PDB Short entry for 1OWG HEADER TRANSCRIPTION/DNA 28-MAR-03 1OWG TITLE CRYSTAL STRUCTURE OF WT IHF COMPLEXED WITH AN ALTERED H' SITE (T44A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHAGE LAMBDA H' SITE; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3'; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*AP*GP*CP*AP COMPND 11 *CP*C)-3'; COMPND 12 CHAIN: E; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: INTEGRATION HOST FACTOR ALPHA-SUBUNIT; COMPND 16 CHAIN: A; COMPND 17 SYNONYM: IHF-ALPHA; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: INTEGRATION HOST FACTOR BETA-SUBUNIT; COMPND 21 CHAIN: B; COMPND 22 SYNONYM: IHF-BETA; COMPND 23 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 9 ORGANISM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 MOL_ID: 5; SOURCE 13 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 14 ORGANISM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-DNA RECOGNITION, INDIRECT READOUT, IHF, DNA BENDING, MINOR KEYWDS 2 GROOVE, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.W.LYNCH,E.K.READ,A.N.MATTIS,J.F.GARDNER,P.A.RICE REVDAT 3 14-FEB-24 1OWG 1 REMARK REVDAT 2 24-FEB-09 1OWG 1 VERSN REVDAT 1 15-JUL-03 1OWG 0 JRNL AUTH T.W.LYNCH,E.K.READ,A.N.MATTIS,J.F.GARDNER,P.A.RICE JRNL TITL INTEGRATION HOST FACTOR: PUTTING A TWIST ON PROTEIN-DNA JRNL TITL 2 RECOGNITION JRNL REF J.MOL.BIOL. V. 330 493 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12842466 JRNL DOI 10.1016/S0022-2836(03)00529-1 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 454447.300 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 51.5 REMARK 3 NUMBER OF REFLECTIONS : 15488 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) : 0.226 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 749 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 8.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 375 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE : 0.4460 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 20 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1522 REMARK 3 NUCLEIC ACID ATOMS : 1426 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 83 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.32000 REMARK 3 B22 (A**2) : 33.13000 REMARK 3 B33 (A**2) : -30.82000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.38 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.42 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.46 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.430 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.320 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.810 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.490 ; 5.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 43.31 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP_NOPUCKERS2.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OWG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26109 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG5000-MME, GLYCEROL, TRIS-HCL, REMARK 280 MAGNESIUM CHLORIDE, SODIUM CHLORIDE, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.33000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 90.65700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.41600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 90.65700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.33000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.41600 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 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, E, A, B 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 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 465 ASP A 98 REMARK 465 GLU A 99 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 PHE A 49 -82.94 -118.71 REMARK 500 LYS A 66 -73.39 -77.74 REMARK 500 PRO A 96 110.14 -33.28 REMARK 500 GLN B 13 -83.88 -49.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IHF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN IHF-DNA COMPLEX: A PROTEIN-INDUCED DNA U- REMARK 900 TURN REMARK 900 RELATED ID: 1OUZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A MUTANT IHF (BETAE44A) COMPLEXED WITH A REMARK 900 VARIANT H' SITE (T44A) DBREF 1OWG A 1 99 UNP P0A6X7 IHFA_ECOLI 1 99 DBREF 1OWG B 1 94 UNP P0A6Y1 IHFB_ECOLI 1 94 DBREF 1OWG C 50 16 PDB 1OWG 1OWG 50 16 DBREF 1OWG D 15 29 PDB 1OWG 1OWG 15 29 DBREF 1OWG E 30 49 PDB 1OWG 1OWG 30 49 SEQRES 1 C 35 DC DG DG DT DG DC DT DA DC DA DA DA DT SEQRES 2 C 35 DT DG DA DT DA DA DG DC DA DA DT DG DC SEQRES 3 C 35 DT DT DT DT DT DT DG DG DC SEQRES 1 D 15 DG DG DC DC DA DA DA DA DA DA DG DC DA SEQRES 2 D 15 DT DT SEQRES 1 E 20 DG DC DT DT DA DT DC DA DA DT DT DT DG SEQRES 2 E 20 DT DA DG DC DA DC DC SEQRES 1 A 99 MET ALA LEU THR LYS ALA GLU MET SER GLU TYR LEU PHE SEQRES 2 A 99 ASP LYS LEU GLY LEU SER LYS ARG ASP ALA LYS GLU LEU SEQRES 3 A 99 VAL GLU LEU PHE PHE GLU GLU ILE ARG ARG ALA LEU GLU SEQRES 4 A 99 ASN GLY GLU GLN VAL LYS LEU SER GLY PHE GLY ASN PHE SEQRES 5 A 99 ASP LEU ARG ASP LYS ASN GLN ARG PRO GLY ARG ASN PRO SEQRES 6 A 99 LYS THR GLY GLU ASP ILE PRO ILE THR ALA ARG ARG VAL SEQRES 7 A 99 VAL THR PHE ARG PRO GLY GLN LYS LEU LYS SER ARG VAL SEQRES 8 A 99 GLU ASN ALA SER PRO LYS ASP GLU SEQRES 1 B 94 MET THR LYS SER GLU LEU ILE GLU ARG LEU ALA THR GLN SEQRES 2 B 94 GLN SER HIS ILE PRO ALA LYS THR VAL GLU ASP ALA VAL SEQRES 3 B 94 LYS GLU MET LEU GLU HIS MET ALA SER THR LEU ALA GLN SEQRES 4 B 94 GLY GLU ARG ILE GLU ILE ARG GLY PHE GLY SER PHE SER SEQRES 5 B 94 LEU HIS TYR ARG ALA PRO ARG THR GLY ARG ASN PRO LYS SEQRES 6 B 94 THR GLY ASP LYS VAL GLU LEU GLU GLY LYS TYR VAL PRO SEQRES 7 B 94 HIS PHE LYS PRO GLY LYS GLU LEU ARG ASP ARG ALA ASN SEQRES 8 B 94 ILE TYR GLY FORMUL 6 HOH *83(H2 O) HELIX 1 1 THR A 4 GLY A 17 1 14 HELIX 2 2 SER A 19 ASN A 40 1 22 HELIX 3 3 GLY A 84 GLU A 92 1 9 HELIX 4 4 THR B 2 GLN B 14 1 13 HELIX 5 5 PRO B 18 GLN B 39 1 22 HELIX 6 6 GLY B 83 ASN B 91 1 9 SHEET 1 A 3 VAL A 44 LEU A 46 0 SHEET 2 A 3 GLY A 50 LYS A 57 -1 O PHE A 52 N VAL A 44 SHEET 3 A 3 ARG A 76 PRO A 83 -1 O THR A 80 N ASP A 53 SHEET 1 B 2 ARG A 60 ARG A 63 0 SHEET 2 B 2 ASP A 70 ILE A 73 -1 O ILE A 73 N ARG A 60 SHEET 1 C 3 ILE B 43 ILE B 45 0 SHEET 2 C 3 GLY B 49 ARG B 56 -1 O PHE B 51 N ILE B 43 SHEET 3 C 3 LYS B 75 PRO B 82 -1 O LYS B 75 N ARG B 56 SHEET 1 D 2 ARG B 59 ARG B 62 0 SHEET 2 D 2 LYS B 69 LEU B 72 -1 O VAL B 70 N GLY B 61 CRYST1 46.660 58.832 181.314 90.00 90.00 90.00 P 21 21 21 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 0.021432 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016998 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005515 0.00000