HEADER DNA 17-NOV-15 5ET9 TITLE RACEMIC CRYSTAL STRUCTURES OF PRIBNOW BOX CONSENSUS PROMOTER SEQUENCE TITLE 2 (P21/N) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PRIBNOW BOX TEMPLATE STRAND CONTAINING CONSENSUS COMPND 6 SEQUENCE TATAAT; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PRIBNOW BOX NON-TEMPLATE STRAND; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: PRIBNOW BOX CONSENSUS SEQUENCE TATAAT; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630 KEYWDS RACEMIC DNA CRYSTALLOGRAPHY, PRIBNOW BOX, BACTERIAL PROMOTER, B-DNA, KEYWDS 2 DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,S.C.SRIVASTAVA,I.HUC REVDAT 2 20-JUL-16 5ET9 1 JRNL REVDAT 1 18-MAY-16 5ET9 0 JRNL AUTH P.K.MANDAL,G.W.COLLIE,S.C.SRIVASTAVA,B.KAUFFMANN,I.HUC JRNL TITL STRUCTURE ELUCIDATION OF THE PRIBNOW BOX CONSENSUS PROMOTER JRNL TITL 2 SEQUENCE BY RACEMIC DNA CRYSTALLOGRAPHY. JRNL REF NUCLEIC ACIDS RES. V. 44 5936 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27137886 JRNL DOI 10.1093/NAR/GKW367 REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 10599 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.299 REMARK 3 R VALUE (WORKING SET) : 0.298 REMARK 3 FREE R VALUE : 0.329 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.690 REMARK 3 FREE R VALUE TEST SET COUNT : 497 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 34.1499 - 2.9048 0.94 2572 131 0.2432 0.2561 REMARK 3 2 2.9048 - 2.3057 0.97 2648 121 0.3971 0.5040 REMARK 3 3 2.3057 - 2.0143 0.97 2664 134 0.4292 0.5028 REMARK 3 4 2.0143 - 1.8302 0.80 2218 111 0.4781 0.5355 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.780 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 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 : 0.010 544 REMARK 3 ANGLE : 1.073 836 REMARK 3 CHIRALITY : 0.047 94 REMARK 3 PLANARITY : 0.010 24 REMARK 3 DIHEDRAL : 32.821 232 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.9236 85.2181 7.7445 REMARK 3 T TENSOR REMARK 3 T11: 0.5211 T22: 0.4054 REMARK 3 T33: 0.5376 T12: 0.0140 REMARK 3 T13: 0.0419 T23: -0.0884 REMARK 3 L TENSOR REMARK 3 L11: -1.6789 L22: 1.6922 REMARK 3 L33: -0.2052 L12: -0.3111 REMARK 3 L13: -1.2938 L23: 1.4430 REMARK 3 S TENSOR REMARK 3 S11: 0.1657 S12: 0.3031 S13: 0.1281 REMARK 3 S21: 0.4432 S22: 0.0453 S23: 0.0595 REMARK 3 S31: 0.1596 S32: -0.0831 S33: 0.0724 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.9119 85.4929 9.4029 REMARK 3 T TENSOR REMARK 3 T11: 0.5267 T22: 0.3881 REMARK 3 T33: 0.5053 T12: 0.0031 REMARK 3 T13: -0.0194 T23: -0.0840 REMARK 3 L TENSOR REMARK 3 L11: -1.5112 L22: 2.0228 REMARK 3 L33: -0.3615 L12: 0.4054 REMARK 3 L13: 1.1867 L23: 1.1536 REMARK 3 S TENSOR REMARK 3 S11: 0.1986 S12: -0.2420 S13: -0.0355 REMARK 3 S21: -0.4137 S22: -0.0589 S23: -0.0929 REMARK 3 S31: -0.1077 S32: -0.0791 S33: 0.0354 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 5ET9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10610 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 34.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.01600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.870 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 ID: 1FQ2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DNA CONTAINING D- AND L- SUGARS REMARK 280 (RACEMIC MIXTURE), SODIUM CACODYLATE, BARIUM CHLORIDE, POTASSIUM REMARK 280 CHLORIDE, SPERMINE TETRACHLORIDE, MPD, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21/n 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 3555 -X,-Y,-Z REMARK 290 4555 X+1/2,-Y+1/2,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 14.37807 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 34.14400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 17.10649 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.37807 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.14400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.10649 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: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 A 10 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA A 101 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 3 OP2 REMARK 620 2 HOH A 201 O 78.8 REMARK 620 3 DG A 10 O6 57.9 97.2 REMARK 620 4 HOH A 205 O 77.8 88.4 132.8 REMARK 620 5 HOH A 206 O 81.9 55.4 52.0 141.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 101 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 10 O6 REMARK 620 2 HOH B 205 O 109.3 REMARK 620 3 HOH B 206 O 67.3 143.0 REMARK 620 4 DC B 3 OP2 52.5 133.7 75.5 REMARK 620 5 HOH B 201 O 65.2 91.0 53.2 110.6 REMARK 620 N 1 2 3 4 DBREF 5ET9 A 1 12 PDB 5ET9 5ET9 1 12 DBREF 5ET9 B 1 12 PDB 5ET9 5ET9 1 12 SEQRES 1 A 12 DC DG DC DT DA DT DA DA DT DG DC DG SEQRES 1 B 12 DC DG DC DA DT DT DA DT DA DG DC DG HET BA A 101 1 HET BA B 101 1 HETNAM BA BARIUM ION FORMUL 3 BA 2(BA 2+) FORMUL 5 HOH *13(H2 O) LINK OP2 DC A 3 BA BA A 101 1555 1555 3.06 LINK O6 DG B 10 BA BA B 101 1555 1555 3.03 LINK BA BA A 101 O HOH A 201 1555 1555 2.91 LINK BA BA B 101 O HOH B 205 1555 1555 2.94 LINK BA BA B 101 O HOH B 206 1555 1555 2.57 LINK O6 DG A 10 BA BA A 101 1555 4575 2.96 LINK OP2 DC B 3 BA BA B 101 1555 4475 3.03 LINK BA BA A 101 O HOH A 205 1555 4474 3.02 LINK BA BA A 101 O HOH A 206 1555 4474 2.58 LINK BA BA B 101 O HOH B 201 1555 4574 3.02 CRYST1 28.786 68.288 34.213 90.00 90.05 90.00 P 1 21/n 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 0.034739 0.000000 0.000030 0.00000 SCALE2 0.000000 0.014644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029229 0.00000 MASTER 270 0 2 0 0 0 0 6 0 0 0 2 END