HEADER TRANSCRIPTION 25-AUG-15 5AE4 TITLE STRUCTURES OF INACTIVE AND ACTIVATED DNTR PROVIDE CONCLUSIVE EVIDENCE TITLE 2 FOR THE MECHANISM OF ACTION OF LYSR TRANSCRIPTION FACTORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSR-TYPE REGULATORY PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DNTR; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA CEPACIA; SOURCE 3 ORGANISM_TAXID: 292; SOURCE 4 STRAIN: DNT; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1007065; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PREP4; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PQE-60 KEYWDS TRANSCRIPTION, LYSR-TYPE TRANSCRIPTION REGULATORS, LTTR, KEYWDS 2 TRANSCRIPTION FACTOR, HELIX-TURN-HELIX, DNA BINDING PROTEIN, KEYWDS 3 ROSSMANN-LIKE FOLD, AUTOINDUCING MUTANT, H169T-DNTR EXPDTA X-RAY DIFFRACTION AUTHOR M.LERCHE,C.DIAN,A.ROUND,R.LONNEBORG,P.BRZEZINSKI,G.A.LEONARD REVDAT 3 10-JAN-24 5AE4 1 REMARK REVDAT 2 10-FEB-16 5AE4 1 JRNL REVDAT 1 13-JAN-16 5AE4 0 JRNL AUTH M.LERCHE,C.DIAN,A.ROUND,R.LONNEBORG,P.BRZEZINSKI,G.A.LEONARD JRNL TITL THE SOLUTION CONFIGURATIONS OF INACTIVE AND ACTIVATED DNTR JRNL TITL 2 HAVE IMPLICATIONS FOR THE SLIDING DIMER MECHANISM OF LYSR JRNL TITL 3 TRANSCRIPTION FACTORS. JRNL REF SCI.REP. V. 6 19988 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 26817994 JRNL DOI 10.1038/SREP19988 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 16041 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.5743 - 5.9923 0.98 2699 149 0.2144 0.2748 REMARK 3 2 5.9923 - 4.7581 0.99 2583 117 0.1730 0.2358 REMARK 3 3 4.7581 - 4.1572 1.00 2512 135 0.1401 0.1735 REMARK 3 4 4.1572 - 3.7773 1.00 2496 131 0.1692 0.2213 REMARK 3 5 3.7773 - 3.5067 1.00 2481 139 0.2039 0.2518 REMARK 3 6 3.5067 - 3.3001 1.00 2458 141 0.2599 0.3144 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 79.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 3436 REMARK 3 ANGLE : 0.863 4668 REMARK 3 CHIRALITY : 0.058 517 REMARK 3 PLANARITY : 0.004 611 REMARK 3 DIHEDRAL : 14.439 1249 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 89 THROUGH 303 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.5742 23.6669 -13.4037 REMARK 3 T TENSOR REMARK 3 T11: 0.4322 T22: 0.1579 REMARK 3 T33: 0.3458 T12: 0.0216 REMARK 3 T13: 0.0139 T23: -0.0693 REMARK 3 L TENSOR REMARK 3 L11: 0.7865 L22: 0.2665 REMARK 3 L33: 0.5614 L12: -0.5689 REMARK 3 L13: 0.2018 L23: -0.2986 REMARK 3 S TENSOR REMARK 3 S11: 0.0661 S12: -0.0563 S13: -0.0225 REMARK 3 S21: 0.0159 S22: -0.0536 S23: -0.0179 REMARK 3 S31: -0.2990 S32: 0.0833 S33: -0.0493 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 88 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.1287 29.5540 -29.3949 REMARK 3 T TENSOR REMARK 3 T11: 0.4272 T22: 0.2279 REMARK 3 T33: 0.3717 T12: 0.1185 REMARK 3 T13: 0.0451 T23: 0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.5190 L22: 0.5636 REMARK 3 L33: 0.6946 L12: -0.4211 REMARK 3 L13: 0.1669 L23: 0.1785 REMARK 3 S TENSOR REMARK 3 S11: 0.0804 S12: 0.0664 S13: 0.0647 REMARK 3 S21: -0.0524 S22: -0.0403 S23: -0.0769 REMARK 3 S31: -0.4353 S32: -0.0866 S33: 0.0064 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5AE4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1290064267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : BENT CYLINDRICAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16127 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 43.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.95000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 1UTB REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM TARTRATE, 0.2 M POTASSIUM REMARK 280 THIOCYANATE 0.1 M TRIS-HCL PH 8.5, 20 % (W/V) PEG 8000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 198.51400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 99.25700 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 148.88550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.62850 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 248.14250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 198.51400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 99.25700 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 49.62850 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 148.88550 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 248.14250 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 LEU A 3 REMARK 465 ARG A 4 REMARK 465 ASP A 5 REMARK 465 ILE A 6 REMARK 465 ASP A 7 REMARK 465 LEU A 8 REMARK 465 ASN A 9 REMARK 465 LEU A 10 REMARK 465 LEU A 11 REMARK 465 VAL A 12 REMARK 465 VAL A 13 REMARK 465 PHE A 14 REMARK 465 ASN A 15 REMARK 465 GLN A 16 REMARK 465 LEU A 17 REMARK 465 LEU A 18 REMARK 465 LEU A 19 REMARK 465 ASP A 20 REMARK 465 ARG A 21 REMARK 465 SER A 22 REMARK 465 VAL A 23 REMARK 465 SER A 24 REMARK 465 THR A 25 REMARK 465 ALA A 26 REMARK 465 GLY A 27 REMARK 465 GLU A 28 REMARK 465 LYS A 29 REMARK 465 LEU A 30 REMARK 465 GLY A 31 REMARK 465 LEU A 32 REMARK 465 THR A 33 REMARK 465 GLN A 34 REMARK 465 PRO A 35 REMARK 465 ALA A 36 REMARK 465 VAL A 37 REMARK 465 SER A 38 REMARK 465 ASN A 39 REMARK 465 SER A 40 REMARK 465 LEU A 41 REMARK 465 LYS A 42 REMARK 465 ARG A 43 REMARK 465 LEU A 44 REMARK 465 ARG A 45 REMARK 465 THR A 46 REMARK 465 ALA A 47 REMARK 465 LEU A 48 REMARK 465 ASN A 49 REMARK 465 ASP A 50 REMARK 465 ASP A 51 REMARK 465 LEU A 52 REMARK 465 PHE A 53 REMARK 465 LEU A 54 REMARK 465 ARG A 55 REMARK 465 THR A 56 REMARK 465 SER A 57 REMARK 465 LYS A 58 REMARK 465 GLY A 59 REMARK 465 MET A 60 REMARK 465 GLU A 61 REMARK 465 PRO A 62 REMARK 465 THR A 63 REMARK 465 PRO A 64 REMARK 465 TYR A 65 REMARK 465 ALA A 66 REMARK 465 LEU A 67 REMARK 465 HIS A 68 REMARK 465 LEU A 69 REMARK 465 ALA A 70 REMARK 465 GLU A 71 REMARK 465 PRO A 72 REMARK 465 VAL A 73 REMARK 465 ILE A 74 REMARK 465 TYR A 75 REMARK 465 ALA A 76 REMARK 465 LEU A 77 REMARK 465 ASN A 78 REMARK 465 THR A 79 REMARK 465 LEU A 80 REMARK 465 GLN A 81 REMARK 465 THR A 82 REMARK 465 ALA A 83 REMARK 465 LEU A 84 REMARK 465 THR A 85 REMARK 465 THR A 86 REMARK 465 ARG A 87 REMARK 465 ASP A 88 REMARK 465 HIS A 304 REMARK 465 HIS A 305 REMARK 465 HIS A 306 REMARK 465 HIS A 307 REMARK 465 HIS A 308 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 LEU B 3 REMARK 465 ARG B 4 REMARK 465 ASP B 5 REMARK 465 ILE B 6 REMARK 465 ASP B 7 REMARK 465 LEU B 8 REMARK 465 ASN B 9 REMARK 465 LEU B 10 REMARK 465 LEU B 11 REMARK 465 VAL B 12 REMARK 465 VAL B 13 REMARK 465 PHE B 14 REMARK 465 ASN B 15 REMARK 465 GLN B 16 REMARK 465 LEU B 17 REMARK 465 LEU B 18 REMARK 465 LEU B 19 REMARK 465 ASP B 20 REMARK 465 ARG B 21 REMARK 465 SER B 22 REMARK 465 VAL B 23 REMARK 465 SER B 24 REMARK 465 THR B 25 REMARK 465 ALA B 26 REMARK 465 GLY B 27 REMARK 465 GLU B 28 REMARK 465 LYS B 29 REMARK 465 LEU B 30 REMARK 465 GLY B 31 REMARK 465 LEU B 32 REMARK 465 THR B 33 REMARK 465 GLN B 34 REMARK 465 PRO B 35 REMARK 465 ALA B 36 REMARK 465 VAL B 37 REMARK 465 SER B 38 REMARK 465 ASN B 39 REMARK 465 SER B 40 REMARK 465 LEU B 41 REMARK 465 LYS B 42 REMARK 465 ARG B 43 REMARK 465 LEU B 44 REMARK 465 ARG B 45 REMARK 465 THR B 46 REMARK 465 ALA B 47 REMARK 465 LEU B 48 REMARK 465 ASN B 49 REMARK 465 ASP B 50 REMARK 465 ASP B 51 REMARK 465 LEU B 52 REMARK 465 PHE B 53 REMARK 465 LEU B 54 REMARK 465 ARG B 55 REMARK 465 THR B 56 REMARK 465 SER B 57 REMARK 465 LYS B 58 REMARK 465 GLY B 59 REMARK 465 MET B 60 REMARK 465 GLU B 61 REMARK 465 PRO B 62 REMARK 465 THR B 63 REMARK 465 PRO B 64 REMARK 465 TYR B 65 REMARK 465 ALA B 66 REMARK 465 LEU B 67 REMARK 465 HIS B 68 REMARK 465 LEU B 69 REMARK 465 ALA B 70 REMARK 465 GLU B 71 REMARK 465 PRO B 72 REMARK 465 VAL B 73 REMARK 465 ILE B 74 REMARK 465 TYR B 75 REMARK 465 ALA B 76 REMARK 465 LEU B 77 REMARK 465 ASN B 78 REMARK 465 THR B 79 REMARK 465 LEU B 80 REMARK 465 GLN B 81 REMARK 465 THR B 82 REMARK 465 ALA B 83 REMARK 465 LEU B 84 REMARK 465 THR B 85 REMARK 465 THR B 86 REMARK 465 ARG B 87 REMARK 465 ALA B 301 REMARK 465 ARG B 302 REMARK 465 HIS B 303 REMARK 465 HIS B 304 REMARK 465 HIS B 305 REMARK 465 HIS B 306 REMARK 465 HIS B 307 REMARK 465 HIS B 308 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 SER A 89 OG REMARK 470 GLU A 156 CG CD OE1 OE2 REMARK 470 ARG A 170 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 210 CG OD1 OD2 REMARK 470 LYS A 219 CD CE NZ REMARK 470 LYS A 267 CD CE NZ REMARK 470 ILE A 271 CG2 CD1 REMARK 470 ARG A 302 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 303 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 139 CG CD CE NZ REMARK 470 GLU B 140 CG CD OE1 OE2 REMARK 470 GLU B 143 CG CD OE1 OE2 REMARK 470 GLU B 156 CG CD OE1 OE2 REMARK 470 ARG B 170 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 177 CG CD CE NZ REMARK 470 LYS B 183 CG CD CE NZ REMARK 470 GLU B 214 CD OE1 OE2 REMARK 470 LYS B 219 CG CD CE NZ REMARK 470 LYS B 267 CG CD CE NZ REMARK 470 ILE B 271 CG2 CD1 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 A 154 70.02 39.03 REMARK 500 ALA B 123 79.36 -151.39 REMARK 500 LEU B 154 62.28 34.48 REMARK 500 GLN B 158 -76.23 -131.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN A 1304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN B 1301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AE5 RELATED DB: PDB REMARK 900 STRUCTURES OF INACTIVE AND ACTIVATED DNTR PROVIDE CONCLUSIVE REMARK 900 EVIDENCE FOR THE MECHANISM OF ACTION OF LYSR TRANSCRIPTION FACTORS DBREF 5AE4 A 1 301 UNP Q7WT50 Q7WT50_9BURK 1 301 DBREF 5AE4 B 1 301 UNP Q7WT50 Q7WT50_9BURK 1 301 SEQADV 5AE4 ARG A 302 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS A 303 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS A 304 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS A 305 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS A 306 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS A 307 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS A 308 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 THR A 169 UNP Q7WT50 HIS 169 ENGINEERED MUTATION SEQADV 5AE4 SER A 192 UNP Q7WT50 THR 192 CONFLICT SEQADV 5AE4 ARG B 302 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS B 303 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS B 304 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS B 305 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS B 306 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS B 307 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 HIS B 308 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE4 THR B 169 UNP Q7WT50 HIS 169 ENGINEERED MUTATION SEQADV 5AE4 SER B 192 UNP Q7WT50 THR 192 CONFLICT SEQRES 1 A 308 MET ASP LEU ARG ASP ILE ASP LEU ASN LEU LEU VAL VAL SEQRES 2 A 308 PHE ASN GLN LEU LEU LEU ASP ARG SER VAL SER THR ALA SEQRES 3 A 308 GLY GLU LYS LEU GLY LEU THR GLN PRO ALA VAL SER ASN SEQRES 4 A 308 SER LEU LYS ARG LEU ARG THR ALA LEU ASN ASP ASP LEU SEQRES 5 A 308 PHE LEU ARG THR SER LYS GLY MET GLU PRO THR PRO TYR SEQRES 6 A 308 ALA LEU HIS LEU ALA GLU PRO VAL ILE TYR ALA LEU ASN SEQRES 7 A 308 THR LEU GLN THR ALA LEU THR THR ARG ASP SER PHE ASP SEQRES 8 A 308 PRO PHE ALA SER THR ARG THR PHE ASN LEU ALA MET THR SEQRES 9 A 308 ASP ILE GLY GLU MET TYR PHE MET PRO PRO LEU MET GLU SEQRES 10 A 308 ALA LEU ALA GLN ARG ALA PRO HIS ILE GLN ILE SER THR SEQRES 11 A 308 LEU ARG PRO ASN ALA GLY ASN LEU LYS GLU ASP MET GLU SEQRES 12 A 308 SER GLY ALA VAL ASP LEU ALA LEU GLY LEU LEU PRO GLU SEQRES 13 A 308 LEU GLN THR GLY PHE PHE GLN ARG ARG LEU PHE ARG THR SEQRES 14 A 308 ARG TYR VAL CYS MET PHE ARG LYS ASP HIS PRO SER ALA SEQRES 15 A 308 LYS SER PRO MET SER LEU LYS GLN PHE SER GLU LEU GLU SEQRES 16 A 308 HIS VAL GLY VAL VAL ALA LEU ASN THR GLY HIS GLY GLU SEQRES 17 A 308 VAL ASP GLY LEU LEU GLU ARG ALA GLY ILE LYS ARG ARG SEQRES 18 A 308 MET ARG LEU VAL VAL PRO HIS PHE ILE ALA ILE GLY PRO SEQRES 19 A 308 ILE LEU HIS SER THR ASP LEU ILE ALA THR VAL PRO GLN SEQRES 20 A 308 ARG PHE ALA VAL ARG CYS GLU VAL PRO PHE GLY LEU THR SEQRES 21 A 308 THR SER PRO HIS PRO ALA LYS LEU PRO ASP ILE ALA ILE SEQRES 22 A 308 ASN LEU PHE TRP HIS ALA LYS TYR ASN ARG ASP PRO GLY SEQRES 23 A 308 ASN MET TRP LEU ARG GLN LEU PHE VAL GLU LEU PHE SER SEQRES 24 A 308 GLU ALA ARG HIS HIS HIS HIS HIS HIS SEQRES 1 B 308 MET ASP LEU ARG ASP ILE ASP LEU ASN LEU LEU VAL VAL SEQRES 2 B 308 PHE ASN GLN LEU LEU LEU ASP ARG SER VAL SER THR ALA SEQRES 3 B 308 GLY GLU LYS LEU GLY LEU THR GLN PRO ALA VAL SER ASN SEQRES 4 B 308 SER LEU LYS ARG LEU ARG THR ALA LEU ASN ASP ASP LEU SEQRES 5 B 308 PHE LEU ARG THR SER LYS GLY MET GLU PRO THR PRO TYR SEQRES 6 B 308 ALA LEU HIS LEU ALA GLU PRO VAL ILE TYR ALA LEU ASN SEQRES 7 B 308 THR LEU GLN THR ALA LEU THR THR ARG ASP SER PHE ASP SEQRES 8 B 308 PRO PHE ALA SER THR ARG THR PHE ASN LEU ALA MET THR SEQRES 9 B 308 ASP ILE GLY GLU MET TYR PHE MET PRO PRO LEU MET GLU SEQRES 10 B 308 ALA LEU ALA GLN ARG ALA PRO HIS ILE GLN ILE SER THR SEQRES 11 B 308 LEU ARG PRO ASN ALA GLY ASN LEU LYS GLU ASP MET GLU SEQRES 12 B 308 SER GLY ALA VAL ASP LEU ALA LEU GLY LEU LEU PRO GLU SEQRES 13 B 308 LEU GLN THR GLY PHE PHE GLN ARG ARG LEU PHE ARG THR SEQRES 14 B 308 ARG TYR VAL CYS MET PHE ARG LYS ASP HIS PRO SER ALA SEQRES 15 B 308 LYS SER PRO MET SER LEU LYS GLN PHE SER GLU LEU GLU SEQRES 16 B 308 HIS VAL GLY VAL VAL ALA LEU ASN THR GLY HIS GLY GLU SEQRES 17 B 308 VAL ASP GLY LEU LEU GLU ARG ALA GLY ILE LYS ARG ARG SEQRES 18 B 308 MET ARG LEU VAL VAL PRO HIS PHE ILE ALA ILE GLY PRO SEQRES 19 B 308 ILE LEU HIS SER THR ASP LEU ILE ALA THR VAL PRO GLN SEQRES 20 B 308 ARG PHE ALA VAL ARG CYS GLU VAL PRO PHE GLY LEU THR SEQRES 21 B 308 THR SER PRO HIS PRO ALA LYS LEU PRO ASP ILE ALA ILE SEQRES 22 B 308 ASN LEU PHE TRP HIS ALA LYS TYR ASN ARG ASP PRO GLY SEQRES 23 B 308 ASN MET TRP LEU ARG GLN LEU PHE VAL GLU LEU PHE SER SEQRES 24 B 308 GLU ALA ARG HIS HIS HIS HIS HIS HIS HET SCN A1304 3 HET SCN B1301 3 HETNAM SCN THIOCYANATE ION FORMUL 3 SCN 2(C N S 1-) HELIX 1 1 THR A 104 ALA A 123 1 20 HELIX 2 2 ASN A 137 SER A 144 1 8 HELIX 3 3 SER A 187 LEU A 194 1 8 HELIX 4 4 GLU A 208 ALA A 216 1 9 HELIX 5 5 ALA A 231 THR A 239 1 9 HELIX 6 6 GLN A 247 GLY A 258 1 12 HELIX 7 7 LYS A 280 ASN A 282 5 3 HELIX 8 8 ASP A 284 SER A 299 1 16 HELIX 9 9 THR B 104 ALA B 123 1 20 HELIX 10 10 ASN B 137 SER B 144 1 8 HELIX 11 11 SER B 187 LEU B 194 1 8 HELIX 12 12 THR B 204 GLY B 207 5 4 HELIX 13 13 GLU B 208 ALA B 216 1 9 HELIX 14 14 ALA B 231 THR B 239 1 9 HELIX 15 15 GLN B 247 VAL B 255 1 9 HELIX 16 16 LYS B 280 ASN B 282 5 3 HELIX 17 17 ASP B 284 SER B 299 1 16 SHEET 1 AA10 PHE A 161 THR A 169 0 SHEET 2 AA10 ILE A 271 HIS A 278 -1 O ILE A 271 N THR A 169 SHEET 3 AA10 LEU A 149 GLY A 152 -1 O ALA A 150 N PHE A 276 SHEET 4 AA10 THR A 98 ALA A 102 1 O ALA A 102 N LEU A 151 SHEET 5 AA10 GLN A 127 LEU A 131 1 O GLN A 127 N PHE A 99 SHEET 6 AA10 ARG B 221 VAL B 226 1 O ARG B 223 N ILE A 128 SHEET 7 AA10 GLU B 195 VAL B 199 1 O HIS B 196 N LEU B 224 SHEET 8 AA10 ILE B 242 PRO B 246 1 O ILE B 242 N VAL B 197 SHEET 9 AA10 TYR B 171 ARG B 176 -1 O VAL B 172 N VAL B 245 SHEET 10 AA10 LEU B 259 PRO B 263 -1 O THR B 260 N PHE B 175 SHEET 1 AB10 LEU A 259 PRO A 263 0 SHEET 2 AB10 TYR A 171 ARG A 176 -1 O CYS A 173 N SER A 262 SHEET 3 AB10 ILE A 242 PRO A 246 -1 O ALA A 243 N MET A 174 SHEET 4 AB10 GLU A 195 VAL A 199 1 O GLU A 195 N ILE A 242 SHEET 5 AB10 ARG A 221 VAL A 226 1 O ARG A 221 N HIS A 196 SHEET 6 AB10 GLN B 127 LEU B 131 1 O ILE B 128 N VAL A 225 SHEET 7 AB10 THR B 98 MET B 103 1 O PHE B 99 N SER B 129 SHEET 8 AB10 LEU B 149 GLY B 152 1 O LEU B 149 N ALA B 102 SHEET 9 AB10 ILE B 271 HIS B 278 -1 O ASN B 274 N GLY B 152 SHEET 10 AB10 PHE B 161 THR B 169 -1 O PHE B 162 N TRP B 277 CISPEP 1 SER A 184 PRO A 185 0 -1.56 CISPEP 2 GLY B 136 ASN B 137 0 -1.41 CISPEP 3 SER B 184 PRO B 185 0 -3.28 SITE 1 AC1 1 THR A 104 SITE 1 AC2 1 THR B 104 CRYST1 107.472 107.472 297.771 90.00 90.00 120.00 P 65 2 2 24 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 0.009305 0.005372 0.000000 0.00000 SCALE2 0.000000 0.010744 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003358 0.00000