HEADER DNA/ANTIBIOTIC 27-MAR-22 7XDJ TITLE CRYSTAL STRUCTURE OF ACTINOMYCIN D-ECHINOMYCIN-D(AGCGCGT/ACGAGCT) TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3'); COMPND 3 CHAIN: A, E, I, M; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3'); COMPND 7 CHAIN: B, F, J, N; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA; COMPND 11 CHAIN: L, P, D, H; COMPND 12 MOL_ID: 4; COMPND 13 MOLECULE: THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA; COMPND 14 CHAIN: C, G, K, O 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:A MISMATCH, SINGLE-STRAND DNA TWIST, MISMATCH BINDING ANTIBIOTIC, KEYWDS 2 DNA, DNA-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.M.CHIEN,R.B.SATANGE,M.H.HOU REVDAT 3 29-NOV-23 7XDJ 1 REMARK REVDAT 2 15-NOV-23 7XDJ 1 REMARK LINK ATOM REVDAT 1 14-DEC-22 7XDJ 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. 2.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 24192 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2436 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 24.8300 - 6.2309 1.00 1288 144 0.2186 0.2159 REMARK 3 2 6.2309 - 4.9585 1.00 1270 142 0.1725 0.1629 REMARK 3 3 4.9585 - 4.3355 1.00 1310 140 0.1528 0.1916 REMARK 3 4 4.3355 - 3.9408 1.00 1262 142 0.1762 0.1931 REMARK 3 5 3.9408 - 3.6593 1.00 1324 148 0.2082 0.2423 REMARK 3 6 3.6593 - 3.4441 1.00 1272 142 0.1853 0.2914 REMARK 3 7 3.4441 - 3.2721 1.00 1266 138 0.1559 0.2316 REMARK 3 8 3.2721 - 3.1299 1.00 1272 144 0.1756 0.2112 REMARK 3 9 3.1299 - 3.0096 1.00 1274 148 0.2084 0.2257 REMARK 3 10 3.0096 - 2.9059 1.00 1298 140 0.2416 0.2988 REMARK 3 11 2.9059 - 2.8152 1.00 1300 150 0.2652 0.3123 REMARK 3 12 2.8152 - 2.7348 1.00 1278 144 0.2870 0.4665 REMARK 3 13 2.7348 - 2.6629 1.00 1292 142 0.3137 0.3582 REMARK 3 14 2.6629 - 2.5980 1.00 1244 136 0.2937 0.2879 REMARK 3 15 2.5980 - 2.5390 1.00 1319 152 0.2700 0.3687 REMARK 3 16 2.5390 - 2.4850 0.99 1268 145 0.2854 0.3577 REMARK 3 17 2.4850 - 2.4354 0.94 1219 139 0.2990 0.3327 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.28 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 5.3782 25.8104 11.6789 REMARK 3 T TENSOR REMARK 3 T11: 0.3694 T22: 0.3021 REMARK 3 T33: 0.6560 T12: 0.0356 REMARK 3 T13: -0.0829 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.8136 L22: 1.6557 REMARK 3 L33: 1.9811 L12: 0.7040 REMARK 3 L13: -0.5747 L23: 1.1958 REMARK 3 S TENSOR REMARK 3 S11: 0.0912 S12: 0.1241 S13: -0.0830 REMARK 3 S21: 0.2876 S22: -0.1501 S23: 0.0745 REMARK 3 S31: 0.0812 S32: -0.1211 S33: 0.0897 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 7XDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-22. REMARK 100 THE DEPOSITION ID IS D_1300028598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.91982 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24192 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.75900 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 1.14_3260 REMARK 200 STARTING MODEL: 7DQ0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.25 MM OLIGONUCLEOTIDE, 0.25 MM REMARK 280 ECHINOMYCIN, 0.125 MM ACTINOMYCIN D, 2.5 MM SODIUM CACODYLATE, REMARK 280 3.5 MM MAGNESIUM CHLORIDE, 1 MM SPERMINE TETRAHYDROCHLORIDE, 6 REMARK 280 MM COBALT CHLORIDE, 1% (V/V) 2-METHYL-2,4-PENTANEDIOL, 6% (V/V) REMARK 280 PEG 200, RESERVIOR PEG 200 (30%), PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+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 1.000000 0.000000 0.000000 66.26100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.25581 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.53167 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 66.26100 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 38.25581 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.53167 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 66.26100 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 38.25581 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.53167 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 76.51161 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 33.06333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 76.51161 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 33.06333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 76.51161 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 33.06333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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, P, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, J, L, O 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: M, N, K, 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 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: K, O 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: L, P REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE QUI 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 G 1 O MVA G 5 1.42 REMARK 500 OG1 THR G 7 O MVA G 11 1.57 REMARK 500 OG1 THR C 1 O MVA C 5 1.61 REMARK 500 N DSN D 1 C QUI D 101 1.65 REMARK 500 OG1 THR K 1 O MVA K 5 1.87 REMARK 500 OG1 THR C 7 O MVA C 11 1.91 REMARK 500 OG DSN D 1 O MVA D 8 1.93 REMARK 500 OG DSN H 1 O MVA H 8 1.99 REMARK 500 OG DSN P 1 O MVA P 8 2.03 REMARK 500 OG1 THR O 7 O MVA O 11 2.04 REMARK 500 N THR K 1 O1 PXZ K 6 2.10 REMARK 500 CA DSN D 5 C QUI D 102 2.15 REMARK 500 OG1 THR K 7 O MVA K 11 2.16 REMARK 500 CA DSN H 1 C QUI H 101 2.19 REMARK 500 OG1 THR O 1 O MVA O 5 2.19 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 DA A 1 O3' DA A 1 C3' -0.047 REMARK 500 DSN L 1 C DSN L 1 O 0.180 REMARK 500 DSN L 5 C DSN L 5 O 0.163 REMARK 500 DSN P 1 C DSN P 1 O 0.163 REMARK 500 DSN P 5 C DSN P 5 O 0.172 REMARK 500 DSN D 1 C DSN D 1 O 0.160 REMARK 500 DSN D 5 C DSN D 5 O 0.169 REMARK 500 DSN H 1 C DSN H 1 O 0.164 REMARK 500 DSN H 5 C DSN H 5 O 0.175 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 PRO C 9 C - N - CA ANGL. DEV. = 16.2 DEGREES REMARK 500 PRO C 9 C - N - CD ANGL. DEV. = -28.4 DEGREES REMARK 500 PRO O 9 C - N - CA ANGL. DEV. = 10.4 DEGREES REMARK 500 PRO O 9 C - N - CD ANGL. DEV. = -21.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 DVA C 2 PRO C 3 111.55 REMARK 500 DVA C 8 PRO C 9 101.99 REMARK 500 DVA G 2 PRO G 3 110.19 REMARK 500 DVA G 8 PRO G 9 89.63 REMARK 500 DVA K 2 PRO K 3 116.53 REMARK 500 DVA K 8 PRO K 9 98.57 REMARK 500 DVA O 2 PRO O 3 130.07 REMARK 500 DVA O 8 PRO O 9 92.49 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 L 203 DISTANCE = 6.35 ANGSTROMS 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 D 101 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 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 3 OP1 REMARK 620 2 HOH A 202 O 91.5 REMARK 620 3 DC E 3 OP1 176.0 92.4 REMARK 620 4 HOH E 103 O 97.5 110.8 80.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA N 1 O3' REMARK 620 2 DC N 2 OP2 52.8 REMARK 620 N 1 DBREF 7XDJ A 1 7 PDB 7XDJ 7XDJ 1 7 DBREF 7XDJ B 1 7 PDB 7XDJ 7XDJ 1 7 DBREF 7XDJ E 1 7 PDB 7XDJ 7XDJ 1 7 DBREF 7XDJ F 1 7 PDB 7XDJ 7XDJ 1 7 DBREF 7XDJ I 1 7 PDB 7XDJ 7XDJ 1 7 DBREF 7XDJ J 1 7 PDB 7XDJ 7XDJ 1 7 DBREF 7XDJ L 1 8 PDB 7XDJ 7XDJ 1 8 DBREF 7XDJ M 1 7 PDB 7XDJ 7XDJ 1 7 DBREF 7XDJ N 1 7 PDB 7XDJ 7XDJ 1 7 DBREF 7XDJ P 1 8 PDB 7XDJ 7XDJ 1 8 DBREF 7XDJ C 1 11 NOR 7XDJ 7XDJ 1 11 DBREF 7XDJ G 1 11 NOR 7XDJ 7XDJ 1 11 DBREF 7XDJ K 1 11 NOR 7XDJ 7XDJ 1 11 DBREF 7XDJ O 1 11 NOR 7XDJ 7XDJ 1 11 DBREF 7XDJ D 1 8 PDB 7XDJ 7XDJ 1 8 DBREF 7XDJ H 1 8 PDB 7XDJ 7XDJ 1 8 SEQRES 1 A 7 DA DG DC DG DC DG DT SEQRES 1 B 7 DA DC DG DA DG DC BRU SEQRES 1 E 7 DA DG DC DG DC DG DT SEQRES 1 F 7 DA DC DG DA DG DC BRU SEQRES 1 I 7 DA DG DC DG DC DG DT SEQRES 1 J 7 DA DC DG DA DG DC BRU SEQRES 1 L 8 DSN ALA N2C MVA DSN ALA NCY MVA SEQRES 1 M 7 DA DG DC DG DC DG DT SEQRES 1 N 7 DA DC DG DA DG DC BRU SEQRES 1 P 8 DSN ALA N2C MVA DSN ALA NCY MVA SEQRES 1 C 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA SEQRES 1 G 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA SEQRES 1 K 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA SEQRES 1 O 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA SEQRES 1 D 8 DSN ALA N2C MVA DSN ALA NCY MVA SEQRES 1 H 8 DSN ALA N2C MVA DSN ALA NCY MVA HET BRU B 7 20 HET BRU F 7 20 HET BRU J 7 20 HET DSN L 1 6 HET N2C L 3 8 HET MVA L 4 8 HET DSN L 5 6 HET NCY L 7 7 HET MVA L 8 8 HET BRU N 7 20 HET DSN P 1 6 HET N2C P 3 8 HET MVA P 4 8 HET DSN P 5 6 HET NCY P 7 7 HET MVA P 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 DVA G 2 7 HET SAR G 4 5 HET MVA G 5 8 HET PXZ G 6 22 HET DVA G 8 7 HET SAR G 10 5 HET MVA G 11 8 HET DVA K 2 7 HET SAR K 4 5 HET MVA K 5 8 HET PXZ K 6 22 HET DVA K 8 7 HET SAR K 10 5 HET MVA K 11 8 HET DVA O 2 7 HET SAR O 4 5 HET MVA O 5 8 HET PXZ O 6 22 HET DVA O 8 7 HET SAR O 10 5 HET MVA O 11 8 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 DSN H 1 6 HET N2C H 3 8 HET MVA H 4 8 HET DSN H 5 6 HET NCY H 7 7 HET MVA H 8 8 HET CL A 101 1 HET MG A 102 1 HET CL J 101 1 HET MG J 102 1 HET QUI L 101 12 HET QUI L 102 12 HET CL N 101 1 HET MG N 102 1 HET QUI P 101 12 HET QUI P 102 12 HET QUI D 101 12 HET QUI D 102 12 HET QUI H 101 12 HET QUI H 102 12 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE 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 CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM QUI 2-CARBOXYQUINOXALINE HETSYN PXZ PHENOXAZINE FORMUL 2 BRU 4(C9 H12 BR N2 O8 P) FORMUL 7 DSN 8(C3 H7 N O3) FORMUL 7 N2C 4(C5 H11 N O2 S) FORMUL 7 MVA 16(C6 H13 N O2) FORMUL 7 NCY 4(C4 H9 N O2 S) FORMUL 11 DVA 8(C5 H11 N O2) FORMUL 11 SAR 8(C3 H7 N O2) FORMUL 11 PXZ 4(C16 H12 N2 O4) FORMUL 17 CL 3(CL 1-) FORMUL 18 MG 3(MG 2+) FORMUL 21 QUI 8(C9 H6 N2 O2) FORMUL 31 HOH *34(H2 O) LINK O3' DC B 6 P BRU B 7 1555 1555 1.61 LINK O3' DC F 6 P BRU F 7 1555 1555 1.60 LINK O3' DC J 6 P BRU J 7 1555 1555 1.60 LINK C DSN L 1 N ALA L 2 1555 1555 1.33 LINK OG DSN L 1 C MVA L 8 1555 1555 1.37 LINK N DSN L 1 C QUI L 102 1555 1555 1.43 LINK C ALA L 2 N N2C L 3 1555 1555 1.33 LINK C N2C L 3 N MVA L 4 1555 1555 1.33 LINK CB N2C L 3 SG NCY L 7 1555 1555 1.77 LINK C MVA L 4 OG DSN L 5 1555 1555 1.37 LINK C DSN L 5 N ALA L 6 1555 1555 1.33 LINK N DSN L 5 C QUI L 101 1555 1555 1.50 LINK C ALA L 6 N NCY L 7 1555 1555 1.33 LINK C NCY L 7 N MVA L 8 1555 1555 1.33 LINK O3' DC N 6 P BRU N 7 1555 1555 1.60 LINK C DSN P 1 N ALA P 2 1555 1555 1.33 LINK OG DSN P 1 C MVA P 8 1555 1555 1.39 LINK N DSN P 1 C QUI P 102 1555 1555 1.39 LINK C ALA P 2 N N2C P 3 1555 1555 1.34 LINK C N2C P 3 N MVA P 4 1555 1555 1.33 LINK CB N2C P 3 SG NCY P 7 1555 1555 1.78 LINK C MVA P 4 OG DSN P 5 1555 1555 1.40 LINK C DSN P 5 N ALA P 6 1555 1555 1.33 LINK N DSN P 5 C QUI P 101 1555 1555 1.45 LINK C ALA P 6 N NCY P 7 1555 1555 1.33 LINK C NCY P 7 N MVA P 8 1555 1555 1.33 LINK C THR C 1 N DVA C 2 1555 1555 1.34 LINK OG1 THR C 1 C MVA C 5 1555 1555 1.37 LINK N THR C 1 C0 PXZ C 6 1555 1555 1.43 LINK C DVA C 2 N PRO C 3 1555 1555 1.33 LINK C PRO C 3 N SAR C 4 1555 1555 1.36 LINK C SAR C 4 N MVA C 5 1555 1555 1.34 LINK C0' PXZ C 6 N THR C 7 1555 1555 1.42 LINK C THR C 7 N DVA C 8 1555 1555 1.33 LINK OG1 THR C 7 C MVA C 11 1555 1555 1.37 LINK C DVA C 8 N PRO C 9 1555 1555 1.31 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 C THR G 1 N DVA G 2 1555 1555 1.33 LINK N THR G 1 C0 PXZ G 6 1555 1555 1.43 LINK C DVA G 2 N PRO G 3 1555 1555 1.32 LINK C PRO G 3 N SAR G 4 1555 1555 1.36 LINK C SAR G 4 N MVA G 5 1555 1555 1.33 LINK C0' PXZ G 6 N THR G 7 1555 1555 1.43 LINK C THR G 7 N DVA G 8 1555 1555 1.33 LINK OG1 THR G 7 C MVA G 11 1555 1555 1.38 LINK C DVA G 8 N PRO G 9 1555 1555 1.31 LINK C PRO G 9 N SAR G 10 1555 1555 1.33 LINK C SAR G 10 N MVA G 11 1555 1555 1.33 LINK C THR K 1 N DVA K 2 1555 1555 1.34 LINK OG1 THR K 1 C MVA K 5 1555 1555 1.38 LINK N THR K 1 C0 PXZ K 6 1555 1555 1.43 LINK C DVA K 2 N PRO K 3 1555 1555 1.33 LINK C PRO K 3 N SAR K 4 1555 1555 1.35 LINK C SAR K 4 N MVA K 5 1555 1555 1.34 LINK C0' PXZ K 6 N THR K 7 1555 1555 1.44 LINK C THR K 7 N DVA K 8 1555 1555 1.34 LINK OG1 THR K 7 C MVA K 11 1555 1555 1.37 LINK C DVA K 8 N PRO K 9 1555 1555 1.32 LINK C PRO K 9 N SAR K 10 1555 1555 1.33 LINK C SAR K 10 N MVA K 11 1555 1555 1.33 LINK C THR O 1 N DVA O 2 1555 1555 1.35 LINK OG1 THR O 1 C MVA O 5 1555 1555 1.37 LINK N THR O 1 C0 PXZ O 6 1555 1555 1.43 LINK C DVA O 2 N PRO O 3 1555 1555 1.34 LINK C PRO O 3 N SAR O 4 1555 1555 1.35 LINK C SAR O 4 N MVA O 5 1555 1555 1.34 LINK C0' PXZ O 6 N THR O 7 1555 1555 1.43 LINK C THR O 7 N DVA O 8 1555 1555 1.33 LINK OG1 THR O 7 C MVA O 11 1555 1555 1.37 LINK C DVA O 8 N PRO O 9 1555 1555 1.32 LINK C PRO O 9 N SAR O 10 1555 1555 1.34 LINK C SAR O 10 N MVA O 11 1555 1555 1.33 LINK C DSN D 1 N ALA D 2 1555 1555 1.33 LINK OG DSN D 1 C MVA D 8 1555 1555 1.38 LINK C ALA D 2 N N2C D 3 1555 1555 1.33 LINK C N2C D 3 N MVA D 4 1555 1555 1.33 LINK CB N2C D 3 SG NCY D 7 1555 1555 1.76 LINK C MVA D 4 OG DSN D 5 1555 1555 1.37 LINK C DSN D 5 N ALA D 6 1555 1555 1.33 LINK N DSN D 5 C QUI D 102 1555 1555 1.57 LINK C ALA D 6 N NCY D 7 1555 1555 1.33 LINK C NCY D 7 N MVA D 8 1555 1555 1.33 LINK C DSN H 1 N ALA H 2 1555 1555 1.33 LINK OG DSN H 1 C MVA H 8 1555 1555 1.37 LINK N DSN H 1 C QUI H 101 1555 1555 1.58 LINK C ALA H 2 N N2C H 3 1555 1555 1.33 LINK C N2C H 3 N MVA H 4 1555 1555 1.33 LINK CB N2C H 3 SG NCY H 7 1555 1555 1.78 LINK C MVA H 4 OG DSN H 5 1555 1555 1.37 LINK C DSN H 5 N ALA H 6 1555 1555 1.33 LINK N DSN H 5 C QUI H 102 1555 1555 1.56 LINK C ALA H 6 N NCY H 7 1555 1555 1.33 LINK C NCY H 7 N MVA H 8 1555 1555 1.33 LINK OP1 DC A 3 MG MG A 102 1555 1555 2.08 LINK MG MG A 102 O HOH A 202 1555 1555 2.65 LINK MG MG A 102 OP1 DC E 3 1555 1555 2.08 LINK MG MG A 102 O HOH E 103 1555 1555 2.85 LINK OP2 DC J 2 MG MG J 102 1555 1555 2.55 LINK O3' DA N 1 MG MG N 102 1555 1555 2.51 LINK OP2 DC N 2 MG MG N 102 1555 1555 2.90 CISPEP 1 PRO C 3 SAR C 4 0 8.93 CISPEP 2 PRO C 9 SAR C 10 0 1.55 CISPEP 3 PRO G 3 SAR G 4 0 9.59 CISPEP 4 PRO G 9 SAR G 10 0 2.32 CISPEP 5 PRO K 3 SAR K 4 0 16.28 CISPEP 6 PRO K 9 SAR K 10 0 2.45 CISPEP 7 PRO O 3 SAR O 4 0 7.43 CISPEP 8 PRO O 9 SAR O 10 0 1.42 CRYST1 132.522 132.522 49.595 90.00 90.00 120.00 H 3 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 0.007546 0.004357 0.000000 0.00000 SCALE2 0.000000 0.008713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020163 0.00000