HEADER DNA BINDING PROTEIN/DNA 01-NOV-11 3UFD TITLE C.ESP1396I BOUND TO ITS HIGHEST AFFINITY OPERATOR SITE OM COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATORY PROTEIN; COMPND 3 CHAIN: A, B, E, F; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3'); COMPND 8 CHAIN: C, G; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: OM 19-MER; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'- COMPND 13 D(*TP*TP*GP*TP*CP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*TP*AP*CP*A)-3'); COMPND 14 CHAIN: D, H; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: OM 19-MER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTER SP. RFL1396; SOURCE 3 ORGANISM_TAXID: 211595; SOURCE 4 GENE: ESP1396IC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)GOLD; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS HELIX-TURN-HELIX, BACTERIAL GENE REGULATORY PROTEIN, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.J.BALL,J.E.MCGEEHAN,S.D.STREETER,S.-J.THRESH,G.G.KNEALE REVDAT 5 28-FEB-24 3UFD 1 SEQADV REVDAT 4 12-NOV-14 3UFD 1 AUTHOR REVDAT 3 19-DEC-12 3UFD 1 JRNL REVDAT 2 12-SEP-12 3UFD 1 JRNL REVDAT 1 11-JUL-12 3UFD 0 JRNL AUTH N.J.BALL,J.E.MCGEEHAN,S.D.STREETER,S.J.THRESH,G.G.KNEALE JRNL TITL THE STRUCTURAL BASIS OF DIFFERENTIAL DNA SEQUENCE JRNL TITL 2 RECOGNITION BY RESTRICTION-MODIFICATION CONTROLLER PROTEINS. JRNL REF NUCLEIC ACIDS RES. V. 40 10532 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22941636 JRNL DOI 10.1093/NAR/GKS718 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 15885 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 791 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1106 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2479 REMARK 3 NUCLEIC ACID ATOMS : 1546 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.350 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.279 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.762 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.914 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4233 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5998 ; 1.520 ; 2.447 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 4.714 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;28.486 ;24.141 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 560 ;16.973 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;25.046 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 701 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2498 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1509 ; 0.359 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2450 ; 0.719 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2724 ; 1.146 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3548 ; 1.897 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B E F REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 78 1 REMARK 3 1 B 2 B 78 1 REMARK 3 1 E 2 E 78 1 REMARK 3 1 F 2 F 78 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 610 ; 0.020 ; 0.040 REMARK 3 TIGHT POSITIONAL 1 B (A): 610 ; 0.030 ; 0.040 REMARK 3 TIGHT POSITIONAL 1 E (A): 610 ; 0.020 ; 0.040 REMARK 3 TIGHT POSITIONAL 1 F (A): 610 ; 0.030 ; 0.040 REMARK 3 TIGHT THERMAL 1 A (A**2): 610 ; 0.060 ; 0.500 REMARK 3 TIGHT THERMAL 1 B (A**2): 610 ; 0.060 ; 0.500 REMARK 3 TIGHT THERMAL 1 E (A**2): 610 ; 0.050 ; 0.500 REMARK 3 TIGHT THERMAL 1 F (A**2): 610 ; 0.060 ; 0.500 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 77 REMARK 3 ORIGIN FOR THE GROUP (A): 11.7220 8.2790 8.8050 REMARK 3 T TENSOR REMARK 3 T11: 0.1363 T22: 0.1363 REMARK 3 T33: 0.0939 T12: -0.0395 REMARK 3 T13: 0.0828 T23: -0.0294 REMARK 3 L TENSOR REMARK 3 L11: 1.1355 L22: 1.7215 REMARK 3 L33: 7.1282 L12: -0.5518 REMARK 3 L13: 2.1264 L23: 1.0775 REMARK 3 S TENSOR REMARK 3 S11: -0.0788 S12: -0.1106 S13: 0.0531 REMARK 3 S21: 0.1725 S22: -0.1652 S23: 0.1188 REMARK 3 S31: -0.0405 S32: -0.4802 S33: 0.2439 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 78 REMARK 3 ORIGIN FOR THE GROUP (A): 10.9740 -1.9060 -8.8870 REMARK 3 T TENSOR REMARK 3 T11: 0.1056 T22: 0.0866 REMARK 3 T33: 0.0334 T12: -0.0883 REMARK 3 T13: 0.0026 T23: -0.0136 REMARK 3 L TENSOR REMARK 3 L11: 3.7921 L22: 2.1164 REMARK 3 L33: 7.4291 L12: 0.2754 REMARK 3 L13: -1.6984 L23: 1.9939 REMARK 3 S TENSOR REMARK 3 S11: -0.0448 S12: 0.1420 S13: -0.1839 REMARK 3 S21: -0.0233 S22: -0.0876 S23: 0.1850 REMARK 3 S31: 0.1804 S32: -0.4365 S33: 0.1323 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 19 REMARK 3 ORIGIN FOR THE GROUP (A): 29.4190 1.4610 1.1850 REMARK 3 T TENSOR REMARK 3 T11: 0.0721 T22: 0.1458 REMARK 3 T33: 0.2209 T12: 0.0027 REMARK 3 T13: -0.0146 T23: -0.0458 REMARK 3 L TENSOR REMARK 3 L11: 2.1933 L22: 5.5465 REMARK 3 L33: 5.2736 L12: -0.4670 REMARK 3 L13: -0.5251 L23: 4.9985 REMARK 3 S TENSOR REMARK 3 S11: 0.0376 S12: 0.0170 S13: -0.1353 REMARK 3 S21: 0.0528 S22: 0.7910 S23: -0.5610 REMARK 3 S31: 0.0879 S32: 0.5973 S33: -0.8286 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 19 REMARK 3 ORIGIN FOR THE GROUP (A): 28.8980 -1.1790 0.9930 REMARK 3 T TENSOR REMARK 3 T11: 0.1750 T22: 0.1601 REMARK 3 T33: 0.1463 T12: 0.0215 REMARK 3 T13: -0.0718 T23: -0.0523 REMARK 3 L TENSOR REMARK 3 L11: 2.1584 L22: 3.5245 REMARK 3 L33: 5.7293 L12: 0.9032 REMARK 3 L13: 1.4242 L23: 4.0581 REMARK 3 S TENSOR REMARK 3 S11: 0.2027 S12: -0.0400 S13: -0.1569 REMARK 3 S21: 0.4824 S22: 0.5437 S23: -0.5113 REMARK 3 S31: 0.5170 S32: 0.4151 S33: -0.7464 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 2 E 77 REMARK 3 ORIGIN FOR THE GROUP (A): -6.5920 42.8300 12.1790 REMARK 3 T TENSOR REMARK 3 T11: 0.0945 T22: 0.0819 REMARK 3 T33: 0.1020 T12: 0.0319 REMARK 3 T13: -0.0076 T23: 0.0632 REMARK 3 L TENSOR REMARK 3 L11: 9.4788 L22: 2.1462 REMARK 3 L33: 3.5925 L12: -2.5183 REMARK 3 L13: -1.3013 L23: -0.3089 REMARK 3 S TENSOR REMARK 3 S11: 0.2246 S12: 0.4726 S13: 0.0465 REMARK 3 S21: -0.1937 S22: -0.1408 S23: 0.2045 REMARK 3 S31: -0.2697 S32: -0.0558 S33: -0.0838 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 3 F 78 REMARK 3 ORIGIN FOR THE GROUP (A): 10.9470 32.4080 12.4870 REMARK 3 T TENSOR REMARK 3 T11: 0.1589 T22: 0.0959 REMARK 3 T33: 0.0644 T12: 0.0575 REMARK 3 T13: 0.0446 T23: 0.0329 REMARK 3 L TENSOR REMARK 3 L11: 7.2491 L22: 2.5294 REMARK 3 L33: 2.7099 L12: -2.5838 REMARK 3 L13: 2.2054 L23: 0.6256 REMARK 3 S TENSOR REMARK 3 S11: 0.3355 S12: 0.6491 S13: -0.1135 REMARK 3 S21: -0.2311 S22: -0.1826 S23: -0.0457 REMARK 3 S31: 0.2545 S32: 0.1984 S33: -0.1529 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : G 1 G 19 REMARK 3 ORIGIN FOR THE GROUP (A): 1.8940 40.2220 30.2470 REMARK 3 T TENSOR REMARK 3 T11: 0.1944 T22: 0.2367 REMARK 3 T33: 0.1089 T12: 0.0974 REMARK 3 T13: -0.0394 T23: 0.0538 REMARK 3 L TENSOR REMARK 3 L11: 4.9831 L22: 3.4107 REMARK 3 L33: 2.1222 L12: -3.8108 REMARK 3 L13: 1.7912 L23: -0.9857 REMARK 3 S TENSOR REMARK 3 S11: -0.7845 S12: -0.4883 S13: 0.2806 REMARK 3 S21: 0.5684 S22: 0.6257 S23: -0.1734 REMARK 3 S31: -0.2276 S32: -0.0087 S33: 0.1588 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 19 REMARK 3 ORIGIN FOR THE GROUP (A): 2.1210 37.4480 30.3260 REMARK 3 T TENSOR REMARK 3 T11: 0.1037 T22: 0.1503 REMARK 3 T33: 0.0175 T12: 0.1005 REMARK 3 T13: 0.0321 T23: 0.0453 REMARK 3 L TENSOR REMARK 3 L11: 5.0957 L22: 3.2658 REMARK 3 L33: 2.0206 L12: -3.1713 REMARK 3 L13: -0.6801 L23: 0.2640 REMARK 3 S TENSOR REMARK 3 S11: -0.5120 S12: -0.7067 S13: -0.1683 REMARK 3 S21: 0.4228 S22: 0.5679 S23: 0.2082 REMARK 3 S31: -0.0709 S32: -0.0853 S33: -0.0559 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 : 1.40 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 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 3UFD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9395 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) OR REMARK 200 SI(311) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17783 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 73.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.20100 REMARK 200 R SYM FOR SHELL (I) : 0.20100 REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SPG BUFFER, 25% W/V PEG 1500, 10 REMARK 280 UM SPERMIDINE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K 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 73.55000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 6690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 6680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 HIS A 78 REMARK 465 ASP A 79 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ASP B 79 REMARK 465 GLY E -2 REMARK 465 SER E -1 REMARK 465 HIS E 0 REMARK 465 MET E 1 REMARK 465 HIS E 78 REMARK 465 ASP E 79 REMARK 465 GLY F -2 REMARK 465 SER F -1 REMARK 465 HIS F 0 REMARK 465 MET F 1 REMARK 465 GLU F 2 REMARK 465 ASP F 79 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 GLU A 2 CG CD OE1 OE2 REMARK 470 GLU B 2 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT H 11 O3' DT H 11 C3' -0.041 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 DA C 1 C2 - N3 - C4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA C 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 8 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT C 11 C3' - C2' - C1' ANGL. DEV. = -6.8 DEGREES REMARK 500 DT C 11 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA C 12 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 DC C 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 18 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA C 19 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT D 2 C3' - O3' - P ANGL. DEV. = 10.0 DEGREES REMARK 500 DC D 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT D 11 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT D 11 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA D 12 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 DG D 13 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 DT D 14 O4' - C1' - N1 ANGL. DEV. = -6.5 DEGREES REMARK 500 DT D 14 N3 - C4 - O4 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT D 14 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT D 16 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA D 17 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC D 18 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA D 19 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA G 1 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 DA G 1 N3 - C4 - C5 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT G 2 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG G 3 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA G 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG G 6 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA G 7 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC G 8 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 DA G 10 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DT G 11 C3' - C2' - C1' ANGL. DEV. = -7.8 DEGREES REMARK 500 DA G 12 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG G 13 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG G 13 C3' - O3' - P ANGL. DEV. = 11.4 DEGREES REMARK 500 DT G 14 N3 - C4 - O4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC G 15 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA G 17 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 DA G 19 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT H 1 C4 - C5 - C7 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT H 1 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT H 2 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES REMARK 500 DG H 3 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT H 4 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC H 5 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DC H 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG H 6 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DG H 6 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 DC H 8 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA H 10 O4' - C1' - N9 ANGL. DEV. = -6.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 57 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS B 77 HIS B 78 34.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CLC RELATED DB: PDB REMARK 900 TWO C.ESP1396I DIMERS BOUND TO C/R PROMOTER REMARK 900 RELATED ID: 3G5G RELATED DB: PDB REMARK 900 C.ESP1396I NATIVE FREE PROTEIN REMARK 900 RELATED ID: 3FYA RELATED DB: PDB REMARK 900 C.ESP1396I R35A MUTANT FREE PROTEIN REMARK 900 RELATED ID: 3S8Q RELATED DB: PDB REMARK 900 C.ESP1396I BOUND TO THE DISTAL OPERATOR SITE OF THE C/R PROMOTER DBREF 3UFD A 1 79 UNP Q8GGH0 Q8GGH0_9ENTR 1 79 DBREF 3UFD B 1 79 UNP Q8GGH0 Q8GGH0_9ENTR 1 79 DBREF 3UFD E 1 79 UNP Q8GGH0 Q8GGH0_9ENTR 1 79 DBREF 3UFD F 1 79 UNP Q8GGH0 Q8GGH0_9ENTR 1 79 DBREF 3UFD C 1 19 PDB 3UFD 3UFD 1 19 DBREF 3UFD G 1 19 PDB 3UFD 3UFD 1 19 DBREF 3UFD D 1 19 PDB 3UFD 3UFD 1 19 DBREF 3UFD H 1 19 PDB 3UFD 3UFD 1 19 SEQADV 3UFD GLY A -2 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD SER A -1 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD HIS A 0 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD GLY B -2 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD SER B -1 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD HIS B 0 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD GLY E -2 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD SER E -1 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD HIS E 0 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD GLY F -2 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD SER F -1 UNP Q8GGH0 EXPRESSION TAG SEQADV 3UFD HIS F 0 UNP Q8GGH0 EXPRESSION TAG SEQRES 1 A 82 GLY SER HIS MET GLU SER PHE LEU LEU SER LYS VAL SER SEQRES 2 A 82 PHE VAL ILE LYS LYS ILE ARG LEU GLU LYS GLY MET THR SEQRES 3 A 82 GLN GLU ASP LEU ALA TYR LYS SER ASN LEU ASP ARG THR SEQRES 4 A 82 TYR ILE SER GLY ILE GLU ARG ASN SER ARG ASN LEU THR SEQRES 5 A 82 ILE LYS SER LEU GLU LEU ILE MET LYS GLY LEU GLU VAL SEQRES 6 A 82 SER ASP VAL VAL PHE PHE GLU MET LEU ILE LYS GLU ILE SEQRES 7 A 82 LEU LYS HIS ASP SEQRES 1 B 82 GLY SER HIS MET GLU SER PHE LEU LEU SER LYS VAL SER SEQRES 2 B 82 PHE VAL ILE LYS LYS ILE ARG LEU GLU LYS GLY MET THR SEQRES 3 B 82 GLN GLU ASP LEU ALA TYR LYS SER ASN LEU ASP ARG THR SEQRES 4 B 82 TYR ILE SER GLY ILE GLU ARG ASN SER ARG ASN LEU THR SEQRES 5 B 82 ILE LYS SER LEU GLU LEU ILE MET LYS GLY LEU GLU VAL SEQRES 6 B 82 SER ASP VAL VAL PHE PHE GLU MET LEU ILE LYS GLU ILE SEQRES 7 B 82 LEU LYS HIS ASP SEQRES 1 C 19 DA DT DG DT DA DG DA DC DT DA DT DA DG SEQRES 2 C 19 DT DC DG DA DC DA SEQRES 1 D 19 DT DT DG DT DC DG DA DC DT DA DT DA DG SEQRES 2 D 19 DT DC DT DA DC DA SEQRES 1 E 82 GLY SER HIS MET GLU SER PHE LEU LEU SER LYS VAL SER SEQRES 2 E 82 PHE VAL ILE LYS LYS ILE ARG LEU GLU LYS GLY MET THR SEQRES 3 E 82 GLN GLU ASP LEU ALA TYR LYS SER ASN LEU ASP ARG THR SEQRES 4 E 82 TYR ILE SER GLY ILE GLU ARG ASN SER ARG ASN LEU THR SEQRES 5 E 82 ILE LYS SER LEU GLU LEU ILE MET LYS GLY LEU GLU VAL SEQRES 6 E 82 SER ASP VAL VAL PHE PHE GLU MET LEU ILE LYS GLU ILE SEQRES 7 E 82 LEU LYS HIS ASP SEQRES 1 F 82 GLY SER HIS MET GLU SER PHE LEU LEU SER LYS VAL SER SEQRES 2 F 82 PHE VAL ILE LYS LYS ILE ARG LEU GLU LYS GLY MET THR SEQRES 3 F 82 GLN GLU ASP LEU ALA TYR LYS SER ASN LEU ASP ARG THR SEQRES 4 F 82 TYR ILE SER GLY ILE GLU ARG ASN SER ARG ASN LEU THR SEQRES 5 F 82 ILE LYS SER LEU GLU LEU ILE MET LYS GLY LEU GLU VAL SEQRES 6 F 82 SER ASP VAL VAL PHE PHE GLU MET LEU ILE LYS GLU ILE SEQRES 7 F 82 LEU LYS HIS ASP SEQRES 1 G 19 DA DT DG DT DA DG DA DC DT DA DT DA DG SEQRES 2 G 19 DT DC DG DA DC DA SEQRES 1 H 19 DT DT DG DT DC DG DA DC DT DA DT DA DG SEQRES 2 H 19 DT DC DT DA DC DA HET CL B 80 1 HETNAM CL CHLORIDE ION FORMUL 9 CL CL 1- FORMUL 10 HOH *13(H2 O) HELIX 1 1 SER A 3 LYS A 20 1 18 HELIX 2 2 THR A 23 ASN A 32 1 10 HELIX 3 3 ASP A 34 SER A 45 1 12 HELIX 4 4 THR A 49 LEU A 60 1 12 HELIX 5 5 SER A 63 LYS A 77 1 15 HELIX 6 6 SER B 3 LYS B 20 1 18 HELIX 7 7 THR B 23 ASN B 32 1 10 HELIX 8 8 ASP B 34 SER B 45 1 12 HELIX 9 9 THR B 49 LEU B 60 1 12 HELIX 10 10 SER B 63 LYS B 77 1 15 HELIX 11 11 SER E 3 LYS E 20 1 18 HELIX 12 12 THR E 23 ASN E 32 1 10 HELIX 13 13 ASP E 34 SER E 45 1 12 HELIX 14 14 THR E 49 LEU E 60 1 12 HELIX 15 15 SER E 63 LYS E 77 1 15 HELIX 16 16 PHE F 4 LYS F 20 1 17 HELIX 17 17 THR F 23 ASN F 32 1 10 HELIX 18 18 ASP F 34 SER F 45 1 12 HELIX 19 19 THR F 49 LEU F 60 1 12 HELIX 20 20 SER F 63 LYS F 77 1 15 CRYST1 47.490 147.100 47.780 90.00 93.68 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 0.021057 0.000000 0.001354 0.00000 SCALE2 0.000000 0.006798 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020973 0.00000