HEADER DNA 27-DEC-99 1DPL TITLE A-DNA DECAMER GCGTA(T23)TACGC WITH INCORPORATED 2'-METHOXY-3'- TITLE 2 METHYLENEPHOSPHATE-THYMIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS MODIFIED A-DECAMER AT 0.83 A RESOLUTION, DEOXYRIBONUCLEIC ACID, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.EGLI,V.TERESHKO,M.TEPLOVA,G.MINASOV,A.JOACHIMIAK,R.SANISHVILI, AUTHOR 2 C.M.WEEKS,R.MILLER,M.A.MAIER,H.AN,P.DAN COOK,M.MANOHARAN REVDAT 4 07-FEB-24 1DPL 1 REMARK REVDAT 3 22-JUN-22 1DPL 1 REMARK SEQRES LINK REVDAT 2 24-FEB-09 1DPL 1 VERSN REVDAT 1 04-APR-00 1DPL 0 JRNL AUTH M.EGLI,V.TERESHKO,M.TEPLOVA,G.MINASOV,A.JOACHIMIAK, JRNL AUTH 2 R.SANISHVILI,C.M.WEEKS,R.MILLER,M.A.MAIER,H.AN,P.DAN COOK, JRNL AUTH 3 M.MANOHARAN JRNL TITL X-RAY CRYSTALLOGRAPHIC ANALYSIS OF THE HYDRATION OF A- AND JRNL TITL 2 B-FORM DNA AT ATOMIC RESOLUTION. JRNL REF BIOPOLYMERS V. 48 234 1998 JRNL REFN ISSN 0006-3525 JRNL PMID 10699842 JRNL DOI 10.1002/(SICI)1097-0282(1998)48:4<234::AID-BIP4>3.0.CO;2-H REMARK 2 REMARK 2 RESOLUTION. 0.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.117 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.117 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.121 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4742 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 47403 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 408 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.037 REMARK 3 ANGLE DISTANCES (A) : 0.019 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : PARKINSON ET AL. REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010269. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-99 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47403 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.830 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SPERMINE, MGCL2, NACL, KCL, SODIUM REMARK 280 CACODYLATE BUFFER, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 12.31350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.45300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.35850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.45300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.31350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.35850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC 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 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 DG A 1 C2' DG A 1 C1' -0.067 REMARK 500 DG A 3 C2' DG A 3 C1' -0.108 REMARK 500 DT A 4 C2' DT A 4 C1' -0.063 REMARK 500 DC B 12 C2' DC B 12 C1' -0.066 REMARK 500 DG B 19 C2' DG B 19 C1' -0.086 REMARK 500 DG B 19 O4' DG B 19 C1' 0.099 REMARK 500 DG B 19 O4' DG B 19 C1' 0.100 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 DG A 3 O4' - C1' - C2' ANGL. DEV. = 5.7 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = -6.3 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC A 8 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 11 O4' - C1' - C2' ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 13 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 19 P - O5' - C5' ANGL. DEV. = 11.1 DEGREES REMARK 500 DG B 19 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 DG B 19 C1' - O4' - C4' ANGL. DEV. = -8.2 DEGREES REMARK 500 DG B 19 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 DG B 19 O4' - C1' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 DG B 19 O4' - C1' - C2' ANGL. DEV. = 6.3 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = -8.6 DEGREES REMARK 500 DG B 19 C8 - N9 - C1' ANGL. DEV. = 8.8 DEGREES REMARK 500 DG B 19 C4 - N9 - C1' ANGL. DEV. = -8.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SPM B 222 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 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 302 O REMARK 620 2 HOH A 305 O 91.0 REMARK 620 3 HOH A 306 O 88.3 92.3 REMARK 620 4 HOH A 307 O 92.6 176.5 87.7 REMARK 620 5 HOH B 303 O 177.5 90.5 93.6 85.9 REMARK 620 6 HOH B 304 O 91.1 89.1 178.5 90.9 86.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B1302 O REMARK 620 2 HOH B1303 O 95.8 REMARK 620 3 HOH B1304 O 89.0 100.3 REMARK 620 4 HOH B1305 O 93.8 85.7 173.1 REMARK 620 5 HOH B1306 O 159.8 99.8 100.5 74.8 REMARK 620 6 HOH B1307 O 83.7 175.6 84.1 90.0 79.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM B 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM B 222 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1301 DBREF 1DPL A 1 10 PDB 1DPL 1DPL 1 10 DBREF 1DPL B 11 20 PDB 1DPL 1DPL 11 20 SEQRES 1 A 10 DG DC DG DT DA T23 DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA T23 DA DC DG DC HET T23 A 6 22 HET T23 B 16 22 HET MG A 301 1 HET SPM B 221 14 HET SPM B 222 10 HET MG B1301 1 HETNAM T23 2'-O-METHYL-3'-METHYL-3'-DEOXY-ARABINOFURANOSYL- HETNAM 2 T23 THYMINE-5'-PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM SPM SPERMINE FORMUL 1 T23 2(C12 H19 N2 O8 P) FORMUL 3 MG 2(MG 2+) FORMUL 4 SPM 2(C10 H26 N4) FORMUL 7 HOH *177(H2 O) LINK O3' DA A 5 P T23 A 6 1555 1555 1.60 LINK C3M T23 A 6 P DA A 7 1555 1555 1.74 LINK O3' DA B 15 P T23 B 16 1555 1555 1.59 LINK C3M T23 B 16 P DA B 17 1555 1555 1.74 LINK OP1B DG B 19 N5 SPM B 222 1555 1555 1.80 LINK MG MG A 301 O HOH A 302 1555 1555 2.07 LINK MG MG A 301 O HOH A 305 1555 1555 2.11 LINK MG MG A 301 O HOH A 306 1555 1555 2.03 LINK MG MG A 301 O HOH A 307 1555 1555 2.09 LINK MG MG A 301 O HOH B 303 1555 1555 2.09 LINK MG MG A 301 O HOH B 304 1555 1555 2.05 LINK MG MG B1301 O HOH B1302 1555 1555 2.12 LINK MG MG B1301 O HOH B1303 1555 1555 2.05 LINK MG MG B1301 O HOH B1304 1555 1555 1.83 LINK MG MG B1301 O HOH B1305 1555 1555 2.04 LINK MG MG B1301 O HOH B1306 1555 1555 2.13 LINK MG MG B1301 O HOH B1307 1555 1555 2.14 SITE 1 AC1 11 DG A 9 HOH A 329 HOH A 341 HOH A 358 SITE 2 AC1 11 HOH A 502 DG B 13 DT B 14 DC B 18 SITE 3 AC1 11 DG B 19 HOH B 470 HOH B1222 SITE 1 AC2 9 HOH A 336 HOH A 442 DG B 11 DC B 18 SITE 2 AC2 9 DG B 19 DC B 20 HOH B 362 HOH B 367 SITE 3 AC2 9 HOH B 449 SITE 1 AC3 6 HOH A 302 HOH A 305 HOH A 306 HOH A 307 SITE 2 AC3 6 HOH B 303 HOH B 304 SITE 1 AC4 6 HOH B1302 HOH B1303 HOH B1304 HOH B1305 SITE 2 AC4 6 HOH B1306 HOH B1307 CRYST1 24.627 42.717 46.906 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 0.040606 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023410 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021319 0.00000