HEADER ANTIBIOTIC 23-OCT-12 4HP7 TITLE TRIOXACARCIN D517 AS A PRODUCT OF GUANINE ROBBERY FROM D(AACCGGTT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUGAR (TRIOXACARCIN A ANALOGUE, BOUND FORM); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC SOURCE FORM THE LABORATORY OF ANDREW G. SOURCE 4 MYERS KEYWDS AMINOGLYCOSIDES, ANTI-BACTERIAL AGENTS, ANTITUMOR AGENTS, DNA, KEYWDS 2 ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR D.J.SMALTZ,T.MAGAUER,K.PROEPPER,B.DITTRICH,A.G.MYERS REVDAT 1 23-OCT-13 4HP7 0 JRNL AUTH D.J.SMALTZ,T.MAGAUER,K.PROEPPER,B.DITTRICH,A.G.MYERS JRNL TITL TRIOXACARCIN D517 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-2012 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.153 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1288 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.121 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 871 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 7634 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 242 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 247.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 3 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2187 REMARK 3 NUMBER OF RESTRAINTS : 2331 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.029 REMARK 3 ANGLE DISTANCES (A) : 0.729 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.159 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.491 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.120 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.026 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.000 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4HP7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-NOV-12. REMARK 100 THE RCSB ID CODE IS RCSB075746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.090 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.140 REMARK 200 R MERGE (I) : 0.09950 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.21 REMARK 200 R MERGE FOR SHELL (I) : 0.43390 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.360 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHELXL 2012 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE SOLUTION IN THE RESERVOIR REMARK 280 CONTAINED TRI-AMMONIUM CITRATE (PH 7.0) AND 30% V/V DMSO. THE DNA REMARK 280 -DRUG SOLUTION 2.5 MM DNA (SINGLE-STRAND CONCENTRATION), 2.8MM REMARK 280 TRIOXACARCIN A D5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 4.91300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 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 D 204 DISTANCE = 5.04 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 18Y A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C2J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF TRIOXACARCIN A COVALENTLY REMARK 900 BOUND TO GUANINE EXCISED FROM D(AACCGGTT) HET 18Y A 101 90 HET GUN A 102 15 HET 18Y B 101 84 HET GUN B 102 15 HET 18Y C 101 84 HET GUN C 102 15 HET 18Y D 101 86 HET GUN D 102 15 HET DMS C 106 10 HET DMS C 107 10 HET DMS D 108 20 HETNAM 18Y TRIOXACARCIN A ANALOGUE, BOUND FORM HETNAM GUN GUANINE HETNAM DMS DIMETHYL SULFOXIDE HETSYN 18Y (1S,2R,3AS,4S,13AS)-2-(DIMETHOXYMETHYL)-1,12-DIHYDROXY- HETSYN 2 18Y 7-METHOXY-1,5-DIMETHYL-11-OXO-1,2,3A,4,8,9,10,11- HETSYN 3 18Y OCTAHYDRO-13AH-2,4-EPOXYFURO[3,2-B]NAPHTHO[2,3- HETSYN 4 18Y H]CHROMEN-13A-YL 4-C-ACETYL-2,6-DIDEOXY-ALPHA-L-XYLO- HETSYN 5 18Y HEXOPYRANOSIDE FORMUL 1 18Y 4(C33 H40 O14) FORMUL 2 GUN 4(C5 H5 N5 O) FORMUL 9 DMS 3(C2 H6 O S) FORMUL 12 HOH *7(H2 O) LINK N7 GUN A 102 C17 18Y A 101 1555 1555 1.52 LINK N7 GUN B 102 C17 18Y B 101 1555 1555 1.46 LINK N7 GUN C 102 C17 18Y C 101 1555 1555 1.46 LINK N7 GUN D 102 C17 18Y D 101 1555 1555 1.44 CRYST1 24.086 9.826 35.093 90.00 92.32 90.00 P 1 21 1 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 0.041517 0.000000 0.001678 0.00000 SCALE2 0.000000 0.101771 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028519 0.00000 MASTER 174 0 11 0 0 0 0 6 0 0 0 0 END