HEADER DNA 01-DEC-15 5F26 TITLE CRYSTAL STRUCTURES OF PRIBNOW BOX CONSENSUS PROMOTER SEQUENCE (P63) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRIBNOW BOX CONSENSUS SEQUENCE STRAND; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: COMPLEMENTARY STRAND; COMPND 7 CHAIN: B; COMPND 8 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 4 10-JAN-24 5F26 1 REMARK REVDAT 3 29-NOV-17 5F26 1 REMARK REVDAT 2 20-JUL-16 5F26 1 JRNL REVDAT 1 18-MAY-16 5F26 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 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC REMARK 1 TITL RACEMIC DNA CRYSTALLOGRAPHY REMARK 1 REF ANGEW. CHEM. INT. ED. V. 53 14424 2014 REMARK 1 REFN ESSN 1521-3773 REMARK 1 PMID 25358289 REMARK 1 DOI 10.1002/ANIE.201409014 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 1857 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.289 REMARK 3 R VALUE (WORKING SET) : 0.289 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.360 REMARK 3 FREE R VALUE TEST SET COUNT : 192 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 36.0771 - 3.0004 0.97 3393 192 0.2885 0.2983 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.130 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 : 0.005 501 REMARK 3 ANGLE : 0.720 769 REMARK 3 CHIRALITY : 0.032 87 REMARK 3 PLANARITY : 0.003 22 REMARK 3 DIHEDRAL : 31.817 213 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.7433 11.8404 -9.2497 REMARK 3 T TENSOR REMARK 3 T11: 0.1094 T22: 0.2391 REMARK 3 T33: 0.3577 T12: 0.0107 REMARK 3 T13: -0.1995 T23: 0.1979 REMARK 3 L TENSOR REMARK 3 L11: 0.0408 L22: 0.0006 REMARK 3 L33: 0.1601 L12: -0.0167 REMARK 3 L13: 0.0243 L23: -0.0169 REMARK 3 S TENSOR REMARK 3 S11: -0.0445 S12: 0.0892 S13: -0.0558 REMARK 3 S21: -0.1964 S22: 0.0440 S23: 0.1199 REMARK 3 S31: -0.2328 S32: 0.1035 S33: -0.0075 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.4990 11.5527 11.8286 REMARK 3 T TENSOR REMARK 3 T11: -0.4448 T22: 0.2118 REMARK 3 T33: -1.0746 T12: 0.1252 REMARK 3 T13: 0.2422 T23: -0.4833 REMARK 3 L TENSOR REMARK 3 L11: 0.0301 L22: -0.0179 REMARK 3 L33: 0.0564 L12: -0.0078 REMARK 3 L13: -0.0312 L23: 0.0232 REMARK 3 S TENSOR REMARK 3 S11: -0.1607 S12: 0.1552 S13: 0.0762 REMARK 3 S21: 0.1266 S22: -0.0795 S23: -0.2092 REMARK 3 S31: -0.1000 S32: 0.0179 S33: -0.2332 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 14 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.1027 12.1804 9.6783 REMARK 3 T TENSOR REMARK 3 T11: 0.1599 T22: -0.1977 REMARK 3 T33: -0.2038 T12: -0.2500 REMARK 3 T13: 0.4539 T23: 0.5827 REMARK 3 L TENSOR REMARK 3 L11: 0.0855 L22: 0.0006 REMARK 3 L33: 0.0757 L12: 0.0090 REMARK 3 L13: -0.0443 L23: -0.0343 REMARK 3 S TENSOR REMARK 3 S11: -0.1775 S12: -0.0343 S13: -0.0061 REMARK 3 S21: 0.0459 S22: -0.1661 S23: 0.0190 REMARK 3 S31: 0.0003 S32: 0.0383 S33: -0.2320 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 19 THROUGH 23 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.4251 8.9415 -3.8547 REMARK 3 T TENSOR REMARK 3 T11: 0.3714 T22: 0.5879 REMARK 3 T33: 0.3580 T12: -0.4710 REMARK 3 T13: 0.2909 T23: 0.0562 REMARK 3 L TENSOR REMARK 3 L11: 0.1530 L22: 0.0992 REMARK 3 L33: 0.0787 L12: -0.1158 REMARK 3 L13: 0.0929 L23: -0.0386 REMARK 3 S TENSOR REMARK 3 S11: -0.1512 S12: -0.0536 S13: -0.1690 REMARK 3 S21: -0.0379 S22: -0.1513 S23: -0.2263 REMARK 3 S31: 0.0144 S32: -0.0564 S33: -0.0409 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 5F26 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000215838. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2101 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 1.930 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.97 REMARK 200 R MERGE FOR SHELL (I) : 0.15700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.780 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: 463D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DNA, SODIUM CACODYLATE, BARIUM REMARK 280 CHLORIDE, POTASSIUM CHLORIDE, SPERMINE TETRAHYDROCHLORIDE, 2- REMARK 280 METHYL-2,4-PENTANEDIOL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.83950 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.83950 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.83950 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: 940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 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 DC B 13 REMARK 465 DG B 24 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ET9 RELATED DB: PDB REMARK 900 5ET9, 5EWB, 5EYQ, 5EZF CONTAINS RACEMIC CRYSTAL STRUCTURES OF THE REMARK 900 PRIBNOW BOX CONSENSUS SEQUENCE REMARK 900 RELATED ID: 5EWB RELATED DB: PDB REMARK 900 5ET9, 5EWB, 5EYQ, 5EZF CONTAINS RACEMIC CRYSTAL STRUCTURES OF THE REMARK 900 PRIBNOW BOX CONSENSUS SEQUENCE REMARK 900 RELATED ID: 5EYQ RELATED DB: PDB REMARK 900 5ET9, 5EWB, 5EYQ, 5EZF CONTAINS RACEMIC CRYSTAL STRUCTURES OF THE REMARK 900 PRIBNOW BOX CONSENSUS SEQUENCE REMARK 900 RELATED ID: 5EZF RELATED DB: PDB REMARK 900 5ET9, 5EWB, 5EYQ, 5EZF CONTAINS RACEMIC CRYSTAL STRUCTURES OF THE REMARK 900 PRIBNOW BOX CONSENSUS SEQUENCE DBREF 5F26 A 1 12 PDB 5F26 5F26 1 12 DBREF 5F26 B 13 24 PDB 5F26 5F26 13 24 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 FORMUL 3 HOH *5(H2 O) CRYST1 49.232 49.232 67.679 90.00 90.00 120.00 P 63 6 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 0.020312 0.011727 0.000000 0.00000 SCALE2 0.000000 0.023454 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014776 0.00000