10 20 30 40 50 60 70 80 2FVP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/DNA 31-JAN-06 2FVP
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*TP*TP*CP*AP*TP*TP*GP*CP*AP*AP*TP*GP*AP*AP*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 2FVP 1 VERSN REVDAT 1 12-DEC-06 2FVP 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. 2.25 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) : 2.25 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 : 17609 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) : 0.224 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 900 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 : 170 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.37 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 2FVP 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 RCSB036368.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-03 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18291 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 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 (%) : 98.4 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) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 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 (%): 55.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 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 27.36000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 73.06300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.36000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 73.06300 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 SYMMETRY OPERATOR: -X, -Y, Z TRANSLATION 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 109.44000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 146.12600 REMARK 350 BIOMT3 2 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 41 114.79 -170.29 REMARK 500 PRO A 104 100.88 -28.94 REMARK 500 PRO A 175 -76.35 -84.71 REMARK 500 VAL A 223 -109.22 57.93 REMARK 500 CYS A 262 65.16 35.98 REMARK 500 LYS A 274 134.31 -175.16 REMARK 500 REMARK 500 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 A 355 DISTANCE = 5.13 ANGSTROMS REMARK 525 HOH A 427 DISTANCE = 5.21 ANGSTROMS
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FVQ RELATED DB: PDB REMARK 900 RELATED ID: 2FVR RELATED DB: PDB REMARK 900 RELATED ID: 2FVS RELATED DB: PDB
DBREF 2FVP A 24 278 UNP P03355 POL_MLVMO 144 398 DBREF 2FVP B 1 16 PDB 2FVP 2FVP 1 16
SEQRES 1 B 16 DT DT DT DC DA DT DT DG DC DA DA DT DG SEQRES 2 B 16 DA DA 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 *170(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 GLY A 138 1 8 HELIX 6 6 ALA A 154 LEU A 158 5 5 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 LYS A 102 0 SHEET 2 B 2 TYR A 109 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 54.720 146.126 46.863 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 0.018275 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006843 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021339 0.00000