HEADER DNA 10-MAY-06 2GYX TITLE CRYSTAL STRUCTURE OF DB884- D(CGCGAATTCGCG)2 COMPLEX AT 1.86 A TITLE 2 RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: AT-RICH REGION IN THE GENOME OF ORGANISMS. KEYWDS B-TYPE DUPLEX DNA, DOUBLE HELIX, DODECAMER, COMPOUND DB 884., DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.P.H.LEE,S.NEIDLE REVDAT 5 30-AUG-23 2GYX 1 REMARK LINK REVDAT 4 24-JUL-19 2GYX 1 REMARK REVDAT 3 18-OCT-17 2GYX 1 REMARK REVDAT 2 24-FEB-09 2GYX 1 VERSN REVDAT 1 22-MAY-07 2GYX 0 JRNL AUTH M.MUNDE,M.P.H.LEE,S.NEIDLE,R.ARAFA,D.W.BOYKIN,Y.LIU, JRNL AUTH 2 C.BAILLY,W.D.WILSON JRNL TITL INDUCED FIT CONFORMATIONAL CHANGES OF A "REVERSED AMIDINE" JRNL TITL 2 HETEROCYCLE: OPTIMIZED INTERACTIONS IN A DNA MINOR GROOVE JRNL TITL 3 COMPLEX. JRNL REF J.AM.CHEM.SOC. V. 129 5688 2007 JRNL REFN ISSN 0002-7863 JRNL PMID 17425312 JRNL DOI 10.1021/JA069003N REMARK 2 REMARK 2 RESOLUTION. 1.86 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.236 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.230 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.327 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.129 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 550 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 5430 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.225 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.219 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.310 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.102 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 483 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 4781 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 566.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2267 REMARK 3 NUMBER OF RESTRAINTS : 2584 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.012 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.005 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.013 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.071 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GYX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037719. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 105.0 REMARK 200 PH : 7.00 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) : 1.54178 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : OSMIC FOCUSING MIRROR SYSTEM REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : DENZO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5536 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 2.850 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.9306 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.310 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, MPD, DNA, COMPOUND REMARK 280 DB 884, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K, PH 7.00 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 12.19000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.81350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.05100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.81350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.19000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.05100 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 DA A 5 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG A 10 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = -6.6 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = -7.1 DEGREES 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 26 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 65 O REMARK 620 2 HOH A 66 O 89.4 REMARK 620 3 HOH A 67 O 89.6 89.9 REMARK 620 4 HOH B 64 O 90.6 179.9 90.1 REMARK 620 5 HOH B 65 O 179.8 90.4 90.4 89.6 REMARK 620 6 HOH B 66 O 90.4 90.3 179.8 89.6 89.6 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 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RKA A 25 DBREF 2GYX A 1 12 PDB 2GYX 2GYX 1 12 DBREF 2GYX B 13 24 PDB 2GYX 2GYX 13 24 SEQRES 1 A 12 DC DG DC DG DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA DT DT DC DG DC DG HET MG A 26 1 HET RKA A 25 35 HETNAM MG MAGNESIUM ION HETNAM RKA N,N'-(1H-PYRROLE-2,5-DIYLDI-4,1-PHENYLENE) HETNAM 2 RKA DIBENZENECARBOXIMIDAMIDE FORMUL 3 MG MG 2+ FORMUL 4 RKA C30 H25 N5 FORMUL 5 HOH *44(H2 O) LINK MG MG A 26 O HOH A 65 1555 1555 2.12 LINK MG MG A 26 O HOH A 66 1555 1555 2.13 LINK MG MG A 26 O HOH A 67 1555 1555 2.12 LINK MG MG A 26 O HOH B 64 1555 1555 2.13 LINK MG MG A 26 O HOH B 65 1555 1555 2.12 LINK MG MG A 26 O HOH B 66 1555 1555 2.12 SITE 1 AC1 6 HOH A 65 HOH A 66 HOH A 67 HOH B 64 SITE 2 AC1 6 HOH B 65 HOH B 66 SITE 1 AC2 12 DA A 5 DA A 6 DT A 7 DT A 8 SITE 2 AC2 12 DC A 9 DG A 10 HOH A 60 DA B 18 SITE 3 AC2 12 DT B 19 DT B 20 DC B 21 DG B 22 CRYST1 24.380 40.102 65.627 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 0.041017 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015238 0.00000