HEADER TRANSFERASE/DNA 02-MAR-01 1I6J TITLE CRYSTAL STRUCTURE OF A PSEUDO-16-MER DNA WITH STACKED TITLE 2 GUANINES AND TWO G-A MISPAIRS COMPLEXED WITH THE N- TITLE 3 TERMINAL FRAGMENT OF MOLONEY MURINE LEUKEMIA VIRUS REVERSE TITLE 4 TRANSCRIPTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*TP*CP*GP*TP*C)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*AP*CP*GP*GP*GP*AP*CP*GP*AP*C)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: REVERSE TRANSCRIPTASE; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: N-TERMINAL FRAGMENT; COMPND 13 EC: 2.7.7.49; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: ABI 392 DNA SYNTHESIZER; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: ABI 392 DNA SYNTHESIZER; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: MOLONEY MURINE LEUKEMIA VIRUS; SOURCE 9 ORGANISM_TAXID: 11801; SOURCE 10 GENE: VIRUS; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS MOLONEY MURINE LEUKEMIA VIRUS, REVERSE TRANSCRIPTASE, G-A KEYWDS 2 MISPAIR, TRANSFERASE/DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.L.COTE,M.M.GEORGIADIS REVDAT 2 24-FEB-09 1I6J 1 VERSN REVDAT 1 07-SEP-01 1I6J 0 JRNL AUTH M.L.COTE,M.M.GEORGIADIS JRNL TITL STRUCTURE OF A PSEUDO-16-MER DNA WITH STACKED JRNL TITL 2 GUANINES AND TWO G-A MISPAIRS COMPLEXED WITH THE JRNL TITL 3 N-TERMINAL FRAGMENT OF MOLONEY MURINE LEUKEMIA JRNL TITL 4 VIRUS REVERSE TRANSCRIPTASE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 1238 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11526315 JRNL DOI 10.1107/S090744490100943X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 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) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 24781 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1204 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 : 2049 REMARK 3 NUCLEIC ACID ATOMS : 324 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.00 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 1.26 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.00 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 1I6J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-01. REMARK 100 THE RCSB ID CODE IS RCSB012966. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 108.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24781 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 1.100 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.29800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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: PDB ENTRY 1D1U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, NACL, ADA, MGCL2, HEPES, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 27.13200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 73.32400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.13200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 73.32400 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 SECOND PART OF THE DNA IS GENERATED BY THE 2-FOLD: - REMARK 300 X-1, -Y, Z 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 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 41 117.63 -171.23 REMARK 500 PRO A 104 39.76 21.81 REMARK 500 ASN A 107 50.87 -90.57 REMARK 500 MET A 177 89.73 52.27 REMARK 500 VAL A 223 -108.17 55.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D1U RELATED DB: PDB REMARK 900 1D1U CONTAINS THE SAME PROTEIN. DBREF 1I6J A 24 278 UNP P03355 POL_MLVMO 144 398 DBREF 1I6J B 1 6 PDB 1I6J 1I6J 1 6 DBREF 1I6J C 7 16 PDB 1I6J 1I6J 7 16 SEQADV 1I6J MET A 23 UNP P03355 INITIATING MET SEQRES 1 B 6 DG DT DC DG DT DC SEQRES 1 C 10 DA DC DG DG DG DA DC DG DA DC SEQRES 1 A 256 MET THR TRP LEU SER ASP PHE PRO GLN ALA TRP ALA GLU SEQRES 2 A 256 THR GLY GLY MET GLY LEU ALA VAL ARG GLN ALA PRO LEU SEQRES 3 A 256 ILE ILE PRO LEU LYS ALA THR SER THR PRO VAL SER ILE SEQRES 4 A 256 LYS GLN TYR PRO MET SER GLN GLU ALA ARG LEU GLY ILE SEQRES 5 A 256 LYS PRO HIS ILE GLN ARG LEU LEU ASP GLN GLY ILE LEU SEQRES 6 A 256 VAL PRO CYS GLN SER PRO TRP ASN THR PRO LEU LEU PRO SEQRES 7 A 256 VAL LYS LYS PRO GLY THR ASN ASP TYR ARG PRO VAL GLN SEQRES 8 A 256 ASP LEU ARG GLU VAL ASN LYS ARG VAL GLU ASP ILE HIS SEQRES 9 A 256 PRO THR VAL PRO ASN PRO TYR ASN LEU LEU SER GLY LEU SEQRES 10 A 256 PRO PRO SER HIS GLN TRP TYR THR VAL LEU ASP LEU LYS SEQRES 11 A 256 ASP ALA PHE PHE CYS LEU ARG LEU HIS PRO THR SER GLN SEQRES 12 A 256 PRO LEU PHE ALA PHE GLU TRP ARG ASP PRO GLU MET GLY SEQRES 13 A 256 ILE SER GLY GLN LEU THR TRP THR ARG LEU PRO GLN GLY SEQRES 14 A 256 PHE LYS ASN SER PRO THR LEU PHE ASP GLU ALA LEU HIS SEQRES 15 A 256 ARG ASP LEU ALA ASP PHE ARG ILE GLN HIS PRO ASP LEU SEQRES 16 A 256 ILE LEU LEU GLN TYR VAL ASP ASP LEU LEU LEU ALA ALA SEQRES 17 A 256 THR SER GLU LEU ASP CYS GLN GLN GLY THR ARG ALA LEU SEQRES 18 A 256 LEU GLN THR LEU GLY ASN LEU GLY TYR ARG ALA SER ALA SEQRES 19 A 256 LYS LYS ALA GLN ILE CYS GLN LYS GLN VAL LYS TYR LEU SEQRES 20 A 256 GLY TYR LEU LEU LYS GLU GLY GLN ARG FORMUL 4 HOH *204(H2 O) HELIX 1 1 MET A 23 PHE A 29 1 7 HELIX 2 2 TRP A 33 GLY A 38 1 6 HELIX 3 3 SER A 67 GLN A 84 1 18 HELIX 4 4 PRO A 104 THR A 106 5 3 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 GLN A 182 N CYS A 90 SHEET 3 A 3 PHE A 170 GLU A 171 -1 O PHE A 170 N LEU A 183 SHEET 1 B 2 LEU A 98 LYS A 102 0 SHEET 2 B 2 TYR A 109 GLN A 113 -1 O ARG A 110 N VAL A 101 SHEET 1 C 4 ILE A 218 TYR A 222 0 SHEET 2 C 4 ASP A 225 ALA A 230 -1 N ASP A 225 O TYR A 222 SHEET 3 C 4 TRP A 145 ASP A 150 -1 O TRP A 145 N ALA A 230 SHEET 4 C 4 GLN A 260 GLN A 263 -1 O GLN A 260 N VAL A 148 SHEET 1 D 2 GLN A 265 TYR A 268 0 SHEET 2 D 2 TYR A 271 LYS A 274 -1 O TYR A 271 N TYR A 268 CRYST1 54.264 146.648 46.708 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 0.018428 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006819 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021410 0.00000 MASTER 237 0 0 11 11 0 0 6 0 0 0 22 END