HEADER TRANSCRIPTION REGULATOR/DNA 27-JUN-12 4FTH TITLE CRYSTAL STRUCTURE OF NTRC4 DNA-BINDING DOMAIN BOUND TO DOUBLE-STRANDED TITLE 2 DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR (NTRC FAMILY); COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 374-442); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*AP*CP*TP*TP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*AP*AP*AP*TP COMPND 8 *GP*CP*AP*T)-3'; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: LPXC UPSTREAM DNA-BINDING SITE, FORWARD STRAND; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(P*GP*AP*TP*GP*CP*AP*TP*TP*TP*GP*CP*AP*AP*AP*TP*TP*TP*G COMPND 14 P*CP*AP*A)-3'; COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: LPXC UPSTREAM DNA-BINDING SITE, REVERSE STRAND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 GENE: AQ_164, NTRC4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: ROSETTA.PLYSS; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS SIGMA-54, TRANSCRIPTIONAL ACTIVATOR, DNA-BINDING DOMAIN, NTRC, FIS, KEYWDS 2 HELIX-TURN-HELIX, DNA-BINDING, TRANSCRIPTION REGULATOR-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.K.VIDANGOS,J.HEIDEKER,A.Y.LYUBIMOV,M.LAMERS,Y.HUO,J.G.PELTON,J.TON, AUTHOR 2 J.D.GRALLA,J.KURIYAN,J.M.BERGER,D.E.WEMMER REVDAT 4 13-SEP-23 4FTH 1 REMARK REVDAT 3 12-NOV-14 4FTH 1 JRNL REVDAT 2 08-OCT-14 4FTH 1 JRNL REVDAT 1 29-AUG-12 4FTH 0 JRNL AUTH N.K.VIDANGOS,J.HEIDEKER,A.LYUBIMOV,M.LAMERS,Y.HUO, JRNL AUTH 2 J.G.PELTON,J.TON,J.GRALLA,J.BERGER,D.E.WEMMER JRNL TITL DNA RECOGNITION BY A SIGMA (54) TRANSCRIPTIONAL ACTIVATOR JRNL TITL 2 FROM AQUIFEX AEOLICUS. JRNL REF J.MOL.BIOL. V. 426 3553 2014 JRNL REFN ISSN 0022-2836 JRNL PMID 25158097 JRNL DOI 10.1016/J.JMB.2014.08.009 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.2_432) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 5777 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.690 REMARK 3 FREE R VALUE TEST SET COUNT : 560 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 48.1139 - 4.7677 0.99 1381 166 0.2219 0.2493 REMARK 3 2 4.7677 - 3.7848 1.00 1370 138 0.2322 0.2630 REMARK 3 3 3.7848 - 3.3065 0.98 1319 139 0.2666 0.2624 REMARK 3 4 3.3065 - 3.0042 0.85 1147 117 0.3251 0.3605 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.89 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 64.07 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.500 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.230 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) : -32.57540 REMARK 3 B22 (A**2) : 17.60150 REMARK 3 B33 (A**2) : 14.97390 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.65430 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 : 0.004 2082 REMARK 3 ANGLE : 0.802 2968 REMARK 3 CHIRALITY : 0.043 332 REMARK 3 PLANARITY : 0.003 223 REMARK 3 DIHEDRAL : 24.252 872 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 4FTH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073335. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : KHOZU DOUBLE FLAT CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5777 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.06300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 15.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3E7L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 MM NA-CACODYLATE PH 6.0, 140 MM REMARK 280 SPERMIDINE, 50 MM POTASSIUM THIOCYANATE, AND 15% (POLY)ETHYLENE REMARK 280 GLYCOL MW 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 14.39900 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SER A 79 REMARK 465 LEU B 11 REMARK 465 LYS B 12 REMARK 465 GLU B 13 REMARK 465 LYS B 14 REMARK 465 SER B 15 REMARK 465 TRP B 16 REMARK 465 SER B 78 REMARK 465 SER B 79 REMARK 465 DA C 0 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 LYS A 14 CG CD CE NZ REMARK 470 ARG B 17 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 DC C 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA C 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 19 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 21 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA D 6 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DA D 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT D 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3E7L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SIGMA-54 ACTIVATOR NTRC4'S DNA BINDING DOMAIN DBREF 4FTH A 11 79 UNP O66551 O66551_AQUAE 374 442 DBREF 4FTH B 11 79 UNP O66551 O66551_AQUAE 374 442 DBREF 4FTH C 0 21 PDB 4FTH 4FTH 0 21 DBREF 4FTH D 1 21 PDB 4FTH 4FTH 1 21 SEQRES 1 A 69 LEU LYS GLU LYS SER TRP ARG ASP LEU SER TYR LEU LEU SEQRES 2 A 69 LYS ILE LYS GLU LEU LYS GLU ALA LYS LYS GLU PHE GLU SEQRES 3 A 69 LYS ILE PHE ILE GLU GLU LYS LEU ARG GLU TYR ASP TYR SEQRES 4 A 69 ASP LEU LYS ARG THR ALA GLU GLU ILE GLY ILE ASP LEU SEQRES 5 A 69 SER ASN LEU TYR ARG LYS ILE LYS SER LEU ASN ILE ARG SEQRES 6 A 69 VAL LYS SER SER SEQRES 1 B 69 LEU LYS GLU LYS SER TRP ARG ASP LEU SER TYR LEU LEU SEQRES 2 B 69 LYS ILE LYS GLU LEU LYS GLU ALA LYS LYS GLU PHE GLU SEQRES 3 B 69 LYS ILE PHE ILE GLU GLU LYS LEU ARG GLU TYR ASP TYR SEQRES 4 B 69 ASP LEU LYS ARG THR ALA GLU GLU ILE GLY ILE ASP LEU SEQRES 5 B 69 SER ASN LEU TYR ARG LYS ILE LYS SER LEU ASN ILE ARG SEQRES 6 B 69 VAL LYS SER SER SEQRES 1 C 22 DA DC DT DT DG DC DA DA DA DT DT DT DG SEQRES 2 C 22 DC DA DA DA DT DG DC DA DT SEQRES 1 D 21 DG DA DT DG DC DA DT DT DT DG DC DA DA SEQRES 2 D 21 DA DT DT DT DG DC DA DA FORMUL 5 HOH *(H2 O) HELIX 1 1 GLU A 27 TYR A 47 1 21 HELIX 2 2 ASP A 50 ILE A 58 1 9 HELIX 3 3 ASP A 61 LEU A 72 1 12 HELIX 4 4 GLU B 27 TYR B 47 1 21 HELIX 5 5 ASP B 50 ILE B 58 1 9 HELIX 6 6 ASP B 61 ASN B 73 1 13 CRYST1 67.436 28.798 74.931 90.00 94.55 90.00 P 1 21 1 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 0.014829 0.000000 0.001179 0.00000 SCALE2 0.000000 0.034725 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013388 0.00000