HEADER TRANSCRIPTION 16-SEP-10 2XRL TITLE TET-REPRESSOR CLASS D T103A WITH DOXYCYCLINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETRACYCLINE REPRESSOR PROTEIN CLASS D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-208; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: K-12; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: RB791; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PWH610 KEYWDS TRANSCRIPTION, ANTIBIOTIC RESISTANCE, DNA-BINDING, HELIX-TURN-HELIX EXPDTA X-RAY DIFFRACTION AUTHOR G.J.PALM,P.WAACK,W.HINRICHS REVDAT 4 20-DEC-23 2XRL 1 REMARK HETSYN LINK REVDAT 3 18-MAR-20 2XRL 1 JRNL REVDAT 2 08-MAY-19 2XRL 1 REMARK REVDAT 1 05-OCT-11 2XRL 0 JRNL AUTH G.J.PALM,I.BUCHHOLZ,S.WERTEN,B.GIRBARDT,L.BERNDT,M.DELCEA, JRNL AUTH 2 W.HINRICHS JRNL TITL THERMODYNAMICS, COOPERATIVITY AND STABILITY OF THE JRNL TITL 2 TETRACYCLINE REPRESSOR (TETR) UPON TETRACYCLINE BINDING. JRNL REF BIOCHIM BIOPHYS ACTA V.1868 40404 2020 JRNL REF 2 PROTEINS PROTEOM JRNL REFN ISSN 1878-1454 JRNL PMID 32114262 JRNL DOI 10.1016/J.BBAPAP.2020.140404 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 17378 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 912 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1238 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.3900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1639 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.87000 REMARK 3 B22 (A**2) : 0.87000 REMARK 3 B33 (A**2) : -1.75000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.187 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.169 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.238 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1715 ; 0.023 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1157 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2334 ; 1.854 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2803 ; 1.156 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 208 ; 6.531 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;39.936 ;23.529 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 292 ;14.161 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;23.890 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 264 ; 0.155 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1920 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 353 ; 0.001 ; 0.020 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): 1036 ; 1.076 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 420 ; 0.321 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1656 ; 1.796 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 679 ; 2.785 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 678 ; 4.130 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 45 REMARK 3 RESIDUE RANGE : A 46 A 64 REMARK 3 RESIDUE RANGE : A 1209 A 1210 REMARK 3 ORIGIN FOR THE GROUP (A): 18.8930 28.2130 13.9100 REMARK 3 T TENSOR REMARK 3 T11: 0.1624 T22: 0.2075 REMARK 3 T33: 0.0959 T12: -0.0042 REMARK 3 T13: -0.0350 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.8533 L22: 0.0662 REMARK 3 L33: 2.8412 L12: -0.2216 REMARK 3 L13: 1.4237 L23: -0.3209 REMARK 3 S TENSOR REMARK 3 S11: 0.0673 S12: 0.0735 S13: -0.0574 REMARK 3 S21: -0.0042 S22: 0.0063 S23: 0.0270 REMARK 3 S31: 0.1101 S32: 0.1694 S33: -0.0736 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 65 A 93 REMARK 3 RESIDUE RANGE : A 94 A 100 REMARK 3 RESIDUE RANGE : A 101 A 106 REMARK 3 ORIGIN FOR THE GROUP (A): 22.5830 28.3140 36.1530 REMARK 3 T TENSOR REMARK 3 T11: 0.1834 T22: 0.1834 REMARK 3 T33: 0.0893 T12: 0.0705 REMARK 3 T13: -0.0151 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 0.2917 L22: 0.0728 REMARK 3 L33: 2.9205 L12: 0.0948 REMARK 3 L13: 0.5876 L23: 0.3932 REMARK 3 S TENSOR REMARK 3 S11: 0.0274 S12: 0.0340 S13: -0.0777 REMARK 3 S21: 0.0312 S22: 0.0155 S23: 0.0185 REMARK 3 S31: 0.0746 S32: -0.0891 S33: -0.0429 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 166 A 181 REMARK 3 RESIDUE RANGE : A 107 A 123 REMARK 3 RESIDUE RANGE : A 124 A 165 REMARK 3 RESIDUE RANGE : A 182 A 208 REMARK 3 ORIGIN FOR THE GROUP (A): 32.2330 30.9630 39.5720 REMARK 3 T TENSOR REMARK 3 T11: 0.2183 T22: 0.1368 REMARK 3 T33: 0.1022 T12: 0.1054 REMARK 3 T13: -0.0098 T23: -0.0377 REMARK 3 L TENSOR REMARK 3 L11: 1.2417 L22: 0.0617 REMARK 3 L33: 1.0748 L12: -0.2666 REMARK 3 L13: 0.2161 L23: -0.0150 REMARK 3 S TENSOR REMARK 3 S11: 0.1650 S12: 0.1085 S13: -0.1532 REMARK 3 S21: -0.0304 S22: -0.0433 S23: 0.0447 REMARK 3 S31: 0.0190 S32: -0.0031 S33: -0.1217 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 : A 1211 A 1215 REMARK 3 ORIGIN FOR THE GROUP (A): 20.7070 36.2020 35.4190 REMARK 3 T TENSOR REMARK 3 T11: 0.2109 T22: 0.2111 REMARK 3 T33: 0.0798 T12: 0.1446 REMARK 3 T13: -0.0111 T23: 0.0254 REMARK 3 L TENSOR REMARK 3 L11: 2.7813 L22: 3.5387 REMARK 3 L33: 4.5464 L12: 0.4519 REMARK 3 L13: -2.4649 L23: 2.4602 REMARK 3 S TENSOR REMARK 3 S11: 0.1374 S12: 0.3785 S13: 0.0713 REMARK 3 S21: 0.0095 S22: -0.0772 S23: 0.0154 REMARK 3 S31: -0.1404 S32: -0.4508 S33: -0.0602 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. REMARK 4 REMARK 4 2XRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1290045124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU-MSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19733 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 33.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 9.170 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.43 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 2O7O REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP VAPOR DIFFUSION WITH 2 UL REMARK 280 (14 MG/ML PROTEIN) AND 2 UL (0.6 M NACL, 15 % PEG 4000, 0.1 M REMARK 280 MES PH 6.5). CRYSTAL WAS CRYOCOOLED WITH PARAFFIN OIL AS REMARK 280 CRYOPROTECTANT., VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 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 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+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 33.94400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 33.94400 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 90.21900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.94400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.10950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.94400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 135.32850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.94400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 135.32850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.94400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.10950 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 33.94400 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 33.94400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 90.21900 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 33.94400 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 33.94400 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 90.21900 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 33.94400 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 135.32850 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 33.94400 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 45.10950 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 33.94400 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 45.10950 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 33.94400 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 135.32850 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 33.94400 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 33.94400 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 90.21900 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: 8430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 -1.000000 0.000000 0.000000 67.88800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 67.88800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, THR 103 TO ALA 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 GLU A 58 CB GLU A 58 CG 0.115 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 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.3 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 TYR A 66 60.26 -115.47 REMARK 500 ASP A 163 20.80 -76.11 REMARK 500 ASP A 178 63.00 -101.04 REMARK 500 ASP A 180 -156.73 -124.99 REMARK 500 ASP A 181 46.35 -101.66 REMARK 500 LEU A 204 -118.16 53.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12, REMARK 600 12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11, REMARK 600 12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE (DXT): COMMON NAME REMARK 600 DOXYCYCLINE 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 MG A1212 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 100 NE2 REMARK 620 2 DXT A1211 O11 163.0 REMARK 620 3 DXT A1211 O12 90.1 75.3 REMARK 620 4 HOH A1213 O 98.0 96.4 171.6 REMARK 620 5 HOH A1214 O 96.0 93.1 92.1 89.5 REMARK 620 6 HOH A1215 O 90.6 82.7 96.2 81.4 169.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DXT A 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1212 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XGC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DESIGNED HETERODIMERIC VARIANT T -A(I)B OF REMARK 900 THE TETRACYCLINE REPRESSOR REMARK 900 RELATED ID: 2XPW RELATED DB: PDB REMARK 900 TETR(D) IN COMPLEX WITH OXYTETRACYCLINE AND MAGNESIUM. REMARK 900 RELATED ID: 1BJZ RELATED DB: PDB REMARK 900 TETRACYCLINE CHELATED MG2+ -ION INITIATES HELIX UNWINDING FOR TET REMARK 900 REPRESSOR INDUCTION REMARK 900 RELATED ID: 3ZQG RELATED DB: PDB REMARK 900 STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH ANTIINDUCER REMARK 900 PEPTIDE-TAP2 REMARK 900 RELATED ID: 2X9D RELATED DB: PDB REMARK 900 TET REPRESSOR (CLASS D) IN COMPLEX WITH ISO-7- CHLORTETRACYCLINE REMARK 900 RELATED ID: 3ZQH RELATED DB: PDB REMARK 900 STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH INDUCER PEPTIDE- REMARK 900 TIP3 REMARK 900 RELATED ID: 2TRT RELATED DB: PDB REMARK 900 TETRACYCLINE REPRESSOR CLASS D REMARK 900 RELATED ID: 2XPV RELATED DB: PDB REMARK 900 TETR(D) IN COMPLEX WITH MINOCYCLINE AND MG. REMARK 900 RELATED ID: 2VKV RELATED DB: PDB REMARK 900 TETR (BD) VARIANT L17G WITH REVERSE PHENOTYPE REMARK 900 RELATED ID: 1ORK RELATED DB: PDB REMARK 900 TET REPRESSOR, CLASS D IN COMPLEX WITH 9-(N,N- DIMETHYLGLYCYLAMIDO)- REMARK 900 6-DEMETHYL-6-DEOXY-TETRACYCLINE REMARK 900 RELATED ID: 2XGE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DESIGNED HETERODIMERIC VARIANT T -A(A)B OF REMARK 900 THE TETRACYCLINE REPRESSOR REMARK 900 RELATED ID: 2X6O RELATED DB: PDB REMARK 900 TET REPRESSOR CLASS D IN COMPLEX WITH 7-CHLOR-2- CYANO-ISO- REMARK 900 TETRACYCLINE REMARK 900 RELATED ID: 1A6I RELATED DB: PDB REMARK 900 TET REPRESSOR, CLASS D VARIANT REMARK 900 RELATED ID: 1QPI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX REMARK 900 RELATED ID: 2VKE RELATED DB: PDB REMARK 900 TET REPRESSOR CLASS D COMPLEXED WITH COBALT AND TETRACYCLINE REMARK 900 RELATED ID: 2XGD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DESIGNED HOMODIMERIC VARIANT T- A(L)A(L) OF REMARK 900 THE TETRACYCLINE REPRESSOR REMARK 900 RELATED ID: 1DU7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TET REPRESSOR CLASS D WITH 4- EPI- TETRACYCLINE REMARK 900 RELATED ID: 2XPT RELATED DB: PDB REMARK 900 TETR(D) IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM. REMARK 900 RELATED ID: 2XPU RELATED DB: PDB REMARK 900 TETR(D) IN COMPLEX WITH ANHYDROTETRACYCLINE. REMARK 900 RELATED ID: 2XB5 RELATED DB: PDB REMARK 900 TET REPRESSOR (CLASS D) IN COMPLEX WITH 7- IODOTETRACYCLINE REMARK 900 RELATED ID: 3ZQI RELATED DB: PDB REMARK 900 STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH INDUCER PEPTIDE- REMARK 900 TIP2 REMARK 900 RELATED ID: 3ZQF RELATED DB: PDB REMARK 900 STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH ANTIINDUCER REMARK 900 PEPTIDE-TAP1 REMARK 900 RELATED ID: 1BJ0 RELATED DB: PDB REMARK 900 TETRACYCLINE CHELATED MG2+ -ION INITIATES HELIX UNWINDING FOR TET REMARK 900 REPRESSOR INDUCTION REMARK 900 RELATED ID: 2XPS RELATED DB: PDB REMARK 900 TETR(D) IN COMPLEX WITH ANHYDROTETRACYCLINE AND MAGNESIUM REMARK 900 RELATED ID: 2TCT RELATED DB: PDB REMARK 900 MOL_ID: 1; MOLECULE: TETRACYCLINE REPRESSOR; CHAIN: NULL ; SYNONYM: REMARK 900 TET REPRESSOR, CLASS D; ENGINEERED: YES REMARK 900 RELATED ID: 1BJY RELATED DB: PDB REMARK 900 TETRACYCLINE CHELATED MG2+ -ION INITIATES HELIX UNWINDING FOR TET REMARK 900 REPRESSOR INDUCTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 C-TERMINAL 10 RESIDUES WERE REMOVED FOR IMPROVED CRYSTALLIZATION. DBREF 2XRL A 3 208 UNP P0ACT4 TETR4_ECOLX 3 208 SEQADV 2XRL SER A 2 UNP P0ACT4 ALA 2 CLONING ARTIFACT SEQADV 2XRL ALA A 103 UNP P0ACT4 THR 103 ENGINEERED MUTATION SEQRES 1 A 207 SER ARG LEU ASN ARG GLU SER VAL ILE ASP ALA ALA LEU SEQRES 2 A 207 GLU LEU LEU ASN GLU THR GLY ILE ASP GLY LEU THR THR SEQRES 3 A 207 ARG LYS LEU ALA GLN LYS LEU GLY ILE GLU GLN PRO THR SEQRES 4 A 207 LEU TYR TRP HIS VAL LYS ASN LYS ARG ALA LEU LEU ASP SEQRES 5 A 207 ALA LEU ALA VAL GLU ILE LEU ALA ARG HIS HIS ASP TYR SEQRES 6 A 207 SER LEU PRO ALA ALA GLY GLU SER TRP GLN SER PHE LEU SEQRES 7 A 207 ARG ASN ASN ALA MET SER PHE ARG ARG ALA LEU LEU ARG SEQRES 8 A 207 TYR ARG ASP GLY ALA LYS VAL HIS LEU GLY ALA ARG PRO SEQRES 9 A 207 ASP GLU LYS GLN TYR ASP THR VAL GLU THR GLN LEU ARG SEQRES 10 A 207 PHE MET THR GLU ASN GLY PHE SER LEU ARG ASP GLY LEU SEQRES 11 A 207 TYR ALA ILE SER ALA VAL SER HIS PHE THR LEU GLY ALA SEQRES 12 A 207 VAL LEU GLU GLN GLN GLU HIS THR ALA ALA LEU THR ASP SEQRES 13 A 207 ARG PRO ALA ALA PRO ASP GLU ASN LEU PRO PRO LEU LEU SEQRES 14 A 207 ARG GLU ALA LEU GLN ILE MET ASP SER ASP ASP GLY GLU SEQRES 15 A 207 GLN ALA PHE LEU HIS GLY LEU GLU SER LEU ILE ARG GLY SEQRES 16 A 207 PHE GLU VAL GLN LEU THR ALA LEU LEU GLN ILE VAL HET CL A1209 1 HET CL A1210 1 HET DXT A1211 32 HET MG A1212 1 HETNAM CL CHLORIDE ION HETNAM DXT (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12, HETNAM 2 DXT 12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11, HETNAM 3 DXT 12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE HETNAM MG MAGNESIUM ION HETSYN DXT DOXYTETRACYCLINE; DOXYCYCLINE FORMUL 2 CL 2(CL 1-) FORMUL 4 DXT C22 H24 N2 O8 FORMUL 5 MG MG 2+ FORMUL 6 HOH *106(H2 O) HELIX 1 1 ASN A 5 LEU A 25 1 21 HELIX 2 2 THR A 26 GLY A 35 1 10 HELIX 3 3 GLU A 37 VAL A 45 1 9 HELIX 4 4 ASN A 47 HIS A 64 1 18 HELIX 5 5 SER A 74 TYR A 93 1 20 HELIX 6 6 ASP A 95 GLY A 102 1 8 HELIX 7 7 ASP A 106 LYS A 108 5 3 HELIX 8 8 GLN A 109 GLU A 122 1 14 HELIX 9 9 SER A 126 ARG A 158 1 33 HELIX 10 10 PRO A 167 ASP A 178 1 12 HELIX 11 11 GLY A 182 LEU A 204 1 23 LINK NE2 HIS A 100 MG MG A1212 1555 1555 2.28 LINK O11 DXT A1211 MG MG A1212 1555 1555 2.04 LINK O12 DXT A1211 MG MG A1212 1555 1555 1.93 LINK MG MG A1212 O HOH A1213 1555 1555 2.19 LINK MG MG A1212 O HOH A1214 1555 1555 2.25 LINK MG MG A1212 O HOH A1215 1555 1555 2.08 SITE 1 AC1 5 ARG A 3 LEU A 4 GLN A 76 ARG A 80 SITE 2 AC1 5 HOH A2095 SITE 1 AC2 3 ARG A 3 SER A 74 SER A 77 SITE 1 AC3 16 HIS A 64 SER A 67 ASN A 82 PHE A 86 SITE 2 AC3 16 HIS A 100 ARG A 104 PRO A 105 VAL A 113 SITE 3 AC3 16 GLN A 116 ILE A 134 SER A 138 LEU A 174 SITE 4 AC3 16 MG A1212 HOH A1214 HOH A1215 HOH A2105 SITE 1 AC4 5 HIS A 100 DXT A1211 HOH A1213 HOH A1214 SITE 2 AC4 5 HOH A1215 CRYST1 67.888 67.888 180.438 90.00 90.00 90.00 I 41 2 2 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 0.014730 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005542 0.00000