HEADER DEOXYRIBONUCLEIC ACID 10-FEB-92 1D55 OBSLTE 15-OCT-95 1D55 2D55 TITLE CRYSTAL STRUCTURE OF THE 2:1 COMPLEX BETWEEN $D(/GAAGCTTC$) TITLE 2 AND THE ANTICANCER DRUG ACTINOMYCIN D COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE:; COMPND 7 CHAIN: I, J; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2 KEYWDS DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.KAMITORI,F.TAKUSAGAWA REVDAT 2 31-JAN-94 1D55 1 FORMUL REVDAT 1 31-OCT-93 1D55 0 JRNL AUTH S.KAMITORI,F.TAKUSAGAWA JRNL TITL CRYSTAL STRUCTURE OF THE 2:1 COMPLEX BETWEEN JRNL TITL 2 D(/GAAGCTTC) AND THE ANTICANCER DRUG ACTINOMYCIN D JRNL REF J.MOL.BIOL. V. 225 445 1992 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 66 REMARK 3 NUCLEIC ACID ATOMS : 322 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 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: NULL REMARK 4 REMARK 4 1D55 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 1D55 PXZ IS 2-AMINO-1,9-DICARBOXY-4,6 DIMETHYL-3- REMARK 5 PHENOXAZONE. 1D55 REMARK 6 REMARK 6 1D55 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE REMARK 6 CHEMISTS 1D55 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE REMARK 6 MOIETY RATHER 1D55 THAN THAT OF THE NUCLEOSIDE CHEMISTS. REMARK 6 THE RING OXYGEN 1D55 ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 6 1D55 REMARK 7 REMARK 7 1D55 THE HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY REMARK 7 FOLLOW 1D55 THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING REMARK 7 PATTERN. 1D55 THEY HAVE NOT BEEN PRESENTED ON *CONECT* REMARK 7 RECORDS IN THIS 1D55 ENTRY. 1D55 REMARK 8 REMARK 8 1D55 SOME OF THE DISTANCES AND ANGLES IN THIS STRUCTURE REMARK 8 DEVIATE 1D55 FROM EXPECTED VALUES. 1D55 REMARK 9 REMARK 9 1D55 CORRECTION. CORRECT FORMULA FOR SAR ON FORMUL RECORDS. REMARK 9 1D55 31-JAN-94. 1D55 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 : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL 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 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 1/2+X,1/2+Y,Z REMARK 290 4555 1/2-X,1/2+Y,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 25.68500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.04500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.68500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.04500 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 4 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, B, I, 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 N THR I 1 C PXZ 17 1.34 REMARK 500 N THR J 1 C* PXZ 17 1.36 REMARK 500 OG1 THR J 1 C VAL J 5 1.37 REMARK 500 OG1 THR I 1 C VAL I 5 1.40 REMARK 500 N VAL J 5 C CH3 J 5 1.48 REMARK 500 N VAL I 5 C CH3 I 5 1.49 REMARK 500 N THR I 1 O PXZ 17 2.15 REMARK 500 OG1 THR J 1 O VAL J 5 2.16 REMARK 500 OG1 THR I 1 O VAL I 5 2.19 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL I 2 -118.18 104.31 REMARK 500 VAL J 2 -115.80 89.76 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR I 1 VAL I 2 132.54 REMARK 500 PRO I 3 SAR I 4 -47.48 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 32 DISTANCE = 8.79 ANGSTROMS REMARK 525 HOH 39 DISTANCE = 5.31 ANGSTROMS REMARK 525 HOH 45 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH 56 DISTANCE = 8.76 ANGSTROMS REMARK 525 HOH 59 DISTANCE = 5.15 ANGSTROMS REMARK 525 HOH 62 DISTANCE = 8.65 ANGSTROMS REMARK 525 HOH 63 DISTANCE = 7.88 ANGSTROMS REMARK 525 HOH 67 DISTANCE = 10.20 ANGSTROMS REMARK 525 HOH 69 DISTANCE = 9.04 ANGSTROMS REMARK 525 HOH 70 DISTANCE = 5.34 ANGSTROMS REMARK 525 HOH 75 DISTANCE = 7.68 ANGSTROMS REMARK 525 HOH 76 DISTANCE = 5.23 ANGSTROMS REMARK 525 HOH 81 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH 84 DISTANCE = 5.47 ANGSTROMS REMARK 525 HOH 86 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH 89 DISTANCE = 8.31 ANGSTROMS REMARK 525 HOH 93 DISTANCE = 8.75 ANGSTROMS REMARK 525 HOH 100 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH 101 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH 105 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH 110 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH 113 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH 115 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH 116 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH 121 DISTANCE = 5.76 ANGSTROMS REMARK 525 HOH 125 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH 128 DISTANCE = 7.73 ANGSTROMS REMARK 525 HOH 132 DISTANCE = 5.38 ANGSTROMS SEQRES 1 A 8 G A A G C T T C SEQRES 1 B 8 G A A G C T T C SEQRES 1 I 5 THR VAL PRO SAR VAL SEQRES 1 J 5 THR VAL PRO SAR VAL MODRES 1D55 SAR I 4 GLY SARCOSINE MODRES 1D55 SAR J 4 GLY SARCOSINE FTNOTE 1 VALINES 2 I AND 2 J OF ACTINOMYCIN D ARE D-VALINES. FTNOTE 2 THE METHYL GROUP IS ATTACHED TO THE NITROGEN ATOM OF VAL 5 FTNOTE 2 OF THE CYCLIC POLYPEPTIDE RINGS OF ACTINOMYCIN D. HET SAR I 4 5 HET SAR J 4 5 HET PXZ 17 22 HET CH3 I 5 1 HET CH3 J 5 1 HETNAM SAR SARCOSINE HETNAM PXZ 2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO- HETNAM 2 PXZ PHENOXAZIN-3-ONE HETNAM CH3 METHYL GROUP HETSYN PXZ PHENOXAZINE FORMUL 3 SAR 2(C3 H7 N O2) FORMUL 5 PXZ C16 H12 N2 O4 FORMUL 6 CH3 2(C H4) FORMUL 8 HOH *107(H2 O1) CISPEP 1 VAL I 2 PRO I 3 0 14.96 CISPEP 2 VAL J 2 PRO J 3 0 11.10 CISPEP 3 PRO J 3 SAR J 4 0 -4.00 CRYST1 51.370 62.090 25.040 90.00 113.80 90.00 C 1 2 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 0.019467 0.000000 0.008586 0.00000 SCALE2 0.000000 0.016106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.043648 0.00000