HEADER TRANSFERASE/DNA 27-MAY-05 1ZTW TITLE D(CTTAATTCGAATTAAG) COMPLEXED WITH MOLONEY MURINE LEUKEMIA VIRUS TITLE 2 REVERSE TRANSCRIPTASE CATALYTIC FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CTTAATTC; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GAATTAAG; COMPND 7 CHAIN: G; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: REVERSE TRANSCRIPTASE; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: RT CATALYTIC FRAGMENT; COMPND 13 SYNONYM: RT; COMPND 14 EC: 2.7.7.49; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: MOLONEY MURINE LEUKEMIA VIRUS; SOURCE 7 ORGANISM_TAXID: 11801; SOURCE 8 GENE: POL; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MMLV RT, PROTEIN-DNA COMPLEX, DRUG-DNA COMPLEX, NETROPSIN, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.D.GOODWIN,E.C.LONG,M.M.GEORGIADIS REVDAT 4 14-FEB-24 1ZTW 1 REMARK REVDAT 3 24-FEB-09 1ZTW 1 VERSN REVDAT 2 20-SEP-05 1ZTW 1 REMARK REVDAT 1 30-AUG-05 1ZTW 0 JRNL AUTH K.D.GOODWIN,E.C.LONG,M.M.GEORGIADIS JRNL TITL A HOST-GUEST APPROACH FOR DETERMINING DRUG-DNA INTERACTIONS: JRNL TITL 2 AN EXAMPLE USING NETROPSIN. JRNL REF NUCLEIC ACIDS RES. V. 33 4106 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 16049022 JRNL DOI 10.1093/NAR/GKI717 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 34204 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1700 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2041 REMARK 3 NUCLEIC ACID ATOMS : 325 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 237 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.193 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.533 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.551 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.838 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.845 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZTW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033112. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97951 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35445 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MAGNESIUM ACETATE, ADA, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 27.46700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 72.87300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.46700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 72.87300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY CONSISTS OF TWO PROTEIN MOLECULES REMARK 300 BOUND TO THE ENDS OF A 16 BASE PAIR DNA DUPLEX. 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, G, 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 BIOMT1 2 -1.000000 0.000000 0.000000 109.86800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 145.74600 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 O3' DC B 8 P DG G 9 2765 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 41 116.02 -169.73 REMARK 500 PRO A 104 -150.61 -64.78 REMARK 500 THR A 106 19.11 -163.77 REMARK 500 ASN A 107 -141.06 -74.44 REMARK 500 ARG A 110 133.73 179.55 REMARK 500 PRO A 175 -9.35 -46.80 REMARK 500 MET A 177 84.90 68.62 REMARK 500 SER A 180 -70.14 -36.80 REMARK 500 VAL A 223 -106.64 58.96 REMARK 500 CYS A 262 68.98 38.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZTT RELATED DB: PDB REMARK 900 SAME DNA-PROTEIN COMPLEX WITH NETROPSIN BOUND TO DNA DBREF 1ZTW A 24 278 UNP P03355 POL_MLVMO 144 398 DBREF 1ZTW B 1 8 PDB 1ZTW 1ZTW 1 8 DBREF 1ZTW G 9 16 PDB 1ZTW 1ZTW 9 16 SEQRES 1 B 8 DC DT DT DA DA DT DT DC SEQRES 1 G 8 DG DA DA DT DT DA DA DG SEQRES 1 A 255 THR TRP LEU SER ASP PHE PRO GLN ALA TRP ALA GLU THR SEQRES 2 A 255 GLY GLY MET GLY LEU ALA VAL ARG GLN ALA PRO LEU ILE SEQRES 3 A 255 ILE PRO LEU LYS ALA THR SER THR PRO VAL SER ILE LYS SEQRES 4 A 255 GLN TYR PRO MET SER GLN GLU ALA ARG LEU GLY ILE LYS SEQRES 5 A 255 PRO HIS ILE GLN ARG LEU LEU ASP GLN GLY ILE LEU VAL SEQRES 6 A 255 PRO CYS GLN SER PRO TRP ASN THR PRO LEU LEU PRO VAL SEQRES 7 A 255 LYS LYS PRO GLY THR ASN ASP TYR ARG PRO VAL GLN ASP SEQRES 8 A 255 LEU ARG GLU VAL ASN LYS ARG VAL GLU ASP ILE HIS PRO SEQRES 9 A 255 THR VAL PRO ASN PRO TYR ASN LEU LEU SER GLY LEU PRO SEQRES 10 A 255 PRO SER HIS GLN TRP TYR THR VAL LEU ASP LEU LYS ASP SEQRES 11 A 255 ALA PHE PHE CYS LEU ARG LEU HIS PRO THR SER GLN PRO SEQRES 12 A 255 LEU PHE ALA PHE GLU TRP ARG ASP PRO GLU MET GLY ILE SEQRES 13 A 255 SER GLY GLN LEU THR TRP THR ARG LEU PRO GLN GLY PHE SEQRES 14 A 255 LYS ASN SER PRO THR LEU PHE ASP GLU ALA LEU HIS ARG SEQRES 15 A 255 ASP LEU ALA ASP PHE ARG ILE GLN HIS PRO ASP LEU ILE SEQRES 16 A 255 LEU LEU GLN TYR VAL ASP ASP LEU LEU LEU ALA ALA THR SEQRES 17 A 255 SER GLU LEU ASP CYS GLN GLN GLY THR ARG ALA LEU LEU SEQRES 18 A 255 GLN THR LEU GLY ASN LEU GLY TYR ARG ALA SER ALA LYS SEQRES 19 A 255 LYS ALA GLN ILE CYS GLN LYS GLN VAL LYS TYR LEU GLY SEQRES 20 A 255 TYR LEU LEU LYS GLU GLY GLN ARG FORMUL 4 HOH *237(H2 O) HELIX 1 1 THR A 24 PHE A 29 1 6 HELIX 2 2 PRO A 30 ALA A 32 5 3 HELIX 3 3 TRP A 33 GLY A 38 1 6 HELIX 4 4 SER A 67 GLN A 84 1 18 HELIX 5 5 LEU A 115 LYS A 120 1 6 HELIX 6 6 ASN A 131 SER A 137 1 7 HELIX 7 7 ALA A 154 LEU A 158 5 5 HELIX 8 8 SER A 164 ALA A 169 5 6 HELIX 9 9 ASN A 194 LEU A 207 1 14 HELIX 10 10 LEU A 207 HIS A 214 1 8 HELIX 11 11 SER A 232 GLY A 251 1 20 SHEET 1 A 3 LEU A 87 CYS A 90 0 SHEET 2 A 3 GLN A 182 TRP A 185 -1 O THR A 184 N VAL A 88 SHEET 3 A 3 PHE A 170 GLU A 171 -1 N PHE A 170 O LEU A 183 SHEET 1 B 2 LEU A 98 PRO A 100 0 SHEET 2 B 2 PRO A 111 GLN A 113 -1 O VAL A 112 N LEU A 99 SHEET 1 C 4 ILE A 218 TYR A 222 0 SHEET 2 C 4 ASP A 225 ALA A 230 -1 O ALA A 229 N ILE A 218 SHEET 3 C 4 TRP A 145 ASP A 150 -1 N LEU A 149 O LEU A 226 SHEET 4 C 4 GLN A 260 GLN A 263 -1 O GLN A 263 N TYR A 146 SHEET 1 D 2 GLN A 265 TYR A 268 0 SHEET 2 D 2 TYR A 271 LYS A 274 -1 O LEU A 273 N VAL A 266 CRYST1 54.934 145.746 46.855 90.00 90.00 90.00 P 21 21 2 4 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 0.018204 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021342 0.00000