HEADER DNA BINDING PROTEIN 16-AUG-05 2BZF TITLE STRUCTURAL BASIS FOR DNA BRIDGING BY BARRIER-TO-AUTOINTEGRATION FACTOR TITLE 2 (BAF) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BARRIER-TO-AUTOINTEGRATION FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*TP*GP*GP*AP*GP*GP)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(*CP*CP*TP*CP*CP*AP*CP)-3'; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS DNA-BINDING PROTEIN, RETROVIRAL INTEGRATION, NON-SPECIFIC DNA- KEYWDS 2 BINDING, DNA COMPACTION, NUCLEAR ORGANIZATION, LEM FAMILY, DNA KEYWDS 3 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.M.BRADLEY,D.R.RONNING,R.GHIRLANDO,R.CRAIGIE,F.DYDA REVDAT 5 13-DEC-23 2BZF 1 REMARK REVDAT 4 24-FEB-09 2BZF 1 VERSN REVDAT 3 22-MAY-06 2BZF 1 JRNL REVDAT 2 26-SEP-05 2BZF 1 DBREF REVDAT 1 15-SEP-05 2BZF 0 JRNL AUTH C.M.BRADLEY,D.R.RONNING,R.GHIRLANDO,R.CRAIGIE,F.DYDA JRNL TITL STRUCTURAL BASIS FOR DNA BRIDGING BY JRNL TITL 2 BARRIER-TO-AUTOINTEGRATION FACTOR. JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 935 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 16155580 JRNL DOI 10.1038/NSMB989 REMARK 2 REMARK 2 RESOLUTION. 2.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 6060 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) : 0.244 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 697 REMARK 3 NUCLEIC ACID ATOMS : 281 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 5 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.110 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 2BZF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1290025289. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-05 REMARK 200 TEMPERATURE (KELVIN) : 95.0 REMARK 200 PH : 7.40 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU/MSC RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6542 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.870 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.890 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.85 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.050 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1CI4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.40 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 120.96000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.91500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.91500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 181.44000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.91500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.91500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.48000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.91500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.91500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 181.44000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.91500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.91500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.48000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 120.96000 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -241.92000 REMARK 400 REMARK 400 COMPOUND REMARK 400 RESPONSIBLE FOR INHIBITING SELF-DESTRUCTING REMARK 400 AUTOINTEGRATION OF RETROVIRAL DNA, THEREBY REMARK 400 PROMOTING INTEGRATION OF RETROVIRAL DNA REMARK 400 INTO THE HOST CHROMOSOME. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 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 52 27.26 -78.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CI4 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF HUMAN BARRIER-TO- AUTOINTEGRATION FACTOR REMARK 900 (BAF) REMARK 900 RELATED ID: 1QCK RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HUMAN BARRIER-TO- AUTOINTEGRATION FACTOR BAF, REMARK 900 NMR, REGULARIZED MEAN STRUCTURE PLUS 20 INDIVIDUAL SIMULATED REMARK 900 ANNEALING STRUCTURES REMARK 900 RELATED ID: 2EZX RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HUMAN BARRIER-TO- AUTOINTEGRATION FACTOR BAF, REMARK 900 NMR, REGULARIZED MEAN STRUCTURE REMARK 900 RELATED ID: 2EZY RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HUMAN BARRIER-TO- AUTOINTEGRATION FACTOR BAF, REMARK 900 NMR, ENSEMBLE OF 20 SIMULATED ANNEALING STRUCTURES REMARK 900 RELATED ID: 2EZZ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HUMAN BARRIER-TO- AUTOINTEGRATION FACTOR BAF REMARK 900 NMR, ENSEMBLE OF 20 SIMULATED ANNEALING STRUCTURES REMARK 999 REMARK 999 SEQUENCE REMARK 999 MET 1 IS NOT SEEN IN THE STRUCTURE. DBREF 2BZF A 1 89 UNP O75531 BAF_HUMAN 1 89 DBREF 2BZF B 1 7 PDB 2BZF 2BZF 1 7 DBREF 2BZF C 8 14 PDB 2BZF 2BZF 8 14 SEQRES 1 A 89 MET THR THR SER GLN LYS HIS ARG ASP PHE VAL ALA GLU SEQRES 2 A 89 PRO MET GLY GLU LYS PRO VAL GLY SER LEU ALA GLY ILE SEQRES 3 A 89 GLY GLU VAL LEU GLY LYS LYS LEU GLU GLU ARG GLY PHE SEQRES 4 A 89 ASP LYS ALA TYR VAL VAL LEU GLY GLN PHE LEU VAL LEU SEQRES 5 A 89 LYS LYS ASP GLU ASP LEU PHE ARG GLU TRP LEU LYS ASP SEQRES 6 A 89 THR CYS GLY ALA ASN ALA LYS GLN SER ARG ASP CYS PHE SEQRES 7 A 89 GLY CYS LEU ARG GLU TRP CYS ASP ALA PHE LEU SEQRES 1 B 7 DG DT DG DG DA DG DG SEQRES 1 C 7 DC DC DT DC DC DA DC FORMUL 4 HOH *5(H2 O) HELIX 1 1 SER A 4 GLU A 13 1 10 HELIX 2 2 PRO A 19 LEU A 23 5 5 HELIX 3 3 GLY A 27 ARG A 37 1 11 HELIX 4 4 LYS A 41 LEU A 52 1 12 HELIX 5 5 ASP A 55 CYS A 67 1 13 HELIX 6 6 ASN A 70 LEU A 89 1 20 CRYST1 45.830 45.830 241.920 90.00 90.00 90.00 P 43 21 2 8 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 0.021820 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004134 0.00000