PDB Full entry for 416D HEADER DEOXYRIBONUCLEIC ACID 13-JUL-98 416D OBSLTE 26-AUG-03 416D 1O56 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 MAREL, AUTHOR 2 A.H.-J.WANG REVDAT 2 26-AUG-03 416D 1 OBSLTE REVDAT 1 29-JUL-98 416D 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. 0.90 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) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL 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) : 3059 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.109 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 : 0 REMARK 3 SOLVENT ATOMS : 13 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) : 0.032 REMARK 3 ANGLE DISTANCES (A) : NULL 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 416D COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 WARNING REMARK 5 416D: 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, AUX416D.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 UD0002. 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) : 298.0 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 : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : RIGAKU/MSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : RIGAKU/VAX REMARK 200 DATA SCALING SOFTWARE : RIGAKU/VAX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3059 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIRECT METHODS 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 (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED FROM A REMARK 280 SOLUTION THAT CONTAINED MPD, GLYCINE, MGCL2., PH 4.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,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 -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 0.00000 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 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, G 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 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 -0.866025 0.000000 23.32800 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 G 3 LIES ON A SPECIAL POSITION. REMARK 375 HOH G 4 LIES ON A SPECIAL POSITION. REMARK 375 HOH G 5 LIES ON A SPECIAL POSITION. REMARK 375 HOH G 12 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 REMARK 500 O HOH G 13 O HOH G 14 2.17 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 P A D 2 O3* A D 2 3665 1.59 REMARK 500 P A A 1 O3* A A 1 2555 1.61 REMARK 500 O HOH G 13 O HOH G 15 1554 2.17 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH G 3 DISTANCE = 11.10 ANGSTROMS REMARK 525 HOH G 9 DISTANCE = 8.53 ANGSTROMS REMARK 525 HOH G 15 DISTANCE = 11.16 ANGSTROMS DBREF 416D A 1 1 NDB UD0002 UD0002 1 1 DBREF 416D D 2 2 NDB UD0002 UD0002 2 2 FORMUL 3 HOH *13(H2 O1) CRYST1 23.328 23.328 9.680 90.00 90.00 120.00 P 3 3 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 0.042867 0.024749 0.000000 0.00000 SCALE2 0.000000 0.049498 0.000000 0.00000 SCALE3 0.000000 0.000000 0.103306 0.00000 ATOM 1 P A A 1 0.421 4.039 -2.933 1.00 0.10 P ATOM 2 O1P A A 1 0.818 5.069 -3.901 1.00 0.16 O ATOM 3 O2P A A 1 0.311 4.338 -1.509 1.00 0.12 O ATOM 4 O5* A A 1 1.400 2.800 -2.997 1.00 0.11 O ATOM 5 C5* A A 1 1.801 2.311 -4.251 1.00 0.13 C ATOM 6 C4* A A 1 2.995 1.329 -4.062 1.00 0.08 C ATOM 7 O4* A A 1 4.119 2.107 -3.636 1.00 0.08 O ATOM 8 C3* A A 1 2.825 0.234 -2.994 1.00 0.07 C ATOM 9 O3* A A 1 3.486 -0.903 -3.541 1.00 0.09 O ATOM 10 C2* A A 1 3.512 0.802 -1.757 1.00 0.09 C ATOM 11 C1* A A 1 4.621 1.636 -2.392 1.00 0.09 C ATOM 12 N9 A A 1 5.017 2.794 -1.636 1.00 0.08 N ATOM 13 C8 A A 1 4.355 3.964 -1.571 1.00 0.10 C ATOM 14 N7 A A 1 4.943 4.873 -0.817 1.00 0.10 N ATOM 15 C5 A A 1 6.031 4.196 -0.300 1.00 0.08 C ATOM 16 C6 A A 1 7.094 4.570 0.542 1.00 0.07 C ATOM 17 N6 A A 1 7.194 5.794 1.058 1.00 0.08 N ATOM 18 N1 A A 1 8.004 3.701 0.819 1.00 0.09 N ATOM 19 C2 A A 1 7.926 2.564 0.285 1.00 0.10 C ATOM 20 N3 A A 1 6.983 2.026 -0.522 1.00 0.10 N ATOM 21 C4 A A 1 6.068 2.946 -0.788 1.00 0.07 C TER 22 A A 1 ATOM 23 P A D 2 14.944 9.099 5.933 1.00 0.09 P ATOM 24 O1P A D 2 15.269 9.154 4.483 1.00 0.15 O ATOM 25 O2P A D 2 15.672 9.976 6.862 1.00 0.13 O ATOM 26 O5* A D 2 13.348 9.362 5.980 1.00 0.10 O ATOM 27 C5* A D 2 12.696 9.433 7.234 1.00 0.12 C ATOM 28 C4* A D 2 11.318 9.990 7.024 1.00 0.10 C ATOM 29 O4* A D 2 11.421 11.354 6.614 1.00 0.11 O ATOM 30 C3* A D 2 10.430 9.273 5.987 1.00 0.10 C ATOM 31 O3* A D 2 9.132 9.324 6.513 1.00 0.08 O ATOM 32 C2* A D 2 10.633 10.186 4.785 1.00 0.09 C ATOM 33 C1* A D 2 10.804 11.562 5.401 1.00 0.09 C ATOM 34 N9 A D 2 11.568 12.473 4.612 1.00 0.09 N ATOM 35 C8 A D 2 12.900 12.477 4.536 1.00 0.15 C ATOM 36 N7 A D 2 13.380 13.505 3.788 1.00 0.12 N ATOM 37 C5 A D 2 12.238 14.069 3.280 1.00 0.10 C ATOM 38 C6 A D 2 12.104 15.166 2.454 1.00 0.12 C ATOM 39 N6 A D 2 13.096 15.851 1.925 1.00 0.14 N ATOM 40 N1 A D 2 10.788 15.546 2.175 1.00 0.11 N ATOM 41 C2 A D 2 9.927 14.827 2.742 1.00 0.13 C ATOM 42 N3 A D 2 9.928 13.794 3.511 1.00 0.11 N ATOM 43 C4 A D 2 11.185 13.473 3.789 1.00 0.10 C TER 44 A D 2 HETATM 45 O HOH G 3 0.000 0.000 8.705 1.00 0.17 O HETATM 46 O HOH G 4 11.665 6.734 3.904 1.00 0.18 O HETATM 47 O HOH G 5 0.000 0.000 3.307 1.00 0.19 O HETATM 48 O HOH G 6 0.890 2.325 0.214 1.00 0.11 O HETATM 49 O HOH G 7 9.230 7.154 2.752 1.00 0.10 O HETATM 50 O HOH G 8 0.020 5.012 3.134 1.00 0.22 O HETATM 51 O HOH G 9 11.619 1.752 9.559 1.00 0.29 O HETATM 52 O HOH G 10 10.807 4.273 0.669 1.00 0.13 O HETATM 53 O HOH G 11 -0.877 2.489 2.321 1.00 0.14 O HETATM 54 O HOH G 12 11.665 6.734 9.377 1.00 0.21 O HETATM 55 O HOH G 13 0.146 6.831 1.878 1.00 0.17 O HETATM 56 O HOH G 14 1.701 5.931 0.657 1.00 0.24 O HETATM 57 O HOH G 15 -1.182 6.653 9.847 1.00 0.28 O MASTER 259 0 0 0 0 0 0 6 55 2 0 0 END