HEADER DEOXYRIBONUCLEIC ACID 13-JUL-98 415D OBSLTE 26-AUG-03 415D 1O55 TITLE MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TITLE 2 TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*A)-3'); COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS CYCLIC TRINUCLEOTIDE, DEOXYRIBONUCLEIC ACID EXPDTA X-RAY DIFFRACTION AUTHOR Y.-G.GAO,H.ROBINSON,Y.-C.LIAW,J.H.VAN BOOM,G.A.VAN DER AUTHOR 2 MAREL,A.H.-J.WANG REVDAT 2 26-AUG-03 415D 1 OBSLTE REVDAT 1 29-JUL-98 415D 0 JRNL AUTH Y.-G.GAO,H.ROBINSON,Y.-C.LIAW,J.H.VAN BOOM, JRNL AUTH 2 G.A.VAN DER MAREL,A.H.-J.WANG JRNL TITL MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC JRNL TITL 2 TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION JRNL REF TO BE PUBLISHED 1998 JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.04 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) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.144 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL 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) : 2198 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.138 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 : 42 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 17 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) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.031 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 : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 415D COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 WARNING REMARK 5 415D: THIS IS NDB RELEASE. REMARK 5 REMARK 5 PLEASE NOTE THAT THIS ENTRY WAS RELEASED AFTER DEPOSITOR REMARK 5 CHECKING AND APPROVAL. REMARK 5 AN AUXILIARY FILE, AUX415D.RPT, IS AVAILABLE FROM THE REMARK 5 PDB FTP SERVER AND IS ACCESSIBLE THROUGH THE 3DB BROWSER. REMARK 5 THE FILE CONTAINS THE OUTPUT OF THE PROGRAM WHAT_CHECK AND REMARK 5 OTHER DIAGNOSTICS. REMARK 5 REMARK 5 NOMENCLATURE IN THIS ENTRY, INCLUDING HET RESIDUE NAMES REMARK 5 AND HET ATOM NAMES, HAS BEEN STANDARDIZED BY THE NUCLEIC REMARK 5 ACID DATABASE PROCESSING STAFF. A LAYER 2 ENTRY WILL BE REMARK 5 RELEASED BY THE PDB SHORTLY AFTER COMPLETION OF REVIEW REMARK 5 AGAINST THE PDB DATABASE. THE LAYER 2 ENTRY WILL BE REMARK 5 TREATED AS A CORRECTION TO THIS ONE, WITH THE APPROPRIATE REMARK 5 REVDAT RECORD. REMARK 5 REMARK 5 FURTHER INFORMATION INCLUDING VALIDATION CRITERIA USED IN REMARK 5 CHECKING THIS ENTRY AND A LIST OF MANDATORY DATA FIELDS REMARK 5 ARE AVAILABLE FROM THE PDB WEB SITE AT REMARK 5 HTTP://WWW.PDB.BNL.GOV/. REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY THE NUCLEIC ACID DATABASE REMARK 100 ON 15-JUL-1998. REMARK 100 THE NDB ID CODE IS UD0001. REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-DEC-1997 REMARK 200 TEMPERATURE (KELVIN) : 123.0 REMARK 200 PH : 4.50 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) : 1.5406 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX REMARK 200 DATA SCALING SOFTWARE : BIOTEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2198 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.040 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL 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 (%): 26.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED FROM A REMARK 280 SOLUTION THAT CONTAINED , COCL3, GLYCINE, MPD., PH 4.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: R 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 Z,X,Y REMARK 290 3555 Y,Z,X REMARK 290 4555 -Y,-X,-Z REMARK 290 5555 -X,-Z,-Y REMARK 290 6555 -Z,-Y,-X 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 -0.288675 0.507772 0.00000 REMARK 290 SMTRY2 2 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 2.274052 0.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 1.154701 -0.253886 0.00000 REMARK 290 SMTRY2 3 0.000000 0.000000 0.439744 0.00000 REMARK 290 SMTRY3 3 1.969386 1.137026 0.000000 0.00000 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 -0.577350 0.253886 0.00000 REMARK 290 SMTRY2 5 0.000000 0.000000 -0.439744 0.00000 REMARK 290 SMTRY3 5 0.000000 -2.274052 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.577350 -0.507772 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 -1.969386 -1.137026 0.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, D, G, J 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: 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 REMARK 500 O HOH J 113 O HOH J 114 2.09 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 O4* A A 2 N1 A D 5 2565 0.61 REMARK 500 C2 A D 5 C2* A A 2 3455 0.65 REMARK 500 O HOH J 5 C5 A A 2 6565 0.76 REMARK 500 C3* A D 5 C4* A D 5 6555 0.93 REMARK 500 C2* A D 5 C4* A D 5 6555 0.98 REMARK 500 C1* A A 2 N1 A D 5 2565 1.01 REMARK 500 C4 A A 2 O HOH J 5 6565 1.09 REMARK 500 N3 A A 2 N3 A A 2 6565 1.13 REMARK 500 O HOH J 116 O HOH J 109 6565 1.16 REMARK 500 N1 A D 5 C2* A A 2 3455 1.17 REMARK 500 C8 A A 2 C4 A D 5 2565 1.20 REMARK 500 CO CO G 7 C6 A A 2 6565 1.21 REMARK 500 O HOH J 4 C6 A A 2 6565 1.21 REMARK 500 C6 A D 5 O4* A A 2 3455 1.22 REMARK 500 C4* A D 5 O4* A D 5 6555 1.24 REMARK 500 O4* A D 5 C3* A D 5 6555 1.26 REMARK 500 C2 A D 5 O4* A A 2 3455 1.27 REMARK 500 O HOH J 3 N6 A A 2 6565 1.33 REMARK 500 C6 A A 2 O HOH J 5 6565 1.38 REMARK 500 C5* A D 5 C2* A D 5 6555 1.39 REMARK 500 C4* A D 5 C4* A D 5 6555 1.42 REMARK 500 C5 A A 2 CO CO G 7 6565 1.44 REMARK 500 C4* A A 2 N1 A D 5 2565 1.47 REMARK 500 C1* A D 5 C4* A D 5 6555 1.49 REMARK 500 N6 A A 2 CO CO G 7 6565 1.57 REMARK 500 C3* A D 5 C3* A D 5 6555 1.61 REMARK 500 C8 A A 2 N9 A D 5 2565 1.64 REMARK 500 O HOH J 104 O HOH J 104 4665 1.64 REMARK 500 C5* A D 5 C3* A D 5 6555 1.72 REMARK 500 O HOH J 1 C6 A A 2 6565 1.72 REMARK 500 C1* A D 5 C3* A D 5 6555 1.75 REMARK 500 C2* A D 5 C3* A D 5 6555 1.79 REMARK 500 O HOH J 108 N1 A A 2 6565 1.84 REMARK 500 N3 A D 5 C2* A A 2 3455 1.85 REMARK 500 N3 A A 2 O HOH J 5 6565 1.87 REMARK 500 O4* A D 5 O3* A D 5 6555 1.87 REMARK 500 O2P A A 2 N3 A D 5 5565 1.88 REMARK 500 N9 A A 2 C4 A D 5 2565 1.88 REMARK 500 C6 A D 5 C1* A A 2 3455 1.89 REMARK 500 O5* A D 5 C3* A D 5 6555 1.90 REMARK 500 C5 A D 5 O4* A A 2 3455 1.90 REMARK 500 N1 A A 2 O HOH J 5 6565 1.93 REMARK 500 O HOH J 4 N6 A A 2 6565 1.93 REMARK 500 C1* A D 5 O1P A A 2 5556 1.95 REMARK 500 O HOH J 111 O3* A D 5 6555 1.97 REMARK 500 C4 A A 2 N3 A A 2 6565 1.98 REMARK 500 N6 A A 2 O HOH J 2 6565 2.00 REMARK 500 O4* A D 5 C2* A D 5 6555 2.00 REMARK 500 O3* A D 5 O1P A A 2 5556 2.01 REMARK 500 C1* A A 2 C2 A D 5 2565 2.02 REMARK 500 O4* A D 5 O4* A D 5 6555 2.02 REMARK 500 C2 A A 2 O HOH J 5 6565 2.04 REMARK 500 O2P A D 5 O HOH J 109 6565 2.05 REMARK 500 C3* A A 2 N1 A D 5 2565 2.08 REMARK 500 N7 A A 2 O HOH J 5 6565 2.08 REMARK 500 N3 A D 5 O4* A A 2 3455 2.08 REMARK 500 O HOH J 106 O HOH J 115 2555 2.08 REMARK 500 O3* A D 5 C4* A D 5 6555 2.09 REMARK 500 O HOH J 107 O1P A D 5 6565 2.10 REMARK 500 O4* A D 5 O1P A A 2 5556 2.12 REMARK 500 C4 A D 5 O4* A A 2 3455 2.16 REMARK 500 O HOH J 109 O1P A D 5 6565 2.16 DBREF 415D A 2 2 NDB UD0001 UD0001 1 1 DBREF 415D D 5 5 NDB UD0001 UD0001 2 2 HET CO G 7 1 HETNAM CO COBALT (II) ION FORMUL 3 CO CO 2+ FORMUL 4 HOH *23(H2 O1) CRYST1 22.637 22.637 44.581 90.00 90.00 120.00 R 3 2 18 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 0.044175 0.025505 0.000000 0.00000 SCALE2 0.000000 0.051009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022431 0.00000