HEADER DNA/ANTIBIOTIC 22-MAR-24 8YS7 TITLE CRYSTAL STRUCTURE OF ACTINOMYCIN D AND ECHINOMYCIN-D(ACGGGCT/AGCCCCGT) TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*GP*CP*CP*CP*CP*GP*T)-3'); COMPND 3 CHAIN: B, K; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*AP*CP*GP*GP*GP*CP*T)-3'); COMPND 7 CHAIN: C, L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ECHINOMYCIN; COMPND 11 CHAIN: E, A; COMPND 12 MOL_ID: 4; COMPND 13 MOLECULE: ACTINOMYCIN D; COMPND 14 CHAIN: I, D SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: STREPTOMYCES; SOURCE 11 ORGANISM_TAXID: 1883; SOURCE 12 MOL_ID: 4; SOURCE 13 ORGANISM_SCIENTIFIC: STREPTOMYCES; SOURCE 14 ORGANISM_TAXID: 1883 KEYWDS BULGE DNA, ACTINOMYCIN D, ECHINOMYCIN, DNA, DNA-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.Y.LEE,M.H.HOU REVDAT 1 09-APR-25 8YS7 0 JRNL AUTH Y.Y.LEE,M.H.HOU JRNL TITL CRYSTAL STRUCTURE OF ACTINOMYCIN D AND JRNL TITL 2 ECHINOMYCIN-D(ACGGGCT/AGCCCCGT) COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 2687 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.279 REMARK 3 R VALUE (WORKING SET) : 0.277 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 269 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.3200 - 4.0800 0.99 1251 140 0.2710 0.2840 REMARK 3 2 3.3700 - 3.2500 0.96 1167 129 0.2945 0.3157 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.120 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.030 1020 REMARK 3 ANGLE : 2.592 1512 REMARK 3 CHIRALITY : 0.171 160 REMARK 3 PLANARITY : 0.020 84 REMARK 3 DIHEDRAL : 38.779 336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2677 66.7847 26.1148 REMARK 3 T TENSOR REMARK 3 T11: 1.3611 T22: 0.0141 REMARK 3 T33: 2.8524 T12: -0.1879 REMARK 3 T13: 0.0969 T23: 0.6258 REMARK 3 L TENSOR REMARK 3 L11: 1.0668 L22: 6.8116 REMARK 3 L33: 2.7614 L12: 1.2964 REMARK 3 L13: -1.4601 L23: -0.1134 REMARK 3 S TENSOR REMARK 3 S11: 0.9714 S12: -0.9763 S13: -0.5966 REMARK 3 S21: 2.6013 S22: -1.2781 S23: -0.5466 REMARK 3 S31: -0.0704 S32: 3.0250 S33: 0.0451 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.9146 66.8809 16.8426 REMARK 3 T TENSOR REMARK 3 T11: 1.7422 T22: 0.7981 REMARK 3 T33: 1.4473 T12: -0.0062 REMARK 3 T13: 0.1298 T23: 0.2208 REMARK 3 L TENSOR REMARK 3 L11: 1.1812 L22: 6.0777 REMARK 3 L33: 3.6579 L12: 0.4850 REMARK 3 L13: 0.1526 L23: -0.4931 REMARK 3 S TENSOR REMARK 3 S11: 0.9774 S12: 0.6733 S13: 0.9810 REMARK 3 S21: -0.4731 S22: -0.7118 S23: 0.9282 REMARK 3 S31: -0.9373 S32: -0.1296 S33: 0.0003 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'K' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5195 32.3655 20.9740 REMARK 3 T TENSOR REMARK 3 T11: 1.0586 T22: 0.7980 REMARK 3 T33: 1.2632 T12: -0.2890 REMARK 3 T13: -0.2198 T23: 0.0826 REMARK 3 L TENSOR REMARK 3 L11: 1.1325 L22: 5.4078 REMARK 3 L33: 4.4986 L12: -1.2777 REMARK 3 L13: -0.3221 L23: -0.5588 REMARK 3 S TENSOR REMARK 3 S11: -0.4279 S12: 0.7104 S13: -0.1617 REMARK 3 S21: 0.2315 S22: -0.2954 S23: -1.0964 REMARK 3 S31: 0.7016 S32: -0.4753 S33: 0.5451 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2253 35.9604 19.9539 REMARK 3 T TENSOR REMARK 3 T11: 1.1749 T22: 1.1868 REMARK 3 T33: 1.1830 T12: -0.4558 REMARK 3 T13: -0.0142 T23: -0.1807 REMARK 3 L TENSOR REMARK 3 L11: 0.4180 L22: 5.4052 REMARK 3 L33: 3.4672 L12: -1.0668 REMARK 3 L13: -1.5344 L23: -0.2840 REMARK 3 S TENSOR REMARK 3 S11: 0.0186 S12: 0.7807 S13: -0.0158 REMARK 3 S21: 0.6546 S22: -0.7586 S23: 1.4439 REMARK 3 S31: 1.3079 S32: -1.6943 S33: 0.3844 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 2 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.0978 27.5443 22.9282 REMARK 3 T TENSOR REMARK 3 T11: -0.5969 T22: -3.5940 REMARK 3 T33: 1.8691 T12: -4.1812 REMARK 3 T13: -0.0777 T23: 0.6340 REMARK 3 L TENSOR REMARK 3 L11: 0.4011 L22: 4.4008 REMARK 3 L33: 2.8445 L12: -0.8814 REMARK 3 L13: -0.4413 L23: -1.3572 REMARK 3 S TENSOR REMARK 3 S11: 1.0307 S12: -0.0609 S13: -0.5712 REMARK 3 S21: 1.1617 S22: 0.2176 S23: 1.5208 REMARK 3 S31: 1.9406 S32: -1.2026 S33: 0.5357 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.1067 57.9001 23.7642 REMARK 3 T TENSOR REMARK 3 T11: 1.6499 T22: 0.7123 REMARK 3 T33: 1.4458 T12: 0.1663 REMARK 3 T13: 0.2678 T23: -0.4380 REMARK 3 L TENSOR REMARK 3 L11: 0.6569 L22: 2.7881 REMARK 3 L33: 2.8813 L12: -1.2122 REMARK 3 L13: 0.1428 L23: -1.4214 REMARK 3 S TENSOR REMARK 3 S11: 0.1028 S12: -1.7081 S13: 1.1638 REMARK 3 S21: 0.8755 S22: -1.5397 S23: 0.0729 REMARK 3 S31: 1.0884 S32: 2.1242 S33: 0.1856 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3082 40.7655 27.7145 REMARK 3 T TENSOR REMARK 3 T11: 1.1283 T22: 0.8944 REMARK 3 T33: 1.1670 T12: -0.3513 REMARK 3 T13: 0.0531 T23: -0.0360 REMARK 3 L TENSOR REMARK 3 L11: 0.7554 L22: 4.8685 REMARK 3 L33: 2.7739 L12: -1.0216 REMARK 3 L13: -0.9611 L23: -0.2381 REMARK 3 S TENSOR REMARK 3 S11: 0.3927 S12: -0.7270 S13: 1.3583 REMARK 3 S21: 1.7361 S22: 0.9692 S23: 0.5007 REMARK 3 S31: 0.3268 S32: -0.3538 S33: 0.3722 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1530 71.1641 18.7734 REMARK 3 T TENSOR REMARK 3 T11: 1.8323 T22: 2.9547 REMARK 3 T33: 1.4591 T12: 0.6376 REMARK 3 T13: 0.3317 T23: -1.2301 REMARK 3 L TENSOR REMARK 3 L11: 1.8551 L22: 4.2752 REMARK 3 L33: 1.1570 L12: 0.7454 REMARK 3 L13: 0.6663 L23: 1.0016 REMARK 3 S TENSOR REMARK 3 S11: 0.9091 S12: 0.2921 S13: 0.6351 REMARK 3 S21: 0.7836 S22: -0.5876 S23: -0.8771 REMARK 3 S31: -1.5044 S32: 0.3858 S33: -0.0523 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8YS7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300046244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99984 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2721 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000, POTASSIUM CHLORIDE, REMARK 280 MAGNESIUM CHLORIDE HEXAHYDRATE, SODIUM CHLORIDE, BIS-TRIS, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 66.33050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.29593 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 16.68400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 66.33050 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 38.29593 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 16.68400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 66.33050 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 38.29593 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 16.68400 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 66.33050 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 38.29593 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 16.68400 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 66.33050 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 38.29593 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 16.68400 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 66.33050 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 38.29593 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 16.68400 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 76.59186 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 33.36800 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 76.59186 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 33.36800 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 76.59186 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 33.36800 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 76.59186 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 33.36800 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 76.59186 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 33.36800 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 76.59186 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 33.36800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, I, A 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: K, L, E, D 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 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 C 102 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER REMARK 400 OF THE QUINOXALINE CLASS OF ANTIBIOTICS. REMARK 400 HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE REMARK 400 SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI. REMARK 400 ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE REMARK 400 ACTINOMYCIN FAMILY. REMARK 400 HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES) REMARK 400 REMARK 400 THE ACTINOMYCIN D IS POLYPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 THE ECHINOMYCIN IS CYCLIC DEPSIPEPTIDE, A MEMBER OF ANTIBIOTIC REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ACTINOMYCIN D REMARK 400 CHAIN: D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED REMARK 400 BY THE CHROMOPHORE (PXZ) REMARK 400 REMARK 400 GROUP: 2 REMARK 400 NAME: ECHINOMYCIN REMARK 400 CHAIN: E REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE QUI, 2 COPIES REMARK 400 DESCRIPTION: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. REMARK 400 BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE REMARK 400 C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 REMARK 400 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED REMARK 400 TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. 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 DISTANCE REMARK 500 OG1 THR I 7 O MVA I 11 1.46 REMARK 500 O1' PXZ I 6 N THR I 7 1.72 REMARK 500 OG1 THR I 7 C MVA I 11 1.76 REMARK 500 OG1 THR I 1 O MVA I 5 1.93 REMARK 500 CB THR D 1 C MVA D 5 2.05 REMARK 500 OG1 THR D 7 O MVA D 11 2.11 REMARK 500 CA DSN E 1 C QUI E 101 2.11 REMARK 500 CA DSN E 5 C QUI E 102 2.16 REMARK 500 CA DSN A 5 C QUI A 102 2.17 REMARK 500 OG DSN E 1 O MVA E 8 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YS7 B 1 8 PDB 8YS7 8YS7 1 8 DBREF 8YS7 C 1 7 PDB 8YS7 8YS7 1 7 DBREF 8YS7 K 1 8 PDB 8YS7 8YS7 1 8 DBREF 8YS7 L 1 7 PDB 8YS7 8YS7 1 7 DBREF 8YS7 E 1 8 NOR 8YS7 8YS7 1 8 DBREF 8YS7 I 1 11 NOR 8YS7 8YS7 1 11 DBREF 8YS7 D 1 11 NOR 8YS7 8YS7 1 11 DBREF 8YS7 A 1 8 NOR 8YS7 8YS7 1 8 SEQRES 1 B 8 DA DG DC DC DC DC DG DT SEQRES 1 C 7 DA DC DG DG DG DC DT SEQRES 1 K 8 DA DG DC DC DC DC DG DT SEQRES 1 L 7 DA DC DG DG DG DC DT SEQRES 1 E 8 DSN ALA N2C MVA DSN ALA NCY MVA SEQRES 1 I 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA SEQRES 1 D 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA SEQRES 1 A 8 DSN ALA N2C MVA DSN ALA NCY MVA HET DSN E 1 6 HET N2C E 3 8 HET MVA E 4 8 HET DSN E 5 6 HET NCY E 7 7 HET MVA E 8 8 HET DVA I 2 7 HET SAR I 4 5 HET MVA I 5 8 HET PXZ I 6 22 HET DVA I 8 7 HET SAR I 10 5 HET MVA I 11 8 HET DVA D 2 7 HET SAR D 4 5 HET MVA D 5 8 HET PXZ D 6 22 HET DVA D 8 7 HET SAR D 10 5 HET MVA D 11 8 HET DSN A 1 6 HET N2C A 3 8 HET MVA A 4 8 HET DSN A 5 6 HET NCY A 7 7 HET MVA A 8 8 HET QUI E 101 12 HET QUI E 102 12 HET QUI A 101 12 HET QUI A 102 12 HETNAM DSN D-SERINE HETNAM N2C N,S-DIMETHYLCYSTEINE HETNAM MVA N-METHYLVALINE HETNAM NCY N-METHYLCYSTEINE HETNAM DVA D-VALINE HETNAM SAR SARCOSINE HETNAM PXZ 2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO- HETNAM 2 PXZ PHENOXAZIN-3-ONE HETNAM QUI 2-CARBOXYQUINOXALINE HETSYN PXZ PHENOXAZINE FORMUL 5 DSN 4(C3 H7 N O3) FORMUL 5 N2C 2(C5 H11 N O2 S) FORMUL 5 MVA 8(C6 H13 N O2) FORMUL 5 NCY 2(C4 H9 N O2 S) FORMUL 6 DVA 4(C5 H11 N O2) FORMUL 6 SAR 4(C3 H7 N O2) FORMUL 6 PXZ 2(C16 H12 N2 O6) FORMUL 9 QUI 4(C9 H6 N2 O2) FORMUL 13 HOH *5(H2 O) SSBOND 1 N2C E 3 NCY E 7 1555 1555 2.91 SSBOND 2 N2C A 3 NCY A 7 1555 1555 2.41 LINK C DSN E 1 N ALA E 2 1555 1555 1.33 LINK OG DSN E 1 C MVA E 8 1555 1555 1.40 LINK N DSN E 1 C QUI E 101 1555 1555 1.44 LINK C ALA E 2 N N2C E 3 1555 1555 1.33 LINK C N2C E 3 N MVA E 4 1555 1555 1.31 LINK CB N2C E 3 SG NCY E 7 1555 1555 1.77 LINK C MVA E 4 OG DSN E 5 1555 1555 1.43 LINK C DSN E 5 N ALA E 6 1555 1555 1.35 LINK N DSN E 5 C QUI E 102 1555 1555 1.45 LINK C ALA E 6 N NCY E 7 1555 1555 1.33 LINK C NCY E 7 N MVA E 8 1555 1555 1.32 LINK C THR I 1 N DVA I 2 1555 1555 1.34 LINK OG1 THR I 1 C MVA I 5 1555 1555 1.47 LINK N THR I 1 C0 PXZ I 6 1555 1555 1.57 LINK C DVA I 2 N PRO I 3 1555 1555 1.36 LINK C PRO I 3 N SAR I 4 1555 1555 1.38 LINK C SAR I 4 N MVA I 5 1555 1555 1.26 LINK C0' PXZ I 6 N THR I 7 1555 1555 1.22 LINK C THR I 7 N DVA I 8 1555 1555 1.34 LINK C DVA I 8 N PRO I 9 1555 1555 1.35 LINK C PRO I 9 N SAR I 10 1555 1555 1.38 LINK C SAR I 10 N MVA I 11 1555 1555 1.34 LINK C THR D 1 N DVA D 2 1555 1555 1.31 LINK OG1 THR D 1 C MVA D 5 1555 1555 1.34 LINK N THR D 1 C0 PXZ D 6 1555 1555 1.35 LINK C DVA D 2 N PRO D 3 1555 1555 1.35 LINK C PRO D 3 N SAR D 4 1555 1555 1.36 LINK C SAR D 4 N MVA D 5 1555 1555 1.43 LINK C0' PXZ D 6 N THR D 7 1555 1555 1.38 LINK C THR D 7 N DVA D 8 1555 1555 1.37 LINK OG1 THR D 7 C MVA D 11 1555 1555 1.29 LINK C DVA D 8 N PRO D 9 1555 1555 1.36 LINK C PRO D 9 N SAR D 10 1555 1555 1.39 LINK C SAR D 10 N MVA D 11 1555 1555 1.34 LINK C DSN A 1 N ALA A 2 1555 1555 1.32 LINK OG DSN A 1 C MVA A 8 1555 1555 1.46 LINK N DSN A 1 C QUI A 101 1555 1555 1.42 LINK C ALA A 2 N N2C A 3 1555 1555 1.34 LINK C N2C A 3 N MVA A 4 1555 1555 1.32 LINK CB N2C A 3 SG NCY A 7 1555 1555 1.82 LINK C MVA A 4 OG DSN A 5 1555 1555 1.40 LINK C DSN A 5 N ALA A 6 1555 1555 1.25 LINK N DSN A 5 C QUI A 102 1555 1555 1.43 LINK C ALA A 6 N NCY A 7 1555 1555 1.37 LINK C NCY A 7 N MVA A 8 1555 1555 1.32 CISPEP 1 DVA I 2 PRO I 3 0 19.05 CISPEP 2 PRO I 3 SAR I 4 0 -15.86 CISPEP 3 DVA I 8 PRO I 9 0 8.31 CISPEP 4 PRO I 9 SAR I 10 0 0.31 CISPEP 5 DVA D 2 PRO D 3 0 19.76 CISPEP 6 PRO D 3 SAR D 4 0 -16.26 CISPEP 7 DVA D 8 PRO D 9 0 13.59 CISPEP 8 PRO D 9 SAR D 10 0 -18.72 CRYST1 132.661 132.661 50.052 90.00 90.00 120.00 H 3 2 36 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 0.007538 0.004352 0.000000 0.00000 SCALE2 0.000000 0.008704 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019979 0.00000 CONECT 617 618 917 CONECT 618 617 619 621 CONECT 619 618 620 623 CONECT 620 619 CONECT 621 618 622 CONECT 622 621 668 CONECT 623 619 CONECT 625 628 CONECT 628 625 629 633 CONECT 629 628 630 634 CONECT 630 629 631 658 CONECT 631 630 632 658 CONECT 632 631 CONECT 633 628 CONECT 634 629 635 636 CONECT 635 634 CONECT 636 634 637 638 CONECT 637 636 CONECT 638 636 639 642 CONECT 639 638 640 641 CONECT 640 639 CONECT 641 639 CONECT 642 638 643 649 CONECT 643 642 CONECT 644 645 929 CONECT 645 644 646 648 CONECT 646 645 647 650 CONECT 647 646 CONECT 648 645 649 CONECT 649 642 648 CONECT 650 646 CONECT 652 655 CONECT 655 652 656 659 CONECT 656 655 657 660 CONECT 657 656 658 CONECT 658 630 631 657 CONECT 659 655 CONECT 660 656 661 662 CONECT 661 660 CONECT 662 660 663 664 CONECT 663 662 CONECT 664 662 665 668 CONECT 665 664 666 667 CONECT 666 665 CONECT 667 665 CONECT 668 622 664 669 CONECT 669 668 CONECT 671 706 CONECT 673 678 CONECT 676 703 CONECT 678 673 679 CONECT 679 678 680 683 CONECT 680 679 681 682 CONECT 681 680 CONECT 682 680 CONECT 683 679 684 685 CONECT 684 683 CONECT 685 683 CONECT 687 692 CONECT 692 687 693 696 CONECT 693 692 694 CONECT 694 693 695 697 CONECT 695 694 CONECT 696 692 CONECT 697 694 698 699 CONECT 698 697 CONECT 699 697 700 703 CONECT 700 699 701 702 CONECT 701 700 CONECT 702 700 CONECT 703 676 699 704 CONECT 704 703 CONECT 705 706 708 721 CONECT 706 671 705 707 CONECT 707 706 CONECT 708 705 709 710 CONECT 709 708 CONECT 710 708 711 712 CONECT 711 710 CONECT 712 710 722 725 CONECT 713 722 723 CONECT 714 715 723 726 CONECT 715 714 716 CONECT 716 715 717 CONECT 717 716 718 724 CONECT 718 717 719 727 CONECT 719 718 CONECT 720 721 724 CONECT 721 705 720 722 CONECT 722 712 713 721 CONECT 723 713 714 724 CONECT 724 717 720 723 CONECT 725 712 CONECT 726 714 CONECT 727 718 CONECT 729 734 CONECT 734 729 735 CONECT 735 734 736 739 CONECT 736 735 737 738 CONECT 737 736 CONECT 738 736 CONECT 739 735 740 741 CONECT 740 739 CONECT 741 739 CONECT 743 748 CONECT 748 743 749 752 CONECT 749 748 750 CONECT 750 749 751 753 CONECT 751 750 CONECT 752 748 CONECT 753 750 754 755 CONECT 754 753 CONECT 755 753 756 759 CONECT 756 755 757 758 CONECT 757 756 CONECT 758 756 CONECT 759 755 760 CONECT 760 759 CONECT 762 797 CONECT 764 769 CONECT 767 794 CONECT 769 764 770 CONECT 770 769 771 774 CONECT 771 770 772 773 CONECT 772 771 CONECT 773 771 CONECT 774 770 775 776 CONECT 775 774 CONECT 776 774 CONECT 778 783 CONECT 783 778 784 787 CONECT 784 783 785 CONECT 785 784 786 788 CONECT 786 785 CONECT 787 783 CONECT 788 785 789 790 CONECT 789 788 CONECT 790 788 791 794 CONECT 791 790 792 793 CONECT 792 791 CONECT 793 791 CONECT 794 767 790 795 CONECT 795 794 CONECT 796 797 799 812 CONECT 797 762 796 798 CONECT 798 797 CONECT 799 796 800 801 CONECT 800 799 CONECT 801 799 802 803 CONECT 802 801 CONECT 803 801 813 816 CONECT 804 813 814 CONECT 805 806 814 817 CONECT 806 805 807 CONECT 807 806 808 CONECT 808 807 809 815 CONECT 809 808 810 818 CONECT 810 809 CONECT 811 812 815 CONECT 812 796 811 813 CONECT 813 803 804 812 CONECT 814 804 805 815 CONECT 815 808 811 814 CONECT 816 803 CONECT 817 805 CONECT 818 809 CONECT 820 825 CONECT 823 850 CONECT 825 820 826 CONECT 826 825 827 830 CONECT 827 826 828 829 CONECT 828 827 CONECT 829 827 CONECT 830 826 831 832 CONECT 831 830 CONECT 832 830 CONECT 834 839 CONECT 839 834 840 843 CONECT 840 839 841 CONECT 841 840 842 844 CONECT 842 841 CONECT 843 839 CONECT 844 841 845 846 CONECT 845 844 CONECT 846 844 847 850 CONECT 847 846 848 849 CONECT 848 847 CONECT 849 847 CONECT 850 823 846 851 CONECT 851 850 CONECT 853 854 941 CONECT 854 853 855 857 CONECT 855 854 856 859 CONECT 856 855 CONECT 857 854 858 CONECT 858 857 904 CONECT 859 855 CONECT 861 864 CONECT 864 861 865 869 CONECT 865 864 866 870 CONECT 866 865 867 894 CONECT 867 866 868 894 CONECT 868 867 CONECT 869 864 CONECT 870 865 871 872 CONECT 871 870 CONECT 872 870 873 874 CONECT 873 872 CONECT 874 872 875 878 CONECT 875 874 876 877 CONECT 876 875 CONECT 877 875 CONECT 878 874 879 885 CONECT 879 878 CONECT 880 881 953 CONECT 881 880 882 884 CONECT 882 881 883 886 CONECT 883 882 CONECT 884 881 885 CONECT 885 878 884 CONECT 886 882 CONECT 888 891 CONECT 891 888 892 895 CONECT 892 891 893 896 CONECT 893 892 894 CONECT 894 866 867 893 CONECT 895 891 CONECT 896 892 897 898 CONECT 897 896 CONECT 898 896 899 900 CONECT 899 898 CONECT 900 898 901 904 CONECT 901 900 902 903 CONECT 902 901 CONECT 903 901 CONECT 904 858 900 905 CONECT 905 904 CONECT 907 908 915 CONECT 908 907 909 917 CONECT 909 908 910 CONECT 910 909 916 CONECT 911 912 916 CONECT 912 911 913 CONECT 913 912 914 CONECT 914 913 915 CONECT 915 907 914 916 CONECT 916 910 911 915 CONECT 917 617 908 918 CONECT 918 917 CONECT 919 920 927 CONECT 920 919 921 929 CONECT 921 920 922 CONECT 922 921 928 CONECT 923 924 928 CONECT 924 923 925 CONECT 925 924 926 CONECT 926 925 927 CONECT 927 919 926 928 CONECT 928 922 923 927 CONECT 929 644 920 930 CONECT 930 929 CONECT 931 932 939 CONECT 932 931 933 941 CONECT 933 932 934 CONECT 934 933 940 CONECT 935 936 940 CONECT 936 935 937 CONECT 937 936 938 CONECT 938 937 939 CONECT 939 931 938 940 CONECT 940 934 935 939 CONECT 941 853 932 942 CONECT 942 941 CONECT 943 944 951 CONECT 944 943 945 953 CONECT 945 944 946 CONECT 946 945 952 CONECT 947 948 952 CONECT 948 947 949 CONECT 949 948 950 CONECT 950 949 951 CONECT 951 943 950 952 CONECT 952 946 947 951 CONECT 953 880 944 954 CONECT 954 953 MASTER 431 0 30 0 0 0 0 6 951 8 285 8 END