HEADER ANTIBIOTIC/DNA 22-DEC-20 7DQ8 TITLE CRYSTAL STRUCTURE OF ACTINOMYCIN D-ECHINOMYCIN-D(ACGCGCT/AGCTCGT) TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*GP*CP*TP*CP*GP*T)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ECHINOMYCIN; COMPND 11 CHAIN: D; COMPND 12 MOL_ID: 4; COMPND 13 MOLECULE: ACTINOMYCIN D; COMPND 14 CHAIN: C 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 SP.; SOURCE 11 ORGANISM_TAXID: 1931; SOURCE 12 MOL_ID: 4; SOURCE 13 ORGANISM_SCIENTIFIC: STREPTOMYCES SP.; SOURCE 14 ORGANISM_TAXID: 1931 KEYWDS DRUG-DNA COMPLEX, DNA MISMATCH, DNA UNWINDING, DNA DEFORMATION, DNA, KEYWDS 2 ANTIBIOTIC-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.B.SATANGE,M.H.HOU REVDAT 5 10-JUL-24 7DQ8 1 COMPND FORMUL LINK REVDAT 4 29-NOV-23 7DQ8 1 REMARK REVDAT 3 15-NOV-23 7DQ8 1 LINK ATOM REVDAT 2 29-MAR-23 7DQ8 1 JRNL REVDAT 1 29-DEC-21 7DQ8 0 JRNL AUTH R.SATANGE,C.C.CHANG,L.Y.LI,S.H.LIN,S.NEIDLE,M.H.HOU JRNL TITL SYNERGISTIC BINDING OF ACTINOMYCIN D AND ECHINOMYCIN TO DNA JRNL TITL 2 MISMATCH SITES AND THEIR COMBINED ANTI-TUMOUR EFFECTS. JRNL REF NUCLEIC ACIDS RES. 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36919604 JRNL DOI 10.1093/NAR/GKAD156 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 2741 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.268 REMARK 3 R VALUE (WORKING SET) : 0.267 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 276 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 24.9700 - 2.4900 0.97 1252 141 0.2450 0.2599 REMARK 3 2 2.4900 - 2.4035 1.00 1213 135 0.3361 0.3478 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.57 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 : 0.027 489 REMARK 3 ANGLE : 2.105 713 REMARK 3 CHIRALITY : 0.109 74 REMARK 3 PLANARITY : 0.014 40 REMARK 3 DIHEDRAL : 40.714 170 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.9498 6.6738 5.3267 REMARK 3 T TENSOR REMARK 3 T11: 0.2602 T22: 1.0323 REMARK 3 T33: 0.3954 T12: -0.0986 REMARK 3 T13: 0.0473 T23: -0.1089 REMARK 3 L TENSOR REMARK 3 L11: 3.0559 L22: 3.2918 REMARK 3 L33: 5.1886 L12: 0.7096 REMARK 3 L13: -2.5523 L23: -2.3786 REMARK 3 S TENSOR REMARK 3 S11: 0.4564 S12: -0.6152 S13: -0.2196 REMARK 3 S21: 0.4067 S22: 0.2896 S23: -0.2583 REMARK 3 S31: -2.5130 S32: 2.3074 S33: -0.5108 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.9494 -1.5772 3.9786 REMARK 3 T TENSOR REMARK 3 T11: 0.7943 T22: 0.4970 REMARK 3 T33: 0.4000 T12: 0.0410 REMARK 3 T13: -0.0371 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.5613 L22: 2.7964 REMARK 3 L33: 8.5219 L12: -0.3653 REMARK 3 L13: 0.0032 L23: -2.9260 REMARK 3 S TENSOR REMARK 3 S11: 0.7040 S12: 0.4488 S13: -0.7976 REMARK 3 S21: -0.0305 S22: 0.0738 S23: 0.6989 REMARK 3 S31: 0.7198 S32: 1.7110 S33: -0.6895 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7130 1.9838 14.0601 REMARK 3 T TENSOR REMARK 3 T11: 0.2631 T22: 0.5341 REMARK 3 T33: 0.5209 T12: -0.0349 REMARK 3 T13: 0.0217 T23: 0.1635 REMARK 3 L TENSOR REMARK 3 L11: 4.7837 L22: 3.1323 REMARK 3 L33: 6.9165 L12: 2.2411 REMARK 3 L13: -0.6408 L23: -1.8928 REMARK 3 S TENSOR REMARK 3 S11: 1.3235 S12: -0.6071 S13: 1.2140 REMARK 3 S21: 1.2802 S22: -1.5554 S23: -1.1309 REMARK 3 S31: 0.4023 S32: 2.1890 S33: 0.1776 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 2 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.525 0.349 -4.904 REMARK 3 T TENSOR REMARK 3 T11: 0.2515 T22: 0.6268 REMARK 3 T33: 0.5293 T12: 0.2929 REMARK 3 T13: 0.0528 T23: -0.0412 REMARK 3 L TENSOR REMARK 3 L11: 4.0247 L22: 3.2629 REMARK 3 L33: 2.6892 L12: 3.4418 REMARK 3 L13: 0.4788 L23: -0.4661 REMARK 3 S TENSOR REMARK 3 S11: 0.1746 S12: 0.2955 S13: -0.5088 REMARK 3 S21: -0.5167 S22: 0.4250 S23: -1.6683 REMARK 3 S31: 0.3065 S32: 0.9652 S33: 0.0092 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 7DQ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019946. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-18 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 : 2811 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.24100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 0.72600 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 1.10.1_2155 REMARK 200 STARTING MODEL: 7DQ0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 MM SSDNA, 0.2 MM ECHINOMYCIN, 0.1 REMARK 280 MM ACTINOMYCIN D, 2.5 MM SODIUM CACODYLATE (PH 7.0), 1 MM REMARK 280 MAGNESIUM CHLORIDE, 2.5 MM SPERMINE TETRAHYDROCHLORIDE, 1 MM REMARK 280 ZINC CHLORIDE, 1% PEG 200, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z 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 68.96500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 14.86900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 14.86900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.48250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 14.86900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 14.86900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 103.44750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 14.86900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 14.86900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.48250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 14.86900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 14.86900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 103.44750 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 0.00000 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 68.96500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, 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 MG MG B 101 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND 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 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: C 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: D 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 C 7 O MVA C 11 1.94 REMARK 500 OP2 DT A 4 O HOH A 201 2.03 REMARK 500 CA DSN D 5 C QUI D 102 2.09 REMARK 500 OG1 THR C 1 CA MVA C 5 2.13 REMARK 500 OG1 THR C 1 O MVA C 5 2.15 REMARK 500 OG DSN D 1 O MVA D 8 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 MG MG A 102 O HOH A 201 7555 1.45 REMARK 500 OP2 DT A 4 MG MG A 102 7555 1.59 REMARK 500 MG MG A 102 O HOH A 202 7555 1.63 REMARK 500 O HOH A 205 O HOH A 209 5545 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC B 2 O3' DG B 3 P -0.077 REMARK 500 REMARK 500 REMARK: NULL 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 DG B 5 O5' - P - OP2 ANGL. DEV. = -9.5 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 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 203 O REMARK 620 2 HOH A 205 O 90.4 REMARK 620 3 HOH A 206 O 73.8 142.7 REMARK 620 4 HOH A 209 O 79.7 65.5 78.4 REMARK 620 N 1 2 3 DBREF 7DQ8 A 1 7 PDB 7DQ8 7DQ8 1 7 DBREF 7DQ8 B 1 7 PDB 7DQ8 7DQ8 1 7 DBREF 7DQ8 D 1 8 PDB 7DQ8 7DQ8 1 8 DBREF 7DQ8 C 1 11 PDB 7DQ8 7DQ8 1 11 SEQRES 1 A 7 DA DG DC DT DC DG DT SEQRES 1 B 7 DA DC DG DC DG DC DT SEQRES 1 D 8 DSN ALA N2C MVA DSN ALA NCY MVA SEQRES 1 C 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA HET DSN D 1 6 HET N2C D 3 8 HET MVA D 4 8 HET DSN D 5 6 HET NCY D 7 7 HET MVA D 8 8 HET DVA C 2 7 HET SAR C 4 5 HET MVA C 5 8 HET PXZ C 6 22 HET DVA C 8 7 HET SAR C 10 5 HET MVA C 11 8 HET MG A 101 1 HET MG A 102 1 HET MG B 101 1 HET MG B 102 1 HET QUI D 101 12 HET QUI D 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 MG MAGNESIUM ION HETNAM QUI 2-CARBOXYQUINOXALINE HETSYN PXZ PHENOXAZINE FORMUL 3 DSN 2(C3 H7 N O3) FORMUL 3 N2C C5 H11 N O2 S FORMUL 3 MVA 4(C6 H13 N O2) FORMUL 3 NCY C4 H9 N O2 S FORMUL 4 DVA 2(C5 H11 N O2) FORMUL 4 SAR 2(C3 H7 N O2) FORMUL 4 PXZ C16 H12 N2 O6 FORMUL 5 MG 4(MG 2+) FORMUL 9 QUI 2(C9 H6 N2 O2) FORMUL 11 HOH *12(H2 O) SSBOND 1 N2C D 3 NCY D 7 1555 1555 2.61 LINK C DSN D 1 N ALA D 2 1555 1555 1.31 LINK OG DSN D 1 C MVA D 8 1555 1555 1.38 LINK N DSN D 1 C QUI D 101 1555 1555 1.42 LINK C ALA D 2 N N2C D 3 1555 1555 1.34 LINK C N2C D 3 N MVA D 4 1555 1555 1.34 LINK CB N2C D 3 SG NCY D 7 1555 1555 1.77 LINK C MVA D 4 OG DSN D 5 1555 1555 1.38 LINK C DSN D 5 N ALA D 6 1555 1555 1.34 LINK N DSN D 5 C QUI D 102 1555 1555 1.42 LINK C ALA D 6 N NCY D 7 1555 1555 1.32 LINK C NCY D 7 N MVA D 8 1555 1555 1.33 LINK C THR C 1 N DVA C 2 1555 1555 1.32 LINK OG1 THR C 1 C MVA C 5 1555 1555 1.38 LINK N THR C 1 C0 PXZ C 6 1555 1555 1.42 LINK C DVA C 2 N PRO C 3 1555 1555 1.34 LINK C PRO C 3 N SAR C 4 1555 1555 1.33 LINK C SAR C 4 N MVA C 5 1555 1555 1.34 LINK C0' PXZ C 6 N THR C 7 1555 1555 1.43 LINK C THR C 7 N DVA C 8 1555 1555 1.32 LINK OG1 THR C 7 C MVA C 11 1555 1555 1.37 LINK C DVA C 8 N PRO C 9 1555 1555 1.34 LINK C PRO C 9 N SAR C 10 1555 1555 1.33 LINK C SAR C 10 N MVA C 11 1555 1555 1.33 LINK MG MG A 101 O HOH A 203 1555 1555 1.99 LINK MG MG A 101 O HOH A 205 1555 1555 1.73 LINK MG MG A 101 O HOH A 206 1555 1555 1.77 LINK MG MG A 101 O HOH A 209 1555 5545 2.17 LINK MG MG A 102 O HOH A 207 1555 7555 2.22 CISPEP 1 DVA C 2 PRO C 3 0 10.43 CISPEP 2 PRO C 3 SAR C 4 0 -3.88 CISPEP 3 DVA C 8 PRO C 9 0 10.45 CISPEP 4 PRO C 9 SAR C 10 0 -4.53 CRYST1 29.738 29.738 137.930 90.00 90.00 90.00 P 41 21 2 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 0.033627 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033627 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007250 0.00000