PDB Short entry for 1VZK HEADER NUCLEIC ACID 20-MAY-04 1VZK TITLE A THIOPHENE BASED DIAMIDINE FORMS A "SUPER" AT BINDING MINOR GROOVE TITLE 2 AGENT 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 KEYWDS NUCLEIC ACID, NUCLEIC ACIDS, MINOR GROOVE BINDER, DOUBLE HELIX, DNA- KEYWDS 2 DRUG COMPLEX, MAGNESIUM-WATER COMPLEX, DNA HYDRATION EXPDTA X-RAY DIFFRACTION AUTHOR S.MALLENA,M.P.H.LEE,C.BAILLY,S.NEIDLE,A.KUMAR,D.W.BOYKIN,W.D.WILSON REVDAT 4 13-DEC-23 1VZK 1 LINK REVDAT 3 22-MAY-19 1VZK 1 REMARK REVDAT 2 24-FEB-09 1VZK 1 VERSN REVDAT 1 25-OCT-04 1VZK 0 JRNL AUTH S.MALLENA,M.P.H.LEE,C.BAILLY,S.NEIDLE,A.KUMAR,D.W.BOYKIN, JRNL AUTH 2 W.D.WILSON JRNL TITL THIOPHENE-BASED DIAMIDINE FORMS A "SUPER" AT BINDING MINOR JRNL TITL 2 GROOVE AGENT JRNL REF J.AM.CHEM.SOC. V. 142 13659 2004 JRNL REFN ISSN 0002-7863 JRNL PMID 15493923 JRNL DOI 10.1021/JA048175M REMARK 2 REMARK 2 RESOLUTION. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE 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) : 0.223 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.227 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 662 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 5894 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.215 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.220 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 617 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 5495 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 : 27 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 573.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2307 REMARK 3 NUMBER OF RESTRAINTS : 2538 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.002 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.006 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.004 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.040 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 AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 1VZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1290015035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-03 REMARK 200 TEMPERATURE (KELVIN) : 103.0 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 FOCUSSING MIRRORS 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6667 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 17.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 6.580 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 70.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.13500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 13.16 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 (%): 56.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MGCL2, DNA, COMPOUND DB818, MPD, REMARK 280 SPERMINE, SODIUM CACODYLATE BUFFER., 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 12.83850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.59250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.96050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.59250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.83850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.96050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG A 10 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -7.7 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = -7.5 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = -5.8 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 A2003 DISTANCE = 5.96 ANGSTROMS 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 A1014 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2009 O REMARK 620 2 HOH A2011 O 89.7 REMARK 620 3 HOH A2015 O 179.8 90.5 REMARK 620 4 HOH A2016 O 90.2 179.8 89.6 REMARK 620 5 HOH A2020 O 90.1 89.8 89.8 90.4 REMARK 620 6 HOH B2019 O 90.4 90.2 89.8 89.6 179.6 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 A1014 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D1B A1013 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DBE RELATED DB: PDB REMARK 900 DNA (5'- D( CP GP CP GP AP AP TP TP CP GP CP GP)-3') COMPLEXED WITH REMARK 900 BERENIL (DIMINAZENE ACETURATE) (1,3-BIS(4'-AMIDINOPHENYL)TRIAZENE) DBREF 1VZK A 1 12 PDB 1VZK 1VZK 1 12 DBREF 1VZK B 13 24 PDB 1VZK 1VZK 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 D1B A1013 26 HET MG A1014 1 HETNAM D1B 2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-THIENYL)-1H- HETNAM 2 D1B BENZIMIDAZOLE-6- CARBOXIMIDAMIDE DIHYDROCHLORIDE HETNAM MG MAGNESIUM ION FORMUL 3 D1B C19 H16 N6 S FORMUL 4 MG MG 2+ FORMUL 5 HOH *60(H2 O) LINK MG MG A1014 O HOH A2009 1555 1555 2.13 LINK MG MG A1014 O HOH A2011 1555 1555 2.12 LINK MG MG A1014 O HOH A2015 1555 3655 2.11 LINK MG MG A1014 O HOH A2016 1555 3655 2.13 LINK MG MG A1014 O HOH A2020 1555 3655 2.12 LINK MG MG A1014 O HOH B2019 1555 1555 2.13 SITE 1 AC1 6 HOH A2009 HOH A2011 HOH A2015 HOH A2016 SITE 2 AC1 6 HOH A2020 HOH B2019 SITE 1 AC2 10 DA A 6 DT A 7 DT A 8 DC A 9 SITE 2 AC2 10 HOH A2034 DA B 17 DA B 18 DT B 19 SITE 3 AC2 10 DT B 20 DC B 21 CRYST1 25.677 39.921 65.185 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 0.038945 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015341 0.00000