HEADER DNA-BINDING/REGULATORY PROTEIN 05-APR-05 2BNW TITLE STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX OMEGA TITLE 2 REPRESSOR TO DIRECT DNA HEPTAD REPEATS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORF OMEGA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RIBBON-HELIX-HELIX DOMAIN, RESIDUES 20-71; COMPND 5 SYNONYM: OMEGA TRANSCRIPTIONAL REPRESSOR, ORF OMEGA'; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP COMPND 9 *TP*CP*AP*CP*AP*AP*GP*C)-3'; COMPND 10 CHAIN: E, G; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: SEQUENCE\: 5'- GAA TCA CAA ATC ACA AGC -3', 18MER DNA COMPND 13 OLIGONUCLEOTIDE, FIRST STRAND, DIRECT DNA HEPTAD REPEATS (5'-AATCACA COMPND 14 -3'); COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: 5'-D(*CP*TP*TP*GP*TP*GP*AP*TP*TP*TP COMPND 17 *GP*TP*GP*AP*TP*TP*CP*G)-3'; COMPND 18 CHAIN: F, H; COMPND 19 ENGINEERED: YES; COMPND 20 OTHER_DETAILS: SEQUENCE\: 5'- CTT GTG ATT TGT GAT TCG -3', 18MER DNA COMPND 21 OLIGONUCLEOTIDE, SECOND STRAND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_COMMON: STREPTOCOCCUS; SOURCE 4 ORGANISM_TAXID: 1314; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A-DELTA19OMEGA; SOURCE 10 OTHER_DETAILS: OMEGA TRANSCRIPTIONAL REPRESSOR IS ENCODED BY PLASMID SOURCE 11 PSM19035 OF THE INC18 FAMILY OF PLASMIDS; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 OTHER_DETAILS: DIRECT DNA HEPTAD REPEATS OCCUR IN PROMOTERS SOURCE 17 PRECEEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL EPRESSOR, INC18 SOURCE 18 FAMILY OF PLASMIDS; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630; SOURCE 23 OTHER_DETAILS: DIRECT DNA HEPTAD REPEATS OCCUR IN PROMOTERS SOURCE 24 PRECEEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL EPRESSOR, INC18 SOURCE 25 FAMILY OF PLASMIDS KEYWDS DNA-BINDING-REGULATORY PROTEIN COMPLEX, RIBBON-HELIX-HELIX, RHH, KEYWDS 2 METJ/ARC SUPERFAMILY, COOPERATIVE DNA BINDING, INVERTED REPEATS, DNA KEYWDS 3 HEPTAD, INC18 FAMILY, DNA-BINDING REGULATORY PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.A.WEIHOFEN,A.CICEK,F.PRATTO,J.C.ALONSO,W.SAENGER REVDAT 4 29-JUL-20 2BNW 1 SOURCE REVDAT 3 13-JUL-11 2BNW 1 VERSN REVDAT 2 24-FEB-09 2BNW 1 VERSN REVDAT 1 15-MAR-06 2BNW 0 JRNL AUTH W.A.WEIHOFEN,A.CICEK,F.PRATTO,J.C.ALONSO,W.SAENGER JRNL TITL STRUCTURES OF OMEGA REPRESSORS BOUND TO DIRECT AND INVERTED JRNL TITL 2 DNA REPEATS EXPLAIN MODULATION OF TRANSCRIPTION. JRNL REF NUCLEIC ACIDS RES. V. 34 1450 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 16528102 JRNL DOI 10.1093/NAR/GKL015 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 24191 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 + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1044 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1416 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1634 REMARK 3 NUCLEIC ACID ATOMS : 1440 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.88000 REMARK 3 B22 (A**2) : 1.44000 REMARK 3 B33 (A**2) : -3.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.10000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.296 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.236 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.188 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3262 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2285 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4686 ; 1.385 ; 2.520 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5449 ; 0.798 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 198 ; 5.761 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;32.310 ;24.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 355 ;17.072 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;21.229 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 529 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2482 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 290 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 664 ; 0.214 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2576 ; 0.203 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1404 ; 0.211 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 1428 ; 0.091 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 215 ; 0.203 ; 0.400 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 29 ; 0.181 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 49 ; 0.188 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.264 ; 0.400 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1305 ; 0.585 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1617 ; 0.663 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3011 ; 0.882 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3069 ; 1.426 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 24 A 50 REMARK 3 RESIDUE RANGE : B 24 B 50 REMARK 3 ORIGIN FOR THE GROUP (A): 53.2231 31.5073 11.6711 REMARK 3 T TENSOR REMARK 3 T11: -0.0396 T22: -0.1254 REMARK 3 T33: -0.1228 T12: 0.0408 REMARK 3 T13: 0.0035 T23: 0.0281 REMARK 3 L TENSOR REMARK 3 L11: 1.9682 L22: 0.9489 REMARK 3 L33: 1.8611 L12: 0.0562 REMARK 3 L13: -1.2346 L23: 0.3063 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: 0.1302 S13: -0.0071 REMARK 3 S21: 0.0846 S22: 0.1002 S23: -0.0480 REMARK 3 S31: -0.0327 S32: 0.0025 S33: -0.0811 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 51 A 67 REMARK 3 RESIDUE RANGE : B 51 B 67 REMARK 3 ORIGIN FOR THE GROUP (A): 51.0294 38.0868 8.1859 REMARK 3 T TENSOR REMARK 3 T11: -0.0639 T22: -0.0932 REMARK 3 T33: -0.1298 T12: 0.0036 REMARK 3 T13: -0.0009 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 3.4430 L22: 2.3854 REMARK 3 L33: 2.0260 L12: -1.0444 REMARK 3 L13: -2.0659 L23: -0.6488 REMARK 3 S TENSOR REMARK 3 S11: -0.1297 S12: 0.0703 S13: 0.1951 REMARK 3 S21: 0.0243 S22: 0.2731 S23: 0.0488 REMARK 3 S31: -0.0383 S32: -0.0639 S33: -0.1434 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 24 C 50 REMARK 3 RESIDUE RANGE : D 24 D 50 REMARK 3 ORIGIN FOR THE GROUP (A): 32.4287 16.7063 27.4890 REMARK 3 T TENSOR REMARK 3 T11: -0.0228 T22: -0.0648 REMARK 3 T33: -0.1370 T12: 0.0382 REMARK 3 T13: -0.0040 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.9294 L22: 3.1046 REMARK 3 L33: 1.6052 L12: 0.8157 REMARK 3 L13: -0.2321 L23: -0.4522 REMARK 3 S TENSOR REMARK 3 S11: 0.0960 S12: 0.0663 S13: 0.0392 REMARK 3 S21: -0.0253 S22: 0.0300 S23: 0.1864 REMARK 3 S31: 0.0529 S32: -0.1613 S33: -0.1260 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 51 C 67 REMARK 3 RESIDUE RANGE : D 51 D 67 REMARK 3 ORIGIN FOR THE GROUP (A): 30.7914 19.0140 34.8059 REMARK 3 T TENSOR REMARK 3 T11: -0.0209 T22: -0.0776 REMARK 3 T33: -0.1091 T12: 0.0354 REMARK 3 T13: 0.0022 T23: 0.0290 REMARK 3 L TENSOR REMARK 3 L11: 2.2355 L22: 3.3617 REMARK 3 L33: 1.9818 L12: 1.3970 REMARK 3 L13: -0.9748 L23: 1.3592 REMARK 3 S TENSOR REMARK 3 S11: 0.0161 S12: 0.0113 S13: 0.1010 REMARK 3 S21: -0.0313 S22: 0.1142 S23: 0.0534 REMARK 3 S31: -0.0179 S32: -0.2027 S33: -0.1304 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 18 REMARK 3 ORIGIN FOR THE GROUP (A): 45.1815 17.0725 15.4878 REMARK 3 T TENSOR REMARK 3 T11: -0.0770 T22: -0.1424 REMARK 3 T33: -0.1923 T12: 0.0587 REMARK 3 T13: -0.0286 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 4.5541 L22: 2.2753 REMARK 3 L33: 1.3444 L12: 1.8683 REMARK 3 L13: -1.0265 L23: -0.5047 REMARK 3 S TENSOR REMARK 3 S11: -0.0852 S12: 0.0781 S13: -0.1776 REMARK 3 S21: -0.0831 S22: 0.0764 S23: -0.0308 REMARK 3 S31: 0.1195 S32: -0.0491 S33: 0.0089 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 19 F 36 REMARK 3 ORIGIN FOR THE GROUP (A): 45.1430 16.7234 16.9562 REMARK 3 T TENSOR REMARK 3 T11: -0.0754 T22: -0.1314 REMARK 3 T33: -0.1797 T12: 0.0502 REMARK 3 T13: -0.0379 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 4.0072 L22: 1.3698 REMARK 3 L33: 1.2503 L12: 1.2707 REMARK 3 L13: -0.4409 L23: 0.1071 REMARK 3 S TENSOR REMARK 3 S11: 0.0460 S12: 0.1273 S13: -0.1354 REMARK 3 S21: 0.0024 S22: -0.0024 S23: -0.0394 REMARK 3 S31: 0.0028 S32: -0.0682 S33: -0.0436 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : G 2 G 18 REMARK 3 RESIDUE RANGE : H 34 H 38 REMARK 3 ORIGIN FOR THE GROUP (A): 93.4962 30.0053 12.4643 REMARK 3 T TENSOR REMARK 3 T11: 0.0420 T22: 0.2421 REMARK 3 T33: 0.1624 T12: -0.0191 REMARK 3 T13: -0.0392 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 2.0497 L22: 0.0609 REMARK 3 L33: 0.0068 L12: 0.3533 REMARK 3 L13: -0.1180 L23: -0.0203 REMARK 3 S TENSOR REMARK 3 S11: -0.1329 S12: -0.1318 S13: 0.0747 REMARK 3 S21: 0.0124 S22: 0.0843 S23: -0.0766 REMARK 3 S31: -0.0328 S32: 0.1261 S33: 0.0486 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. CYTOSINES E18 AND G18 WERE ONLY MODELED FOR THE 5'- REMARK 3 PHOSPATE AND ATOM C5' REMARK 4 REMARK 4 2BNW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-APR-05. REMARK 100 THE DEPOSITION ID IS D_1290023532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83105 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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 1IRQ AND 1CMA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150 MM NA/KPO4, PH 7.0, 2.4 REMARK 280 NA2MALONATE, PH 7.5, 2% AMINOCAPROIC ACID, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 109.71300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.31550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 109.71300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.31550 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 300 REMARK: THE DESIGNATION OF THE QUATERNARY STRUCTURE REMARK 300 AS OCTAMERICREFLECTS THE STANDARD PQS CONVENTION FOR REMARK 300 DESCRIBINGHETEROGENEOUS ASSEMBLIES. HOWEVER, THE REMARK 300 CRYSTALLOGRAPHICASYMMETRIC UNIT ACTUALLY CONTAINS ONE REMARK 300 DNA FRAGMENT(COMPRISED OF CHAINS E AND F) WHICH REMARK 300 IS BOUND TO TWOPROTEIN DIMERS (CHAINS A, B, C REMARK 300 AND D). A FURTHER FREEDNA FRAGMENT (CHAINS G REMARK 300 AND H) IS PRESENT IN THE A.U.THE INTERFACE REMARK 300 BETWEEN THE TWO PROTEIN DIMERS AND DNAIS 1600 REMARK 300 ANGSTROMS**2 AND THE INTERFACE BETWEEN THETWO REMARK 300 PROTEIN DIMERS IS 280 ANSGTROMS**2. 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 19 REMARK 465 ALA A 20 REMARK 465 LYS A 21 REMARK 465 LYS A 22 REMARK 465 MET D 19 REMARK 465 ALA D 20 REMARK 465 LYS D 21 REMARK 465 LYS D 22 REMARK 465 ASP D 23 REMARK 465 ILE D 24 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 DC E 18 C4' O4' C3' O3' C2' C1' N1 REMARK 470 DC E 18 C2 O2 N3 C4 N4 C5 C6 REMARK 470 DC F 19 O5' REMARK 470 DC G 18 C4' O4' C3' O3' C2' C1' N1 REMARK 470 DC G 18 C2 O2 N3 C4 N4 C5 C6 REMARK 470 DC H 19 O5' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O THR C 44 O ASN C 47 2.00 REMARK 500 REMARK 500 REMARK: NULL 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 ASP D 69 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 DC E 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC E 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG G 1 C3' - C2' - C1' ANGL. DEV. = -6.7 DEGREES REMARK 500 DG G 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC G 5 O3' - P - O5' ANGL. DEV. = 19.7 DEGREES REMARK 500 DC G 5 O3' - P - OP2 ANGL. DEV. = -25.2 DEGREES REMARK 500 DC G 5 O3' - P - OP1 ANGL. DEV. = -26.3 DEGREES REMARK 500 DC G 5 OP1 - P - OP2 ANGL. DEV. = 22.0 DEGREES REMARK 500 DC G 5 O5' - P - OP1 ANGL. DEV. = -24.9 DEGREES REMARK 500 DC G 5 O5' - P - OP2 ANGL. DEV. = -20.8 DEGREES REMARK 500 DC G 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA G 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC G 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA G 8 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA G 8 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA G 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC H 19 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT H 26 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT H 33 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT H 34 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 LEU B 67 48.32 -141.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IRQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF OMEGA TRANSCRIPTIONAL REPRESSOR AT1.5A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 2BNZ RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REMARK 900 OMEGA REPRESSOR TO INVERTED DNA HEPTAD REPEATS REMARK 900 RELATED ID: 2CAX RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REMARK 900 REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS REMARK 999 REMARK 999 SEQUENCE REMARK 999 19 N-TERMINAL RESIDUES TRUNCATED, NEW N-TERMINAL MET19 IS REMARK 999 A CLONING ARTEFACT. DBREF 2BNW A 19 19 PDB 2BNW 2BNW 19 19 DBREF 2BNW A 20 71 UNP Q57468 Q57468_STRPY 20 71 DBREF 2BNW B 19 19 PDB 2BNW 2BNW 19 19 DBREF 2BNW B 20 71 UNP Q57468 Q57468_STRPY 20 71 DBREF 2BNW C 19 19 PDB 2BNW 2BNW 19 19 DBREF 2BNW C 20 71 UNP Q57468 Q57468_STRPY 20 71 DBREF 2BNW D 19 19 PDB 2BNW 2BNW 19 19 DBREF 2BNW D 20 71 UNP Q57468 Q57468_STRPY 20 71 DBREF 2BNW E 1 18 PDB 2BNW 2BNW 1 18 DBREF 2BNW F 19 36 PDB 2BNW 2BNW 19 36 DBREF 2BNW G 1 18 PDB 2BNW 2BNW 1 18 DBREF 2BNW H 19 36 PDB 2BNW 2BNW 19 36 SEQRES 1 A 53 MET ALA LYS LYS ASP ILE MET GLY ASP LYS THR VAL ARG SEQRES 2 A 53 VAL ARG ALA ASP LEU HIS HIS ILE ILE LYS ILE GLU THR SEQRES 3 A 53 ALA LYS ASN GLY GLY ASN VAL LYS GLU VAL MET ASP GLN SEQRES 4 A 53 ALA LEU GLU GLU TYR ILE ARG LYS TYR LEU PRO ASP LYS SEQRES 5 A 53 LEU SEQRES 1 B 53 MET ALA LYS LYS ASP ILE MET GLY ASP LYS THR VAL ARG SEQRES 2 B 53 VAL ARG ALA ASP LEU HIS HIS ILE ILE LYS ILE GLU THR SEQRES 3 B 53 ALA LYS ASN GLY GLY ASN VAL LYS GLU VAL MET ASP GLN SEQRES 4 B 53 ALA LEU GLU GLU TYR ILE ARG LYS TYR LEU PRO ASP LYS SEQRES 5 B 53 LEU SEQRES 1 C 53 MET ALA LYS LYS ASP ILE MET GLY ASP LYS THR VAL ARG SEQRES 2 C 53 VAL ARG ALA ASP LEU HIS HIS ILE ILE LYS ILE GLU THR SEQRES 3 C 53 ALA LYS ASN GLY GLY ASN VAL LYS GLU VAL MET ASP GLN SEQRES 4 C 53 ALA LEU GLU GLU TYR ILE ARG LYS TYR LEU PRO ASP LYS SEQRES 5 C 53 LEU SEQRES 1 D 53 MET ALA LYS LYS ASP ILE MET GLY ASP LYS THR VAL ARG SEQRES 2 D 53 VAL ARG ALA ASP LEU HIS HIS ILE ILE LYS ILE GLU THR SEQRES 3 D 53 ALA LYS ASN GLY GLY ASN VAL LYS GLU VAL MET ASP GLN SEQRES 4 D 53 ALA LEU GLU GLU TYR ILE ARG LYS TYR LEU PRO ASP LYS SEQRES 5 D 53 LEU SEQRES 1 E 18 DG DA DA DT DC DA DC DA DA DA DT DC DA SEQRES 2 E 18 DC DA DA DG DC SEQRES 1 F 18 DC DT DT DG DT DG DA DT DT DT DG DT DG SEQRES 2 F 18 DA DT DT DC DG SEQRES 1 G 18 DG DA DA DT DC DA DC DA DA DA DT DC DA SEQRES 2 G 18 DC DA DA DG DC SEQRES 1 H 18 DC DT DT DG DT DG DA DT DT DT DG DT DG SEQRES 2 H 18 DA DT DT DC DG FORMUL 9 HOH *79(H2 O) HELIX 1 1 ALA A 34 GLY A 48 1 15 HELIX 2 2 ASN A 50 LEU A 67 1 18 HELIX 3 3 PRO A 68 LEU A 71 5 4 HELIX 4 4 MET B 19 ILE B 24 1 6 HELIX 5 5 ALA B 34 GLY B 48 1 15 HELIX 6 6 ASN B 50 LEU B 67 1 18 HELIX 7 7 PRO B 68 LEU B 71 5 4 HELIX 8 8 MET C 19 MET C 25 1 7 HELIX 9 9 ALA C 34 ASN C 47 1 14 HELIX 10 10 ASN C 50 LEU C 67 1 18 HELIX 11 11 PRO C 68 LEU C 71 5 4 HELIX 12 12 ALA D 34 ASN D 47 1 14 HELIX 13 13 ASN D 50 LEU D 67 1 18 HELIX 14 14 PRO D 68 LEU D 71 5 4 SHEET 1 AA 2 ASP A 27 ARG A 33 0 SHEET 2 AA 2 ASP B 27 ARG B 33 -1 O LYS B 28 N VAL A 32 SHEET 1 CA 2 ASP C 27 ARG C 33 0 SHEET 2 CA 2 ASP D 27 ARG D 33 -1 O LYS D 28 N VAL C 32 CRYST1 219.426 44.631 75.960 90.00 108.80 90.00 C 1 2 1 16 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 0.004557 0.000000 0.001551 0.00000 SCALE2 0.000000 0.022406 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013907 0.00000 MTRIX1 1 -0.834290 -0.480500 0.270340 109.69965 1 MTRIX2 1 -0.494290 0.434670 -0.752820 53.00224 1 MTRIX3 1 0.244220 -0.761690 -0.600150 29.66882 1 MTRIX1 2 0.915550 0.271370 0.296850 -28.76051 1 MTRIX2 2 0.329630 -0.083400 -0.940420 13.07345 1 MTRIX3 2 -0.230450 0.958850 -0.165810 11.35475 1 MTRIX1 3 -0.814810 -0.564060 -0.133910 95.15180 1 MTRIX2 3 -0.468380 0.504390 0.725400 17.72947 1 MTRIX3 3 -0.341630 0.653780 -0.675170 32.99157 1 MASTER 491 0 0 14 4 0 0 15 0 0 0 28 END