HEADER DNA/ANTIBIOTIC 15-MAR-22 7X9F TITLE CRYSTAL STRUCTURE OF ACTINOMYCIN D-ECHINOMYCIN-D(AGCGCGT/ACGCGCT) TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-3'); COMPND 3 CHAIN: F, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3'); COMPND 7 CHAIN: O, B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA; COMPND 11 CHAIN: G, C; COMPND 12 MOL_ID: 4; COMPND 13 MOLECULE: THR-DVA-PRO-SAR-MVA-PXF-THR-DVA-PRO-SAR-MVA; COMPND 14 CHAIN: H, A 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 G:C CANONICAL DNA, SINGLE-STRAND DNA TWIST, FOUR-WAY JUNCTION, KEYWDS 2 ECHINOMYCIN, ACTINOMYCIN D, DNA, DNA-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.H.KAO,R.B.SATANGE,M.H.HOU REVDAT 3 29-NOV-23 7X9F 1 REMARK REVDAT 2 15-NOV-23 7X9F 1 LINK ATOM REVDAT 1 14-DEC-22 7X9F 0 JRNL AUTH R.SATANGE,S.H.KAO,C.M.CHIEN,S.H.CHOU,C.C.LIN,S.NEIDLE, JRNL AUTH 2 M.H.HOU JRNL TITL STAGGERED INTERCALATION OF DNA DUPLEXES WITH BASE-PAIR JRNL TITL 2 MODULATION BY TWO DISTINCT DRUG MOLECULES INDUCES ASYMMETRIC JRNL TITL 3 BACKBONE TWISTING AND STRUCTURE POLYMORPHISM. JRNL REF NUCLEIC ACIDS RES. V. 50 8867 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35871296 JRNL DOI 10.1093/NAR/GKAC629 REMARK 2 REMARK 2 RESOLUTION. 2.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 4174 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 419 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 27.8000 - 4.2657 1.00 1329 148 0.1909 0.2403 REMARK 3 2 4.2657 - 3.3878 1.00 1228 136 0.2251 0.2729 REMARK 3 3 3.3878 - 2.9601 0.98 1198 135 0.2526 0.3272 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.81 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'F' AND (RESID -5 THROUGH 1 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.0213 8.9902 10.0574 REMARK 3 T TENSOR REMARK 3 T11: 1.2473 T22: 1.0313 REMARK 3 T33: 0.5845 T12: 0.1643 REMARK 3 T13: -0.1808 T23: 0.0625 REMARK 3 L TENSOR REMARK 3 L11: 9.1551 L22: 6.8528 REMARK 3 L33: 2.0327 L12: -4.1044 REMARK 3 L13: 8.2569 L23: -7.7528 REMARK 3 S TENSOR REMARK 3 S11: 0.1022 S12: -1.2650 S13: -0.2649 REMARK 3 S21: 0.6990 S22: 1.2712 S23: 2.2963 REMARK 3 S31: -0.3390 S32: -0.2271 S33: -0.0786 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'O' AND (RESID -5 THROUGH 1 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.8280 1.6210 8.9744 REMARK 3 T TENSOR REMARK 3 T11: 0.7675 T22: 1.0559 REMARK 3 T33: 0.4708 T12: -0.0136 REMARK 3 T13: -0.1122 T23: 0.1052 REMARK 3 L TENSOR REMARK 3 L11: 6.1945 L22: 4.5529 REMARK 3 L33: 6.1374 L12: 4.0309 REMARK 3 L13: 4.0277 L23: 5.2054 REMARK 3 S TENSOR REMARK 3 S11: 0.1559 S12: -0.1680 S13: -0.6239 REMARK 3 S21: 0.6572 S22: 0.7285 S23: -0.1607 REMARK 3 S31: -0.4460 S32: 0.7135 S33: -0.9759 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'G' AND (RESID 2 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.0398 9.9914 17.3452 REMARK 3 T TENSOR REMARK 3 T11: 1.1667 T22: 0.8205 REMARK 3 T33: 0.3986 T12: 0.0856 REMARK 3 T13: 0.0225 T23: -0.2022 REMARK 3 L TENSOR REMARK 3 L11: 7.5380 L22: 2.7880 REMARK 3 L33: 5.4989 L12: 2.0922 REMARK 3 L13: -3.0483 L23: -3.9125 REMARK 3 S TENSOR REMARK 3 S11: -0.1040 S12: 0.4944 S13: 0.1172 REMARK 3 S21: 1.0414 S22: 1.3255 S23: -0.6074 REMARK 3 S31: -0.5986 S32: 1.9312 S33: 0.2143 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.8614 9.8034 0.3886 REMARK 3 T TENSOR REMARK 3 T11: 0.8005 T22: 0.8244 REMARK 3 T33: 0.6767 T12: -0.3127 REMARK 3 T13: -0.2289 T23: 0.3674 REMARK 3 L TENSOR REMARK 3 L11: 8.5349 L22: 7.3876 REMARK 3 L33: 9.4605 L12: 1.1051 REMARK 3 L13: -7.4667 L23: 3.6367 REMARK 3 S TENSOR REMARK 3 S11: 0.5597 S12: 0.6327 S13: 0.8848 REMARK 3 S21: 0.9443 S22: -1.2653 S23: -0.7879 REMARK 3 S31: -0.1494 S32: -0.2010 S33: -0.4303 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID -5 THROUGH 1 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.3892 -11.3913 15.9344 REMARK 3 T TENSOR REMARK 3 T11: 0.7625 T22: 0.8042 REMARK 3 T33: 0.9890 T12: -0.0095 REMARK 3 T13: 0.2030 T23: 0.0642 REMARK 3 L TENSOR REMARK 3 L11: 1.9157 L22: 4.5051 REMARK 3 L33: 2.3329 L12: 2.7405 REMARK 3 L13: 0.6333 L23: -0.3041 REMARK 3 S TENSOR REMARK 3 S11: 1.6788 S12: 1.4306 S13: 2.2778 REMARK 3 S21: 0.8801 S22: 0.1444 S23: 2.7886 REMARK 3 S31: -1.2797 S32: -0.9955 S33: -1.7743 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID -5 THROUGH 1 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.0089 -18.8433 20.0233 REMARK 3 T TENSOR REMARK 3 T11: 0.7903 T22: 1.0408 REMARK 3 T33: 0.6491 T12: -0.0439 REMARK 3 T13: 0.1053 T23: 0.1209 REMARK 3 L TENSOR REMARK 3 L11: 7.3465 L22: 7.1504 REMARK 3 L33: 9.7389 L12: 4.7875 REMARK 3 L13: -3.9708 L23: -6.1840 REMARK 3 S TENSOR REMARK 3 S11: -0.6925 S12: -0.0888 S13: -0.9437 REMARK 3 S21: 0.4756 S22: -1.0740 S23: -0.4021 REMARK 3 S31: 0.4223 S32: -0.3392 S33: 0.8194 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.8268 -10.0032 16.9438 REMARK 3 T TENSOR REMARK 3 T11: 0.7368 T22: 0.8987 REMARK 3 T33: 0.3861 T12: -0.6950 REMARK 3 T13: 0.2334 T23: 0.4068 REMARK 3 L TENSOR REMARK 3 L11: 7.0777 L22: 4.1610 REMARK 3 L33: 0.5244 L12: 0.2389 REMARK 3 L13: 1.8687 L23: -0.2902 REMARK 3 S TENSOR REMARK 3 S11: 0.5711 S12: -1.4064 S13: 0.5393 REMARK 3 S21: 1.6441 S22: -0.5545 S23: 0.6722 REMARK 3 S31: 0.2230 S32: -0.2650 S33: -0.1166 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8640 -14.5939 25.3349 REMARK 3 T TENSOR REMARK 3 T11: 0.9969 T22: 0.7296 REMARK 3 T33: 0.8784 T12: -0.0423 REMARK 3 T13: 0.4663 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 4.0001 L22: 8.1139 REMARK 3 L33: 8.0605 L12: -1.5588 REMARK 3 L13: 5.6341 L23: -3.1549 REMARK 3 S TENSOR REMARK 3 S11: -0.3472 S12: -2.3339 S13: -0.6027 REMARK 3 S21: 0.7863 S22: -0.0943 S23: 0.4173 REMARK 3 S31: -0.6165 S32: -0.4074 S33: 0.9232 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 7X9F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028366. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4205 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.960 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.75000 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 1.9_1692 REMARK 200 STARTING MODEL: 7DQ0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM MES BUFFER (PH 6.0), 5 MM REMARK 280 SPERMINE TETRAHYDROCHLORIDE, 2% PEG200, 3 MM MANGANESE CHLORIDE, REMARK 280 0.25 MM OLIGONUCLEOTIDES, 0.25 MM ECHINOMYCIN, 0.125 MM REMARK 280 ACTINOMYCIN D, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 2 2 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 -Y,X,Z+1/2 REMARK 290 4555 Y,-X,Z+1/2 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z+1/2 REMARK 290 8555 -Y,-X,-Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.77550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.77550 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 23.77550 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 23.77550 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: F, O, G, H 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: D, B, A, C 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 MN MN O 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 101 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 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: H, A 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: G, C REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER 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 N7 DG O 0 MN MN O 101 1.62 REMARK 500 OG1 THR H 1 C MVA H 5 1.80 REMARK 500 OG1 THR H 7 C MVA H 11 1.81 REMARK 500 OG1 THR A 1 C MVA A 5 1.81 REMARK 500 OG1 THR A 7 C MVA A 11 1.84 REMARK 500 N DSN G 5 C QUI F 101 1.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 QUI F 101 DBREF 7X9F F -5 1 PDB 7X9F 7X9F -5 1 DBREF 7X9F O -5 1 PDB 7X9F 7X9F -5 1 DBREF 7X9F G 1 8 PDB 7X9F 7X9F 1 8 DBREF 7X9F H 1 11 PDB 7X9F 7X9F 1 11 DBREF 7X9F D -5 1 PDB 7X9F 7X9F -5 1 DBREF 7X9F B -5 1 PDB 7X9F 7X9F -5 1 DBREF 7X9F A 1 11 PDB 7X9F 7X9F 1 11 DBREF 7X9F C 1 8 PDB 7X9F 7X9F 1 8 SEQRES 1 F 7 DA DC DG DC DG DC DT SEQRES 1 O 7 DA DG DC DG DC DG DT SEQRES 1 G 8 DSN ALA N2C MVA DSN ALA NCY MVA SEQRES 1 H 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA SEQRES 1 D 7 DA DC DG DC DG DC DT SEQRES 1 B 7 DA DG DC DG DC DG DT SEQRES 1 A 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA SEQRES 1 C 8 DSN ALA N2C MVA DSN ALA NCY MVA HET DSN G 1 6 HET N2C G 3 8 HET MVA G 4 8 HET DSN G 5 6 HET NCY G 7 7 HET MVA G 8 8 HET DVA H 2 7 HET SAR H 4 5 HET MVA H 5 8 HET PXZ H 6 22 HET DVA H 8 7 HET SAR H 10 5 HET MVA H 11 8 HET DVA A 2 7 HET SAR A 4 5 HET MVA A 5 8 HET PXZ A 6 22 HET DVA A 8 7 HET SAR A 10 5 HET MVA A 11 8 HET DSN C 1 6 HET N2C C 3 8 HET MVA C 4 8 HET DSN C 5 6 HET NCY C 7 7 HET MVA C 8 8 HET QUI F 101 12 HET MN O 101 1 HET QUI G 101 12 HET QUI C 101 12 HET QUI C 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 HETNAM MN MANGANESE (II) ION HETSYN PXZ PHENOXAZINE FORMUL 3 DSN 4(C3 H7 N O3) FORMUL 3 N2C 2(C5 H11 N O2 S) FORMUL 3 MVA 8(C6 H13 N O2) FORMUL 3 NCY 2(C4 H9 N O2 S) FORMUL 4 DVA 4(C5 H11 N O2) FORMUL 4 SAR 4(C3 H7 N O2) FORMUL 4 PXZ 2(C16 H12 N2 O4) FORMUL 9 QUI 4(C9 H6 N2 O2) FORMUL 10 MN MN 2+ FORMUL 14 HOH *7(H2 O) LINK C DSN G 1 N ALA G 2 1555 1555 1.32 LINK OG DSN G 1 C MVA G 8 1555 1555 1.30 LINK N DSN G 1 C QUI G 101 1555 1555 1.31 LINK C ALA G 2 N N2C G 3 1555 1555 1.33 LINK C N2C G 3 N MVA G 4 1555 1555 1.33 LINK CB N2C G 3 SG NCY G 7 1555 1555 1.82 LINK C MVA G 4 OG DSN G 5 1555 1555 1.37 LINK C DSN G 5 N ALA G 6 1555 1555 1.32 LINK C ALA G 6 N NCY G 7 1555 1555 1.33 LINK C NCY G 7 N MVA G 8 1555 1555 1.44 LINK C THR H 1 N DVA H 2 1555 1555 1.33 LINK N THR H 1 C0 PXZ H 6 1555 1555 1.52 LINK C DVA H 2 N PRO H 3 1555 1555 1.35 LINK C PRO H 3 N SAR H 4 1555 1555 1.33 LINK C SAR H 4 N MVA H 5 1555 1555 1.33 LINK C0' PXZ H 6 N THR H 7 1555 1555 1.54 LINK C THR H 7 N DVA H 8 1555 1555 1.33 LINK C DVA H 8 N PRO H 9 1555 1555 1.34 LINK C PRO H 9 N SAR H 10 1555 1555 1.33 LINK C SAR H 10 N MVA H 11 1555 1555 1.34 LINK C THR A 1 N DVA A 2 1555 1555 1.33 LINK N THR A 1 C0 PXZ A 6 1555 1555 1.51 LINK C DVA A 2 N PRO A 3 1555 1555 1.34 LINK C PRO A 3 N SAR A 4 1555 1555 1.33 LINK C SAR A 4 N MVA A 5 1555 1555 1.34 LINK C0' PXZ A 6 N THR A 7 1555 1555 1.59 LINK C THR A 7 N DVA A 8 1555 1555 1.33 LINK C DVA A 8 N PRO A 9 1555 1555 1.34 LINK C PRO A 9 N SAR A 10 1555 1555 1.33 LINK C SAR A 10 N MVA A 11 1555 1555 1.33 LINK C DSN C 1 N ALA C 2 1555 1555 1.29 LINK OG DSN C 1 C MVA C 8 1555 1555 1.44 LINK N DSN C 1 C QUI C 102 1555 1555 1.66 LINK C ALA C 2 N N2C C 3 1555 1555 1.33 LINK C N2C C 3 N MVA C 4 1555 1555 1.34 LINK CB N2C C 3 SG NCY C 7 1555 1555 1.83 LINK C MVA C 4 OG DSN C 5 1555 1555 1.38 LINK C DSN C 5 N ALA C 6 1555 1555 1.33 LINK N DSN C 5 C QUI C 101 1555 1555 1.59 LINK C ALA C 6 N NCY C 7 1555 1555 1.33 LINK C NCY C 7 N MVA C 8 1555 1555 1.32 CISPEP 1 DVA H 2 PRO H 3 0 5.95 CISPEP 2 PRO H 3 SAR H 4 0 -1.03 CISPEP 3 DVA H 8 PRO H 9 0 7.08 CISPEP 4 PRO H 9 SAR H 10 0 -0.48 CISPEP 5 DVA A 2 PRO A 3 0 3.82 CISPEP 6 PRO A 3 SAR A 4 0 -5.27 CISPEP 7 DVA A 8 PRO A 9 0 9.03 CISPEP 8 PRO A 9 SAR A 10 0 -1.78 CRYST1 87.917 87.917 47.551 90.00 90.00 90.00 P 42 2 2 16 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 0.011374 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011374 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021030 0.00000