HEADER DNA BINDING PROTEIN/DNA 06-APR-05 2BNZ TITLE STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX OMEGA TITLE 2 REPRESSOR TO INVERTED 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*GP COMPND 9 *TP*GP*AP*TP*TP*AP*GP*C)-3'; COMPND 10 CHAIN: E, G; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: SEQUENCE\: 5'- GAA TCA CAA GTG ATT AGC -3', 18MER DNA COMPND 13 OLIGONUCLEOTIDE, FIRST STRAND, INVERTED DNA HEPTAD REPEATS (5'- COMPND 14 AATCAC A/T -3'), NUCLEOTIDES G5 - G16, G18 AND E18 WERE NOT MODELLED; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: 5'-D(*CP*TP*AP*AP*TP*CP*AP*CP*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'- CTA ATC ACT TGT GAT TCG -3', 18MER DNA COMPND 21 OLIGONUCLEOTIDE, SECOND STRAND, NUCLEOTIDES H19 - H31 WERE NOT COMPND 22 MODELLED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_TAXID: 1314; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A-DELTA19OMEGA; SOURCE 9 OTHER_DETAILS: OMEGA TRANSCRIPTIONAL REPRESSOR IS ENCODED BY PLASMID SOURCE 10 PSM19035 OF THE INC18 FAMILY OF PLASMIDS; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: INVERTED REPEATS OCCUR IN PROMOTER REGIONS PRECEDING SOURCE 16 GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR, PLASMID SOURCE 17 PSM19035; SOURCE 18 MOL_ID: 3; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 ORGANISM_TAXID: 32630; SOURCE 22 OTHER_DETAILS: INVERTED REPEATS OCCUR IN PROMOTER REGIONS PRECEDING SOURCE 23 GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR, PLASMID SOURCE 24 PSM19035 KEYWDS DNA BINDING PROTEIN-DNA COMPLEX, RIBBON-HELIX-HELIX, RHH, METJ/ARC KEYWDS 2 SUPERFAMILY, COOPERATIVE DNA BINDING, INC18 FAMILY EXPDTA X-RAY DIFFRACTION AUTHOR W.A.WEIHOFEN,A.CICEK,F.PRATTO,J.C.ALONSO,W.SAENGER REVDAT 5 13-DEC-23 2BNZ 1 REMARK REVDAT 4 21-OCT-15 2BNZ 1 SOURCE REMARK REVDAT 3 13-JUL-11 2BNZ 1 VERSN REVDAT 2 24-FEB-09 2BNZ 1 VERSN REVDAT 1 15-MAR-06 2BNZ 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. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 17564 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) : 0.225 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 944 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 981 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3660 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.4040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1613 REMARK 3 NUCLEIC ACID ATOMS : 927 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 45 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) : 34.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.18000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : 2.42000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.27000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.365 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.268 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.202 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.753 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2665 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2009 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3765 ; 1.044 ; 2.410 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4771 ; 0.727 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 195 ; 6.435 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;33.312 ;24.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 349 ;17.026 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.490 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 426 ; 0.051 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2208 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 287 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 616 ; 0.208 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2265 ; 0.200 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1179 ; 0.206 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 1301 ; 0.088 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 164 ; 0.209 ; 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): 10 ; 0.110 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 46 ; 0.181 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.217 ; 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): 1294 ; 0.878 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1594 ; 1.051 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2201 ; 0.554 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2171 ; 1.035 ; 3.000 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): -11.7706 -13.0601 -2.2275 REMARK 3 T TENSOR REMARK 3 T11: -0.0533 T22: -0.0834 REMARK 3 T33: 0.0287 T12: -0.0011 REMARK 3 T13: -0.0088 T23: 0.0317 REMARK 3 L TENSOR REMARK 3 L11: 2.4214 L22: 0.8484 REMARK 3 L33: 1.1087 L12: 0.0862 REMARK 3 L13: -0.4518 L23: 0.3186 REMARK 3 S TENSOR REMARK 3 S11: -0.1025 S12: -0.0442 S13: -0.0570 REMARK 3 S21: -0.0003 S22: 0.0593 S23: 0.0127 REMARK 3 S31: 0.0301 S32: 0.0366 S33: 0.0431 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): -9.4437 -19.7056 0.8256 REMARK 3 T TENSOR REMARK 3 T11: -0.0425 T22: -0.0456 REMARK 3 T33: 0.0116 T12: 0.0294 REMARK 3 T13: 0.0334 T23: 0.0129 REMARK 3 L TENSOR REMARK 3 L11: 1.4921 L22: 1.7929 REMARK 3 L33: 0.5507 L12: -0.1307 REMARK 3 L13: -0.4571 L23: -0.8153 REMARK 3 S TENSOR REMARK 3 S11: -0.1373 S12: -0.1088 S13: -0.1180 REMARK 3 S21: -0.0515 S22: 0.1765 S23: -0.0885 REMARK 3 S31: 0.2074 S32: -0.0539 S33: -0.0392 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): -32.7993 2.2285 12.2330 REMARK 3 T TENSOR REMARK 3 T11: -0.0835 T22: -0.0381 REMARK 3 T33: -0.0227 T12: 0.0402 REMARK 3 T13: -0.0122 T23: -0.0223 REMARK 3 L TENSOR REMARK 3 L11: 1.7414 L22: 3.1371 REMARK 3 L33: 1.1969 L12: -0.9244 REMARK 3 L13: 0.0054 L23: 0.6820 REMARK 3 S TENSOR REMARK 3 S11: -0.1447 S12: -0.2663 S13: -0.0144 REMARK 3 S21: 0.1131 S22: 0.0843 S23: 0.0168 REMARK 3 S31: 0.0171 S32: 0.0876 S33: 0.0604 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): -40.1214 -0.0091 11.7257 REMARK 3 T TENSOR REMARK 3 T11: -0.0928 T22: -0.0759 REMARK 3 T33: -0.0561 T12: 0.0232 REMARK 3 T13: 0.0193 T23: 0.0192 REMARK 3 L TENSOR REMARK 3 L11: 4.7769 L22: 4.2141 REMARK 3 L33: 2.3797 L12: 0.0582 REMARK 3 L13: 0.0258 L23: 2.6243 REMARK 3 S TENSOR REMARK 3 S11: -0.0378 S12: -0.1026 S13: 0.0817 REMARK 3 S21: 0.0936 S22: 0.0820 S23: 0.0793 REMARK 3 S31: 0.1904 S32: -0.0060 S33: -0.0442 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 17 REMARK 3 ORIGIN FOR THE GROUP (A): -17.5503 1.9413 4.6985 REMARK 3 T TENSOR REMARK 3 T11: -0.1130 T22: -0.0335 REMARK 3 T33: -0.0268 T12: -0.0104 REMARK 3 T13: -0.0163 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 1.6400 L22: 1.1384 REMARK 3 L33: 4.7785 L12: -1.3528 REMARK 3 L13: -2.2065 L23: 1.6186 REMARK 3 S TENSOR REMARK 3 S11: -0.0111 S12: -0.1178 S13: 0.0360 REMARK 3 S21: -0.0067 S22: 0.0572 S23: -0.1418 REMARK 3 S31: -0.1179 S32: 0.0202 S33: -0.0460 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 21 F 36 REMARK 3 ORIGIN FOR THE GROUP (A): -18.9119 2.2400 4.0972 REMARK 3 T TENSOR REMARK 3 T11: -0.0929 T22: -0.1197 REMARK 3 T33: -0.0379 T12: 0.0023 REMARK 3 T13: -0.0114 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 2.1353 L22: 1.4735 REMARK 3 L33: 4.3810 L12: -0.6071 REMARK 3 L13: -1.4997 L23: 1.6292 REMARK 3 S TENSOR REMARK 3 S11: -0.0236 S12: -0.1379 S13: 0.0798 REMARK 3 S21: -0.0230 S22: 0.0852 S23: -0.1519 REMARK 3 S31: -0.0767 S32: 0.1700 S33: -0.0616 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 17 REMARK 3 RESIDUE RANGE : H 34 H 38 REMARK 3 ORIGIN FOR THE GROUP (A): -8.0201 -8.1992 -19.3437 REMARK 3 T TENSOR REMARK 3 T11: 0.2096 T22: 0.2299 REMARK 3 T33: -0.1959 T12: -0.0690 REMARK 3 T13: 0.0574 T23: 0.0640 REMARK 3 L TENSOR REMARK 3 L11: 3.4902 L22: 1.2736 REMARK 3 L33: 6.1415 L12: -1.0287 REMARK 3 L13: -4.2756 L23: 0.3236 REMARK 3 S TENSOR REMARK 3 S11: 0.2926 S12: 0.2465 S13: 0.3769 REMARK 3 S21: -0.4101 S22: 0.0470 S23: -0.2294 REMARK 3 S31: -0.1466 S32: 0.1533 S33: -0.3396 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. NUCLEOTIDES G5-G16, G18, E18 AND H19-H31 WERE NOT REMARK 3 MODELLED DUE TO PATCHY ELECTRON DENSITY REMARK 4 REMARK 4 2BNZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-05. REMARK 100 THE DEPOSITION ID IS D_1290023538. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 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 : 18516 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 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) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2BNW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 120 MM NA/KPO4, PH 7.2, 2.2 M REMARK 280 DINATRIUMMALONATE, PH 7.5, 3 % 2-METHYL-2,4-PENTANDIOL, PH 7.50 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 21.25250 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 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. BUTIS LARGELY REMARK 300 UNOBSERVED IN ELECTRON DENSITY MAPS. 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -104.2 KCAL/MOL 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 MET B 19 REMARK 465 ALA B 20 REMARK 465 LYS B 21 REMARK 465 MET C 19 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 465 DC E 18 REMARK 465 DC G 12 REMARK 465 DA G 13 REMARK 465 DC G 14 REMARK 465 DA G 15 REMARK 465 DA G 16 REMARK 465 DT G 18 REMARK 465 DG G 19 REMARK 465 DA G 20 REMARK 465 DT G 21 REMARK 465 DT G 22 REMARK 465 DA G 23 REMARK 465 DG G 24 REMARK 465 DC G 25 REMARK 465 DC H 19 REMARK 465 DT H 20 REMARK 465 DA H 21 REMARK 465 DA H 22 REMARK 465 DT H 23 REMARK 465 DC H 24 REMARK 465 DA H 25 REMARK 465 DC H 26 REMARK 465 DT H 27 REMARK 465 DT H 28 REMARK 465 DG H 29 REMARK 465 DT H 30 REMARK 465 DG H 31 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 A 23 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 69 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC F 19 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT F 20 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT F 30 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG F 36 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG G 1 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG G 17 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT H 33 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT H 34 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC H 35 O4' - C1' - N1 ANGL. DEV. = 2.6 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 MET A 25 118.33 157.06 REMARK 500 ARG B 33 121.20 -23.68 REMARK 500 ASN B 47 -134.86 -106.35 REMARK 500 LEU B 67 50.12 -141.03 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: 2BNW RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REMARK 900 OMEGA REPRESSOR TO DIRECT 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 2BNZ A 19 19 PDB 2BNZ 2BNZ 19 19 DBREF 2BNZ A 20 71 UNP Q57468 Q57468_STRPY 20 71 DBREF 2BNZ B 19 19 PDB 2BNZ 2BNZ 19 19 DBREF 2BNZ B 20 71 UNP Q57468 Q57468_STRPY 20 71 DBREF 2BNZ C 19 19 PDB 2BNZ 2BNZ 19 19 DBREF 2BNZ C 20 71 UNP Q57468 Q57468_STRPY 20 71 DBREF 2BNZ D 19 19 PDB 2BNZ 2BNZ 19 19 DBREF 2BNZ D 20 71 UNP Q57468 Q57468_STRPY 20 71 DBREF 2BNZ E 1 18 PDB 2BNZ 2BNZ 1 18 DBREF 2BNZ F 19 36 PDB 2BNZ 2BNZ 19 36 DBREF 2BNZ G 1 18 PDB 2BNZ 2BNZ 1 18 DBREF 2BNZ H 19 36 PDB 2BNZ 2BNZ 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 DG DT DG DA SEQRES 2 E 18 DT DT DA DG DC SEQRES 1 F 18 DC DT DA DA DT DC DA DC 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 DG DT DG DA SEQRES 2 G 18 DT DT DA DG DC SEQRES 1 H 18 DC DT DA DA DT DC DA DC DT DT DG DT DG SEQRES 2 H 18 DA DT DT DC DG FORMUL 9 HOH *45(H2 O) HELIX 1 1 ALA A 34 ASN A 47 1 14 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 ALA B 34 ASN B 47 1 14 HELIX 5 5 ASN B 50 LEU B 67 1 18 HELIX 6 6 PRO B 68 LEU B 71 5 4 HELIX 7 7 ALA C 20 MET C 25 1 6 HELIX 8 8 ALA C 34 ASN C 47 1 14 HELIX 9 9 ASN C 50 LEU C 67 1 18 HELIX 10 10 PRO C 68 LEU C 71 5 4 HELIX 11 11 ALA D 34 ASN D 47 1 14 HELIX 12 12 ASN D 50 LEU D 67 1 18 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 75.991 42.505 103.727 90.00 107.17 90.00 P 1 21 1 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 0.013159 0.000000 0.004066 0.00000 SCALE2 0.000000 0.023527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010090 0.00000 MTRIX1 1 -0.811700 -0.520090 0.265800 -27.64397 1 MTRIX2 1 -0.543280 0.505220 -0.670520 -14.37253 1 MTRIX3 1 0.214440 -0.688670 -0.692640 -10.42639 1 MTRIX1 2 -0.049340 0.828370 -0.558000 -23.72695 1 MTRIX2 2 -0.993300 0.017740 0.114180 -9.27670 1 MTRIX3 2 0.104480 0.559890 0.821950 23.01543 1 MTRIX1 3 -0.537710 0.819060 -0.200020 -28.82347 1 MTRIX2 3 0.828270 0.468800 -0.306910 17.26773 1 MTRIX3 3 -0.157610 -0.330690 -0.930490 4.42905 1