PDB Short entry for 1DNX HEADER DNA-RNA HYBRID 16-DEC-99 1DNX TITLE RNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-R(*GP)-D(*CP*GP*TP*AP*TP*AP*CP*GP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA CONFORMATION, RNA/DNA HYBRID, METAL IONS, DNA-RNA COMPLEX, DNA- KEYWDS 2 RNA HYBRID EXPDTA X-RAY DIFFRACTION AUTHOR H.ROBINSON,Y.-G.GAO,R.SANISHVILI,A.JOACHIMIAK,A.H.-J.WANG REVDAT 5 07-FEB-24 1DNX 1 REMARK LINK REVDAT 4 04-OCT-17 1DNX 1 REMARK REVDAT 3 24-FEB-09 1DNX 1 VERSN REVDAT 2 01-APR-03 1DNX 1 JRNL REVDAT 1 10-APR-00 1DNX 0 JRNL AUTH H.ROBINSON,Y.G.GAO,R.SANISHVILI,A.JOACHIMIAK,A.H.WANG JRNL TITL HEXAHYDRATED MAGNESIUM IONS BIND IN THE DEEP MAJOR GROOVE JRNL TITL 2 AND AT THE OUTER MOUTH OF A-FORM NUCLEIC ACID DUPLEXES. JRNL REF NUCLEIC ACIDS RES. V. 28 1760 2000 JRNL REFN ISSN 0305-1048 JRNL PMID 10734195 JRNL DOI 10.1093/NAR/28.8.1760 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 CROSS-VALIDATION METHOD : A POSTERIORI 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) : 0.195 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.194 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 290 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 5659 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.194 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.193 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 285 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 5598 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 406 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 491.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1979 REMARK 3 NUMBER OF RESTRAINTS : 1758 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.074 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.003 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.052 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: SHELXL SWAT OPTION REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : G.PARKINSON ET AL. REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DNX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010233. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK V.4.7 REMARK 200 DATA SCALING SOFTWARE : D*TREK V. 4.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5659 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 47.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.22800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 17.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, CACODYLATE, MGCL2, SPERMINE, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 13.09400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.66150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.97200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.66150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.09400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.97200 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 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 DT A 6 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 8 N1 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG A 9 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC B 12 O4' - C4' - C3' ANGL. DEV. = -5.5 DEGREES REMARK 500 DT B 14 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DC B 18 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 DG B 19 N1 - C6 - O6 ANGL. DEV. = -6.4 DEGREES REMARK 500 DG B 19 C5 - C6 - O6 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC B 20 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC A 2 0.06 SIDE CHAIN REMARK 500 DT A 4 0.07 SIDE CHAIN REMARK 500 DT A 6 0.07 SIDE CHAIN REMARK 500 DC A 8 0.07 SIDE CHAIN REMARK 500 DG A 9 0.06 SIDE CHAIN REMARK 500 DC A 10 0.07 SIDE CHAIN REMARK 500 G B 11 0.09 SIDE CHAIN REMARK 500 DG B 19 0.10 SIDE CHAIN 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 MG A 24 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 179 O REMARK 620 2 HOH A 180 O 179.5 REMARK 620 3 HOH A 181 O 90.0 89.9 REMARK 620 4 HOH A 182 O 88.9 90.7 88.0 REMARK 620 5 HOH A 184 O 91.1 89.3 90.5 178.6 REMARK 620 6 HOH B 183 O 89.7 90.4 177.7 89.7 91.7 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 MG A 24 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DNO RELATED DB: PDB REMARK 900 RELATED ID: 1DNT RELATED DB: PDB DBREF 1DNX A 1 10 PDB 1DNX 1DNX 1 10 DBREF 1DNX B 11 20 PDB 1DNX 1DNX 11 20 SEQRES 1 A 10 G DC DG DT DA DT DA DC DG DC SEQRES 1 B 10 G DC DG DT DA DT DA DC DG DC HET MG A 24 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG MG 2+ FORMUL 4 HOH *84(H2 O) LINK MG MG A 24 O HOH A 179 1555 1555 2.06 LINK MG MG A 24 O HOH A 180 1555 1555 2.05 LINK MG MG A 24 O HOH A 181 1555 1555 2.07 LINK MG MG A 24 O HOH A 182 1555 1555 2.07 LINK MG MG A 24 O HOH A 184 1555 1555 2.05 LINK MG MG A 24 O HOH B 183 1555 1555 2.07 SITE 1 AC1 6 HOH A 179 HOH A 180 HOH A 181 HOH A 182 SITE 2 AC1 6 HOH A 184 HOH B 183 CRYST1 26.188 41.944 43.323 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 0.038185 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023841 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023082 0.00000