HEADER TRANSFERASE/DNA 02-MAR-01 1I6J TITLE CRYSTAL STRUCTURE OF A PSEUDO-16-MER DNA WITH STACKED GUANINES AND TWO TITLE 2 G-A MISPAIRS COMPLEXED WITH THE N-TERMINAL FRAGMENT OF MOLONEY MURINE TITLE 3 LEUKEMIA VIRUS REVERSE 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 MISPAIR, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.L.COTE,M.M.GEORGIADIS REVDAT 4 20-SEP-23 1I6J 1 REMARK REVDAT 3 21-DEC-22 1I6J 1 SEQADV 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 GUANINES AND JRNL TITL 2 TWO G-A MISPAIRS COMPLEXED WITH THE N-TERMINAL FRAGMENT OF JRNL TITL 3 MOLONEY MURINE LEUKEMIA 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 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) : 1.260 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-01. REMARK 100 THE DEPOSITION ID IS D_1000012966. 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, PH REMARK 280 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: -X-1, REMARK 300 -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 METHIONINE 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