HEADER DNA 18-JUN-01 1JES TITLE CRYSTAL STRUCTURE OF A COPPER-MEDIATED BASE PAIR IN DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*(DPY)P*AP*TP*(DRP)P*CP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS CU, COPPER, DNA, Z-DNA, DODECAMER, DUPLEX, UNNATURAL, DESIGNED EXPDTA X-RAY DIFFRACTION AUTHOR S.ATWELL,E.MEGGERS,G.SPRAGGON,P.G.SCHULTZ REVDAT 5 03-APR-24 1JES 1 REMARK REVDAT 4 07-FEB-24 1JES 1 REMARK LINK REVDAT 3 24-FEB-09 1JES 1 VERSN REVDAT 2 07-DEC-01 1JES 1 JRNL REVDAT 1 23-NOV-01 1JES 0 JRNL AUTH S.ATWELL,E.MEGGERS,G.SPRAGGON,P.G.SCHULTZ JRNL TITL STRUCTURE OF A COPPER-MEDIATED BASE PAIR IN DNA JRNL REF J.AM.CHEM.SOC. V. 123 12364 2001 JRNL REFN ISSN 0002-7863 JRNL PMID 11734038 JRNL DOI 10.1021/JA011822E REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.MEGGERS,P.L.HOLLAND,W.B.TOLMAN,F.E.ROMESBERG,P.G.SCHULTZ REMARK 1 TITL A NOVEL COPPER-MEDIATED DNA BASE PAIR REMARK 1 REF J.AM.CHEM.SOC. V. 122 10714 2000 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA0025806 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.G.-J.WANG,G.J.QUIGLEY,F.J.KOLPAK,G.VAN DER MAREL, REMARK 1 AUTH 2 J.H.VAN BOOM,A.RICH REMARK 1 TITL LEFT-HANDED DOUBLE HELICAL DNA: VARIATIONS IN THE BACKBONE REMARK 1 TITL 2 CONFORMATION REMARK 1 REF SCIENCE V. 211 171 1981 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.R.DREW,R.M.WING,T.TAKANO,C.BROKA,S.TANAKA,K.ITAKURA, REMARK 1 AUTH 2 R.E.DICKERSON REMARK 1 TITL STRUCTURE OF A B-DNA DODECAMER: CONFORMATION AND DYNAMICS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 78 2179 1981 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, REMARK 3 A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERS FOR REMARK 3 THE REFINEMENT OF NUCLEIC ACID CONTAINING REMARK 3 STRUCTURES, ACTA CRYST. D, 52, 57-64 (1996). REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 8520 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM 8% REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 682 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 484 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39900 REMARK 3 B22 (A**2) : -0.00700 REMARK 3 B33 (A**2) : 0.40600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.78400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.560 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE FOFC MAPS INDICATED AN ALTERNATE CONFORMATION FOR THE REMARK 3 PHOSPHATE OF B23, REMARK 3 AND SO THE STRUCTURE WAS REFINED WITH TWO CONFORMATIONS FOR THE REMARK 3 PHOSPHATE OF REMARK 3 B23 (EXCEPTING THE O5') AND MOST OF RESIDUE B22 (EXCEPTING O5'), REMARK 3 EACH WITH REMARK 3 0.5 OCCUPANCY. REMARK 4 REMARK 4 1JES COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013688. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 140 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.37991,1.37791,1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : CURVED SI (111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47190 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 46.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.68600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: INITIAL MAP FIT WITH MONONUCLEOTIDES REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% MPD, 40 MM NA CACODYLATE, 12 MM REMARK 280 SPERMINE TETRA-HCL, 80 MM NACL, 20 MM MGCL2, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 17.17950 REMARK 290 SMTRY3 2 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 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 CU A 25 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DPY A 5 N3 REMARK 620 2 DPY A 5 O72 74.6 REMARK 620 3 DPY A 5 O82 79.0 152.8 REMARK 620 4 DRP B 20 N3 171.7 97.5 109.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 26 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DRP A 8 N3 REMARK 620 2 DPY B 17 N3 171.6 REMARK 620 3 DPY B 17 O72 97.1 75.5 REMARK 620 4 DPY B 17 O82 108.7 79.1 153.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 26 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BNA RELATED DB: PDB REMARK 900 STRUCTURE OF 5'-(CPGPCPGPAPAPTPTPCPGPCPG)-3' REMARK 900 RELATED ID: 2ZNA RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF Z(I)-DNA REMARK 900 RELATED ID: 3ZNA RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF Z(II)-DNA DBREF 1JES A 1 12 PDB 1JES 1JES 1 12 DBREF 1JES B 13 24 PDB 1JES 1JES 13 24 SEQRES 1 A 12 DC DG DC DG DPY DA DT DRP DC DG DC DG SEQRES 1 B 12 DC DG DC DG DPY DA DT DRP DC DG DC DG HET DPY A 5 23 HET DRP A 8 17 HET DPY B 17 23 HET DRP B 20 17 HET CU A 25 1 HET CU B 26 1 HETNAM DPY 2-DEOXYRIBOFURANOSYL-PYRIDINE-2,6-DICARBOXYLIC ACID-5'- HETNAM 2 DPY MONOPHOSPHATE HETNAM DRP 2-DEOXYRIBOFURANOSYL-PYRIDINE-5'-MONOPHOSPHATE HETNAM CU COPPER (II) ION FORMUL 1 DPY 2(C12 H14 N O10 P) FORMUL 1 DRP 2(C10 H14 N O6 P) FORMUL 3 CU 2(CU 2+) FORMUL 5 HOH *82(H2 O) LINK O3' DG A 4 P DPY A 5 1555 1555 1.59 LINK O3' DPY A 5 P DA A 6 1555 1555 1.61 LINK O3' DT A 7 P DRP A 8 1555 1555 1.62 LINK O3' DRP A 8 P DC A 9 1555 1555 1.62 LINK O3' DG B 16 P DPY B 17 1555 1555 1.59 LINK O3' DPY B 17 P DA B 18 1555 1555 1.61 LINK O3' DT B 19 P DRP B 20 1555 1555 1.61 LINK O3' DRP B 20 P DC B 21 1555 1555 1.60 LINK N3 DPY A 5 CU CU A 25 1555 1555 1.91 LINK O72 DPY A 5 CU CU A 25 1555 1555 2.28 LINK O82 DPY A 5 CU CU A 25 1555 1555 2.33 LINK N3 DRP A 8 CU CU B 26 1555 1555 1.86 LINK CU CU A 25 N3 DRP B 20 1555 1555 1.89 LINK N3 DPY B 17 CU CU B 26 1555 1555 1.92 LINK O72 DPY B 17 CU CU B 26 1555 1555 2.22 LINK O82 DPY B 17 CU CU B 26 1555 1555 2.26 SITE 1 AC1 4 DG A 4 DPY A 5 DT B 19 DRP B 20 SITE 1 AC2 4 DT A 7 DRP A 8 DG B 16 DPY B 17 CRYST1 25.343 34.359 31.093 90.00 101.13 90.00 P 1 21 1 4 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 0.039459 0.000000 0.007763 0.00000 SCALE2 0.000000 0.029104 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032778 0.00000