10 20 30 40 50 60 70 80 2FVR - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/DNA 31-JAN-06 2FVR
TITLE A STRUCTURAL STUDY OF THE CA DINUCLEOTIDE STEP IN THE TITLE 2 INTEGRASE PROCESSING SITE OF MOLONEY MURINE LEUKEMIA VIRUS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*TP*CP*TP*TP*TP*CP*AP*TP*AP*TP*GP*AP*AP*AP*GP*A)-3'; COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: REVERSE TRANSCRIPTASE; COMPND 8 CHAIN: A; COMPND 9 SYNONYM: RT; COMPND 10 EC: 2.7.7.49; COMPND 11 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: MOLONEY MURINE LEUKEMIA VIRUS; SOURCE 5 ORGANISM_TAXID: 11801; SOURCE 6 GENE: POL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS LTR, MMLV, INTEGRASE, TRANSFERASE/DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.P.MONTANO,M.L.COTE,M.J.ROTH,M.M.GEORGIADIS
REVDAT 2 24-FEB-09 2FVR 1 VERSN REVDAT 1 12-DEC-06 2FVR 0
JRNL AUTH S.P.MONTANO,M.L.COTE,M.J.ROTH,M.M.GEORGIADIS JRNL TITL CRYSTAL STRUCTURES OF OLIGONUCLEOTIDES INCLUDING JRNL TITL 2 THE INTEGRASE PROCESSING SITE OF THE MOLONEY JRNL TITL 3 MURINE LEUKEMIA VIRUS. JRNL REF NUCLEIC ACIDS RES. V. 34 5353 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 17003051 JRNL DOI 10.1093/NAR/GKL693
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 17964 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) : 0.231 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 871 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 : 153 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.23 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) : 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 2FVR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-06. REMARK 100 THE RCSB ID CODE IS RCSB036370.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-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) : 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) : 1.54 REMARK 200 MONOCHROMATOR : CONFOCAL MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18321 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 92.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 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 <I/SIGMA(I)> 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: PDB ENTRY 1D1U REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.39 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 27.39700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 72.95050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.39700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 72.95050 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 BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY PERFORMING THIS TRANSFORMATION ON THE ASYMMETRIC UNIT: REMARK 300 OPERATOR: -X, -Y, Z VECTOR: 2 1 -1
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: B, 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 109.58800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 145.90100 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 OH TYR A 271 OH TYR A 271 2665 2.01 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 41 117.59 -170.75 REMARK 500 PRO A 104 160.48 -45.98 REMARK 500 THR A 106 49.32 174.66 REMARK 500 ASP A 108 116.40 33.06 REMARK 500 PRO A 175 -77.04 -9.24 REMARK 500 GLU A 176 -8.16 -57.46 REMARK 500 MET A 177 100.46 163.12 REMARK 500 SER A 180 -102.88 22.00 REMARK 500 VAL A 223 -109.36 57.61 REMARK 500 CYS A 262 55.59 34.15 REMARK 500 GLU A 275 19.33 59.30 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FVP RELATED DB: PDB REMARK 900 RELATED ID: 2FVQ RELATED DB: PDB REMARK 900 RELATED ID: 2FVS RELATED DB: PDB
DBREF 2FVR A 24 278 UNP P03355 POL_MLVMO 144 398 DBREF 2FVR B 1 16 PDB 2FVR 2FVR 1 16
SEQRES 1 B 16 DT DC DT DT DT DC DA DT DA DT DG DA DA SEQRES 2 B 16 DA DG DA 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 3 HOH *153(H2 O)
HELIX 1 1 THR A 24 PHE A 29 1 6 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 LEU A 115 LYS A 120 1 6 HELIX 5 5 ASN A 131 SER A 137 1 7 HELIX 6 6 ASP A 153 LEU A 158 1 6 HELIX 7 7 SER A 164 ALA A 169 5 6 HELIX 8 8 ASN A 194 LEU A 207 1 14 HELIX 9 9 LEU A 207 HIS A 214 1 8 HELIX 10 10 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 VAL A 101 0 SHEET 2 B 2 ARG A 110 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 THR A 147 O LEU A 228 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 54.794 145.901 46.929 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 0.018250 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006854 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021309 0.00000