KONDO,Y.NOMURA,Y.KITAHARA,S.OBIKA,H.TORIGOE JRNL TITL THE CRYSTAL STRUCTURE OF A 2',4'-BNA(NC)[N-ME]-MODIFIED JRNL TITL 2 ANTISENSE GAPMER IN COMPLEX WITH THE TARGET RNA. JRNL REF CHEM.COMMUN.(CAMB.) V. 52 2354 2016 JRNL REFN ESSN 1364-548X JRNL PMID 26731288 JRNL DOI 10.1039/C5CC08300A REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 21282 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2111 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1895 REMARK 3 BIN R VALUE (WORKING SET) : 0.2584 REMARK 3 BIN FREE R VALUE : 0.2649 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 214 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 780 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 355 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44100 REMARK 3 B22 (A**2) : 0.00400 REMARK 3 B33 (A**2) : -0.44500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.000 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.153 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.516 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 45.56 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : DNA-RNA_201312.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 4 : NCO_XPLOR.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4U6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000202750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-13; 25-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A; BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98; 1.60465, 1.60830, 0.98 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R; ADSC QUANTUM REMARK 200 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21282 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.820 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.98 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: PHENIX, SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA CACODYLATE, NACL, HEXAMMINE COBALT, REMARK 280 MPD, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 51.22000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.22000 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 1.000000 0.000000 0.000000 21.96000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.48000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.96000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.48000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.22000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.96000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 29.48000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.22000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.96000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 29.48000 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 A 214 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 284 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 150 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 204 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 277 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 282 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 292 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 155 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 165 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 208 O HOH A 296 2.02 REMARK 500 O HOH D 124 O HOH D 148 2.07 REMARK 500 O HOH C 263 O HOH D 145 2.13 REMARK 500 O HOH A 295 O HOH A 296 2.14 REMARK 500 O HOH A 296 O HOH A 299 2.15 REMARK 500 O HOH A 282 O HOH C 276 2.18 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 281 O HOH B 173 8556 2.09 REMARK 500 O HOH A 250 O HOH B 107 8556 2.11 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 A A 2 P A A 2 OP1 0.116 REMARK 500 A A 2 P A A 2 OP2 0.119 REMARK 500 A A 3 P A A 3 OP1 0.116 REMARK 500 A A 3 P A A 3 OP2 0.119 REMARK 500 G A 4 P G A 4 OP1 0.107 REMARK 500 G A 4 P G A 4 OP2 0.113 REMARK 500 A A 5 P A A 5 OP1 0.111 REMARK 500 A A 5 P A A 5 OP2 0.113 REMARK 500 A A 6 P A A 6 OP1 0.111 REMARK 500 A A 6 P A A 6 OP2 0.125 REMARK 500 G A 7 P G A 7 OP1 0.107 REMARK 500 G A 7 P G A 7 OP2 0.118 REMARK 500 A A 8 P A A 8 OP1 0.108 REMARK 500 A A 8 P A A 8 OP2 0.113 REMARK 500 G A 9 P G A 9 OP1 0.109 REMARK 500 G A 9 P G A 9 OP2 0.118 REMARK 500 DC B 3 P DC B 3 OP1 0.113 REMARK 500 DC B 3 P DC B 3 OP2 0.127 REMARK 500 DT B 4 P DT B 4 OP1 0.109 REMARK 500 DT B 4 P DT B 4 OP2 0.111 REMARK 500 DT B 5 P DT B 5 OP1 0.115 REMARK 500 DT B 5 P DT B 5 OP2 0.118 REMARK 500 DC B 6 P DC B 6 OP1 0.114 REMARK 500 DC B 6 P DC B 6 OP2 0.120 REMARK 500 DT B 7 P DT B 7 OP1 0.110 REMARK 500 DT B 7 P DT B 7 OP2 0.114 REMARK 500 A C 2 P A C 2 OP1 0.114 REMARK 500 A C 2 P A C 2 OP2 0.121 REMARK 500 A C 3 P A C 3 OP1 0.116 REMARK 500 A C 3 P A C 3 OP2 0.120 REMARK 500 G C 4 P G C 4 OP1 0.117 REMARK 500 G C 4 P G C 4 OP2 0.122 REMARK 500 A C 5 P A C 5 OP1 0.118 REMARK 500 A C 5 P A C 5 OP2 0.124 REMARK 500 A C 6 P A C 6 OP1 0.118 REMARK 500 A C 6 P A C 6 OP2 0.121 REMARK 500 G C 7 P G C 7 OP1 0.115 REMARK 500 G C 7 P G C 7 OP2 0.126 REMARK 500 A C 8 P A C 8 OP1 0.113 REMARK 500 A C 8 P A C 8 OP2 0.121 REMARK 500 G C 9 P G C 9 OP1 0.116 REMARK 500 G C 9 P G C 9 OP2 0.117 REMARK 500 DC D 3 P DC D 3 OP1 0.115 REMARK 500 DC D 3 P DC D 3 OP2 0.118 REMARK 500 DT D 4 P DT D 4 OP1 0.116 REMARK 500 DT D 4 P DT D 4 OP2 0.122 REMARK 500 DT D 5 P DT D 5 OP1 0.116 REMARK 500 DT D 5 P DT D 5 OP2 0.122 REMARK 500 DC D 6 P DC D 6 OP1 0.110 REMARK 500 DC D 6 P DC D 6 OP2 0.122 REMARK 500 REMARK 500 THIS ENTRY HAS 52 BOND DEVIATIONS. 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 3 O5' - P - OP2 ANGL. DEV. = -5.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 302 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH C 292 DISTANCE = 5.99 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues NCU B 1 and NTT B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues NTT B 8 and NCU B 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues NCU D 1 and NTT D 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide NTT D 2 and DC D REMARK 800 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DT D 7 and NTT D REMARK 800 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues NTT D 8 and NCU D 9 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4U6L RELATED DB: PDB REMARK 900 RELATED ID: 4U6M RELATED DB: PDB DBREF 4U6K A 1 9 PDB 4U6K 4U6K 1 9 DBREF 4U6K B 1 9 PDB 4U6K 4U6K 1 9 DBREF 4U6K C 1 9 PDB 4U6K 4U6K 1 9 DBREF 4U6K D 1 9 PDB 4U6K 4U6K 1 9 SEQRES 1 A 9 G A A G A A G A G SEQRES 1 B 9 NCU NTT DC DT DT DC DT NTT NCU SEQRES 1 C 9 G A A G A A G A G SEQRES 1 D 9 NCU NTT DC DT DT DC DT NTT NCU HET NCU B 1 21 HET NTT B 2 24 HET NTT B 8 24 HET NCU B 9 24 HET NCU D 1 21 HET NTT D 2 24 HET NTT D 8 24 HET NCU D 9 24 HET NCO A 101 7 HET NCO A 102 7 HET NCO C 101 7 HETNAM NCU [(1R,5R,7R,8S)-7-(4-AMINO-5-METHYL-2-OXOPYRIMIDIN- HETNAM 2 NCU 1(2H)-YL)-8-HYDROXY-3-METHYL-2,6-DIOXA-3- HETNAM 3 NCU AZABICYCLO[3.2.1]OCT-5-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM NTT [(1R,5R,7R,8S)-8-HYDROXY-3-METHYL-7-(5-METHYL-2,4- HETNAM 2 NTT DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,6-DIOXA-3- HETNAM 3 NTT AZABICYCLO[3.2.1]OCT-5-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM NCO COBALT HEXAMMINE(III) FORMUL 2 NCU 4(C12 H19 N4 O8 P) FORMUL 2 NTT 4(C12 H18 N3 O9 P) FORMUL 5 NCO 3(CO H18 N6 3+) FORMUL 8 HOH *355(H2 O) LINK O3' NCU B 1 P NTT B 2 1555 1555 1.55 LINK O3' NTT B 2 P DC B 3 1555 1555 1.62 LINK O3' DT B 7 P NTT B 8 1555 1555 1.60 LINK O3' NTT B 8 P NCU B 9 1555 1555 1.61 LINK O3' NCU D 1 P NTT D 2 1555 1555 1.55 LINK O3' NTT D 2 P DC D 3 1555 1555 1.60 LINK O3' DT D 7 P NTT D 8 1555 1555 1.61 LINK O3' NTT D 8 P NCU D 9 1555 1555 1.61 SITE 1 AC1 6 A A 3 G A 4 HOH A 233 HOH A 261 SITE 2 AC1 6 HOH A 262 HOH A 264 SITE 1 AC2 8 A A 8 G A 9 HOH A 209 NCU B 1 SITE 2 AC2 8 A C 8 G C 9 HOH C 205 HOH C 228 SITE 1 AC3 7 A C 3 G C 4 HOH C 226 HOH C 231 SITE 2 AC3 7 HOH C 249 HOH C 253 HOH C 254 SITE 1 AC4 18 A A 2 A A 8 G A 9 NCO A 102 SITE 2 AC4 18 DC B 3 NTT B 8 NCU B 9 HOH B 109 SITE 3 AC4 18 HOH B 113 HOH B 115 HOH B 116 HOH B 121 SITE 4 AC4 18 HOH B 136 HOH B 140 HOH B 146 G C 9 SITE 5 AC4 18 NCU D 1 HOH D 128 SITE 1 AC5 23 G A 1 A A 2 A A 3 G A 9 SITE 2 AC5 23 NCU B 1 NTT B 2 DT B 7 HOH B 103 SITE 3 AC5 23 HOH B 104 HOH B 110 HOH B 114 HOH B 117 SITE 4 AC5 23 HOH B 123 HOH B 130 HOH B 133 HOH B 135 SITE 5 AC5 23 HOH B 137 HOH B 138 HOH B 139 HOH B 144 SITE 6 AC5 23 G C 1 NCU D 1 HOH D 113 SITE 1 AC6 14 G A 9 NCU B 1 NCU B 9 A C 8 SITE 2 AC6 14 G C 9 HOH C 215 DC D 3 HOH D 113 SITE 3 AC6 14 HOH D 115 HOH D 116 HOH D 120 HOH D 125 SITE 4 AC6 14 HOH D 128 HOH D 137 SITE 1 AC7 15 G C 7 A C 8 G C 9 NCU D 1 SITE 2 AC7 15 DT D 4 HOH D 108 HOH D 109 HOH D 115 SITE 3 AC7 15 HOH D 116 HOH D 120 HOH D 125 HOH D 126 SITE 4 AC7 15 HOH D 133 HOH D 137 HOH D 142 SITE 1 AC8 12 A C 2 A C 3 G C 4 DC D 6 SITE 2 AC8 12 NCU D 9 HOH D 102 HOH D 111 HOH D 112 SITE 3 AC8 12 HOH D 121 HOH D 122 HOH D 124 HOH D 130 SITE 1 AC9 19 G A 1 G C 1 A C 2 A C 3 SITE 2 AC9 19 DT D 7 HOH D 101 HOH D 102 HOH D 106 SITE 3 AC9 19 HOH D 107 HOH D 111 HOH D 114 HOH D 119 SITE 4 AC9 19 HOH D 121 HOH D 122 HOH D 129 HOH D 130 SITE 5 AC9 19 HOH D 132 HOH D 134 HOH D 139 CRYST1 43.920 58.960 102.440 90.00 90.00 90.00 C 2 2 21 16 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 0.022769 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009762 0.00000