HEADER DNA 21-OCT-99 1D7Z TITLE CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT TITLE 2 2.2 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC) COMPND 3 P*(6HA)P*(6HC))-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE SUGAR MOIETIES ARE NOT DEOXYRIBOSE BUT COMPND 7 D-ARABINO-HEXITOL SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE MOLECULE WAS CHEMICALLY SYNTESISED (SEE SOURCE 4 REFERENCE 1) KEYWDS HEXITOL NUCLEIC ACID, DNA ANALOGUE, DOUBLE HELIX EXPDTA X-RAY DIFFRACTION AUTHOR R.DECLERCQ,L.VAN MEERVELT REVDAT 3 24-FEB-09 1D7Z 1 VERSN REVDAT 2 01-APR-03 1D7Z 1 JRNL REVDAT 1 28-JUN-02 1D7Z 0 JRNL AUTH R.DECLERCQ,A.VAN AERSCHOT,R.J.READ,P.HERDEWIJN, JRNL AUTH 2 L.VAN MEERVELT JRNL TITL CRYSTAL STRUCTURE OF DOUBLE HELICAL HEXITOL JRNL TITL 2 NUCLEIC ACIDS. JRNL REF J.AM.CHEM.SOC. V. 124 928 2002 JRNL REFN ISSN 0002-7863 JRNL PMID 11829600 JRNL DOI 10.1021/JA016570W REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.VAN AERSCHOT,I VERHEGGEN,C.HENDRIX,P.HERDEWIJN REMARK 1 TITL 1',5'-ANHYDROHEXITOL NUCLEIC ACIDS, A NEW REMARK 1 TITL 2 PROMISING ANTISENSE CONSTRUCT REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 34 1338 1995 REMARK 1 REFN ISSN 1433-7851 REMARK 1 DOI 10.1002/ANIE.199513381 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.DECLERCQ,P.HERDEWIJN,L.VAN MEERVELT REMARK 1 TITL 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(GUANIN-9-YL)-D- REMARK 1 TITL 2 ARABINO-HEXITOL REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 52 1213 1995 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.DECLERCQ,A.VAN AERSCHOT,P.HERDEWIJN, REMARK 1 AUTH 2 L.VAN MEERVELT REMARK 1 TITL OLIGONUCLEOTIDES WITH 1',5'-ANHYDROHEXITOL REMARK 1 TITL 2 NUCLEOSIDE BUILDING BLOCKS: CRYSTALLIZATION AND REMARK 1 TITL 3 PRELIMINARY X-RAY STUDIES OF H(GTGTACAC) REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 279 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 2.21 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.8 REMARK 3 CROSS-VALIDATION METHOD : NONE USED REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.233 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.233 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 1329 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 : 169 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 38 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) : 0.018 REMARK 3 ANGLE DISTANCES (A) : 0.022 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 : BASES: TAYLOR AND KENNARD REMARK 3 VALUES; THE REST: VALUES BASED REMARK 3 ON SINGLE CRYSTAL STRUCTURE OF REMARK 3 HNA BUILDING BLOCKS REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D7Z COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB ON 25-OCT-99. REMARK 100 THE RCSB ID CODE IS RCSB009877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9116 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 1344 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 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 (%) : 83.8 REMARK 200 DATA REDUNDANCY : 16.800 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.16800 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: NULL REMARK 200 SOFTWARE USED: GLRF REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CACODYLATE BUFFER, KCL, BACL2, REMARK 280 SPERMINE TETRACHLORIDE AND MPD, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP AT 277K 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 46.08067 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 23.04033 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 46.08067 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 23.04033 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 46.08067 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 23.04033 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 46.08067 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 23.04033 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 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 0.500000 -0.866025 0.000000 18.18200 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 31.49215 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 46.08067 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 21 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 56 LIES ON A SPECIAL POSITION. 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 16 DISTANCE = 8.03 ANGSTROMS REMARK 525 HOH A 24 DISTANCE = 7.88 ANGSTROMS REMARK 525 HOH A 42 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH A 55 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH A 58 DISTANCE = 6.83 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HD0001 RELATED DB: NDB REMARK 900 HD0001 CONTAINS THE SAME MOLECULE CRYSTALLIZED IN P 32 1 2 REMARK 900 AND SOLVED AT 1.6 A RESOLUTION DBREF 1D7Z A 1 8 PDB 1D7Z 1D7Z 1 8 SEQRES 1 A 8 6HG 6HT 6HG 6HT 6HA 6HC 6HA 6HC MODRES 1D7Z 6HG A 1 DG MODRES 1D7Z 6HT A 2 DT MODRES 1D7Z 6HG A 3 DG MODRES 1D7Z 6HT A 4 DT MODRES 1D7Z 6HA A 5 DA MODRES 1D7Z 6HC A 6 DC MODRES 1D7Z 6HA A 7 DA MODRES 1D7Z 6HC A 8 DC HET 6HG A 1 20 HET 6HT A 2 21 HET 6HG A 3 23 HET 6HT A 4 21 HET 6HA A 5 22 HET 6HC A 6 20 HET 6HA A 7 22 HET 6HC A 8 20 HETNAM 6HG 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(GUANIN-9-YL)-6'-O- HETNAM 2 6HG PHOSPHORYL-D-ARABINO-HEXITOL HETNAM 6HT 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(THYMIN-1-YL)-6'-O- HETNAM 2 6HT PHOSPHORYL-D-ARABINO-HEXITOL HETNAM 6HA 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(ADENIN-9-YL)-6'-O- HETNAM 2 6HA PHOSPHORYL-D-ARABINO-HEXITOL HETNAM 6HC 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(CYTOSIN-1-YL)-6'-O- HETNAM 2 6HC PHOSPHORYL-D-ARABINO-HEXITOL FORMUL 1 6HG 2(C11 H16 N5 O7 P) FORMUL 1 6HT 2(C11 H17 N2 O8 P) FORMUL 1 6HA 2(C11 H16 N5 O6 P) FORMUL 1 6HC 2(C10 H16 N3 O7 P) FORMUL 2 HOH *38(H2 O) LINK O3' 6HG A 1 P 6HT A 2 1555 1555 1.62 LINK O3' 6HT A 2 P 6HG A 3 1555 1555 1.65 LINK O3' 6HG A 3 P 6HT A 4 1555 1555 1.57 LINK O3' 6HT A 4 P 6HA A 5 1555 1555 1.62 LINK O3' 6HA A 5 P 6HC A 6 1555 1555 1.60 LINK O3' 6HC A 6 P 6HA A 7 1555 1555 1.72 LINK O3' 6HA A 7 P 6HC A 8 1555 1555 1.63 CRYST1 36.364 36.364 69.121 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 0.027500 0.015877 0.000000 0.00000 SCALE2 0.000000 0.031754 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014467 0.00000 MASTER 267 0 8 0 0 0 0 6 0 0 0 1 END