HEADER GENE REGULATION, STRUCTURAL PROTEIN/DNA 18-JAN-13 4ITQ TITLE CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN SCO1480 BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN SCO1480; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SIHF; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(P*CP*CP*GP*CP*GP*CP*GP*C)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(P*GP*CP*GP*CP*GP*CP*GP*G)-3'; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR; SOURCE 3 ORGANISM_TAXID: 100226; SOURCE 4 STRAIN: A3(2); SOURCE 5 GENE: SCO1480; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834(DE3) PRARE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, H2TH MOTIF, NUCLEOID-ASSOCIATED PROTEIN, GENE KEYWDS 2 REGULATION, STRUCTURAL PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.GUARNE,T.NANJI,M.GLOYD,J.P.SWIERCZ,M.A.ELLIOT REVDAT 2 22-MAY-13 4ITQ 1 JRNL REVDAT 1 27-MAR-13 4ITQ 0 JRNL AUTH J.P.SWIERCZ,T.NANJI,M.GLOYD,A.GUARNE,M.A.ELLIOT JRNL TITL A NOVEL NUCLEOID-ASSOCIATED PROTEIN SPECIFIC TO THE JRNL TITL 2 ACTINOBACTERIA. JRNL REF NUCLEIC ACIDS RES. V. 41 4171 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23427309 JRNL DOI 10.1093/NAR/GKT095 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 4613 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.267 REMARK 3 R VALUE (WORKING SET) : 0.262 REMARK 3 FREE R VALUE : 0.315 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.690 REMARK 3 FREE R VALUE TEST SET COUNT : 447 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.4404 - 3.8922 1.00 1455 157 0.2501 0.2903 REMARK 3 2 3.8922 - 3.0904 0.99 1362 149 0.2428 0.3276 REMARK 3 3 3.0904 - 2.7001 0.98 1349 141 0.3679 0.4179 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.27 REMARK 3 B_SOL : 29.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.560 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 29.98190 REMARK 3 B22 (A**2) : -13.18650 REMARK 3 B33 (A**2) : -18.39950 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 1042 REMARK 3 ANGLE : 0.789 1464 REMARK 3 CHIRALITY : 0.038 168 REMARK 3 PLANARITY : 0.001 136 REMARK 3 DIHEDRAL : 22.447 421 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ITQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-13. REMARK 100 THE RCSB ID CODE IS RCSB077197. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DOUBLE SILICON(111) CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000 REMARK 200 DATA SCALING SOFTWARE : HKL2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5202 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.53900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX.AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG 3350, 210 MM KSCN, 5% ETHYLENE REMARK 280 GLYCOL, 100 MM HEPES PH 7.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 51.46250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.46250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 21.71000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.89100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.71000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.89100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.46250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.71000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.89100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.46250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.71000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.89100 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 PRO A 4 REMARK 465 PRO A 5 REMARK 465 LEU A 6 REMARK 465 THR A 7 REMARK 465 PRO A 8 REMARK 465 GLU A 9 REMARK 465 GLN A 10 REMARK 465 ARG A 11 REMARK 465 ALA A 12 REMARK 465 ALA A 13 REMARK 465 SER A 104 REMARK 465 THR A 105 REMARK 465 GLY A 106 REMARK 465 SER A 107 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 15 CG CD1 CD2 REMARK 470 LYS A 17 CG CD CE NZ REMARK 470 ARG A 23 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 30 CG OD1 ND2 REMARK 470 HIS A 40 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 99 CG CD OE1 OE2 REMARK 470 ARG A 100 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG C 1 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG C 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE ORIGINAL SEQUENCE OF THE DNA DUPLEX INCLUDED IN THE REMARK 999 CRYSTALLIZATION DROPS IS: 5' GAGGGAGTGCGTGGGTCTGA 3'/5' REMARK 999 CTCAGACCCACGCACTCCCT 3'. THE DUPLEX WAS PARTLY DISORDERED IN THE REMARK 999 CRYSTAL STRUCTURE (PROBABLY BECAUSE THE PROTEIN BINDS DNA REMARK 999 UNSPECIFICALLY AND COULD BIND ALL ALONG THE DUPLEX). AS A RESULT REMARK 999 ONLY 8 BP ARE VISIBLE IN THE ASYMMETRIC UNIT. THE DENSITY COULD NOT REMARK 999 BE ASSIGNED TO ANY PARTICULAR SEQUENCE OF THE 19 BP DUPLEX AND REMARK 999 HENCE THE ELECTRON DENSITY WAS MODELED BASED ON THE RELATIVE SIZE REMARK 999 OF THE NUCLEOTIDE MOIETY (USING GUANOSINE FOR "PURINE-LIKE" REMARK 999 DENSITIES AND CYTOSINE FOR "PYRIMIDINE-LIKE" DENSITIES). DBREF 4ITQ A 1 107 UNP Q9KXR9 Q9KXR9_STRCO 1 107 DBREF 4ITQ B 1 8 PDB 4ITQ 4ITQ 1 8 DBREF 4ITQ C 1 8 PDB 4ITQ 4ITQ 1 8 SEQRES 1 A 107 MSE ALA LEU PRO PRO LEU THR PRO GLU GLN ARG ALA ALA SEQRES 2 A 107 ALA LEU GLU LYS ALA ALA ALA ALA ARG ARG GLU ARG ALA SEQRES 3 A 107 GLU VAL LYS ASN ARG LEU LYS HIS SER GLY ALA SER LEU SEQRES 4 A 107 HIS GLU VAL ILE LYS GLN GLY GLN GLU ASN ASP VAL ILE SEQRES 5 A 107 GLY LYS MSE LYS VAL SER ALA LEU LEU GLU SER LEU PRO SEQRES 6 A 107 GLY VAL GLY LYS VAL ARG ALA LYS GLN ILE MSE GLU ARG SEQRES 7 A 107 LEU GLY ILE SER GLU SER ARG ARG VAL ARG GLY LEU GLY SEQRES 8 A 107 SER ASN GLN ILE ALA SER LEU GLU ARG GLU PHE GLY SER SEQRES 9 A 107 THR GLY SER SEQRES 1 B 8 DC DC DG DC DG DC DG DC SEQRES 1 C 8 DG DC DG DC DG DC DG DG MODRES 4ITQ MSE A 55 MET SELENOMETHIONINE MODRES 4ITQ MSE A 76 MET SELENOMETHIONINE HET MSE A 55 8 HET MSE A 76 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 4 HOH *6(H2 O) HELIX 1 1 ALA A 14 HIS A 34 1 21 HELIX 2 2 SER A 38 GLN A 47 1 10 HELIX 3 3 ASN A 49 LYS A 54 1 6 HELIX 4 4 LYS A 56 SER A 63 1 8 HELIX 5 5 GLY A 68 GLY A 80 1 13 HELIX 6 6 GLY A 91 PHE A 102 1 12 LINK C LYS A 54 N MSE A 55 1555 1555 1.33 LINK C MSE A 55 N LYS A 56 1555 1555 1.33 LINK C ILE A 75 N MSE A 76 1555 1555 1.33 LINK C MSE A 76 N GLU A 77 1555 1555 1.33 CISPEP 1 PHE A 102 GLY A 103 0 -0.84 CRYST1 43.420 71.782 102.925 90.00 90.00 90.00 C 2 2 21 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 0.023031 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009716 0.00000