HEADER TRANSCRIPTION 25-AUG-15 5AE5 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 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, APO-DNTR EXPDTA X-RAY DIFFRACTION AUTHOR M.LERCHE,C.DIAN,A.ROUND,R.LONNEBORG,P.BRZEZINSKI,G.A.LEONARD REVDAT 3 10-JAN-24 5AE5 1 REMARK REVDAT 2 10-FEB-16 5AE5 1 JRNL REVDAT 1 13-JAN-16 5AE5 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. 2.65 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 30423 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1537 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 47.1496 - 5.8789 1.00 2898 145 0.2312 0.2668 REMARK 3 2 5.8789 - 4.6676 1.00 2690 144 0.1950 0.2094 REMARK 3 3 4.6676 - 4.0780 1.00 2663 141 0.1596 0.1675 REMARK 3 4 4.0780 - 3.7053 1.00 2617 154 0.1704 0.2075 REMARK 3 5 3.7053 - 3.4398 1.00 2611 137 0.1793 0.1934 REMARK 3 6 3.4398 - 3.2370 1.00 2590 145 0.1992 0.2599 REMARK 3 7 3.2370 - 3.0750 1.00 2586 148 0.1978 0.2266 REMARK 3 8 3.0750 - 2.9411 1.00 2601 124 0.2281 0.2736 REMARK 3 9 2.9411 - 2.8279 1.00 2555 135 0.2308 0.2503 REMARK 3 10 2.8279 - 2.7303 1.00 2589 133 0.2526 0.3337 REMARK 3 11 2.7303 - 2.6450 0.97 2486 131 0.2709 0.3099 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 93.22 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 4554 REMARK 3 ANGLE : 0.969 6188 REMARK 3 CHIRALITY : 0.065 706 REMARK 3 PLANARITY : 0.005 808 REMARK 3 DIHEDRAL : 14.341 1633 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.2711 60.5459 28.2270 REMARK 3 T TENSOR REMARK 3 T11: 1.2188 T22: 1.6555 REMARK 3 T33: 1.8902 T12: 0.0979 REMARK 3 T13: 0.0708 T23: 0.2030 REMARK 3 L TENSOR REMARK 3 L11: 3.0335 L22: 0.5751 REMARK 3 L33: 5.8090 L12: -1.3415 REMARK 3 L13: 4.0058 L23: -1.5942 REMARK 3 S TENSOR REMARK 3 S11: 0.8682 S12: -0.5878 S13: 0.3867 REMARK 3 S21: 0.6676 S22: 0.5581 S23: -0.0330 REMARK 3 S31: 1.2913 S32: -1.6691 S33: -1.0344 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 34 THROUGH 84 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.6898 61.3713 25.3716 REMARK 3 T TENSOR REMARK 3 T11: 1.0965 T22: 1.1356 REMARK 3 T33: 3.0282 T12: -0.0954 REMARK 3 T13: -0.0365 T23: -0.1382 REMARK 3 L TENSOR REMARK 3 L11: 4.0414 L22: 7.7842 REMARK 3 L33: 2.1015 L12: -4.6414 REMARK 3 L13: 1.2014 L23: -3.4343 REMARK 3 S TENSOR REMARK 3 S11: 0.1374 S12: -0.0632 S13: -1.6285 REMARK 3 S21: 0.4348 S22: 1.6792 S23: 0.2155 REMARK 3 S31: 0.2373 S32: -0.5361 S33: -1.1899 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 85 THROUGH 303 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.6726 23.6862 -13.1821 REMARK 3 T TENSOR REMARK 3 T11: 0.5434 T22: 0.2418 REMARK 3 T33: 0.3752 T12: 0.0399 REMARK 3 T13: -0.0047 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.6429 L22: 2.1734 REMARK 3 L33: 3.8075 L12: -0.2143 REMARK 3 L13: 0.4175 L23: 0.7645 REMARK 3 S TENSOR REMARK 3 S11: -0.0627 S12: -0.0799 S13: 0.1426 REMARK 3 S21: 0.1387 S22: -0.0070 S23: -0.0953 REMARK 3 S31: -0.5671 S32: 0.1031 S33: 0.0573 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 5 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.9141 55.6364 -63.4420 REMARK 3 T TENSOR REMARK 3 T11: 1.4381 T22: 1.3681 REMARK 3 T33: 1.4297 T12: -0.1109 REMARK 3 T13: 0.3017 T23: -0.0644 REMARK 3 L TENSOR REMARK 3 L11: 6.3484 L22: 5.7937 REMARK 3 L33: 5.0359 L12: -0.0377 REMARK 3 L13: 0.9509 L23: 1.0117 REMARK 3 S TENSOR REMARK 3 S11: -0.3851 S12: -0.6574 S13: 0.4289 REMARK 3 S21: 0.1753 S22: 0.9821 S23: 0.5957 REMARK 3 S31: -0.2238 S32: 0.3918 S33: -0.8018 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 66 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.4575 30.5694 -32.1920 REMARK 3 T TENSOR REMARK 3 T11: 0.6996 T22: 0.3736 REMARK 3 T33: 0.4649 T12: 0.1720 REMARK 3 T13: 0.0215 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 2.4178 L22: 1.9786 REMARK 3 L33: 3.3523 L12: -1.0920 REMARK 3 L13: -0.7221 L23: 1.0736 REMARK 3 S TENSOR REMARK 3 S11: 0.3034 S12: 0.3601 S13: 0.4062 REMARK 3 S21: -0.2399 S22: -0.1620 S23: -0.1102 REMARK 3 S31: -1.1033 S32: -0.4388 S33: -0.1516 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 5AE5 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_1290064266. 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 : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : SI(111) AND SI (311) REMARK 200 OPTICS : MIRRORS 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 : 30522 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.640 REMARK 200 RESOLUTION RANGE LOW (A) : 47.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 65.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM POTASSIUM TARTRATE, 0.1 M REMARK 280 TRIS-HCL PH 8.0, 5 % (W/V) PEG 6000 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 198.56267 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 99.28133 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 148.92200 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 49.64067 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 248.20333 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 198.56267 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 99.28133 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 49.64067 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 148.92200 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 248.20333 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 53470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.8 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 350 BIOMT1 2 0.500000 0.866025 0.000000 -53.56600 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 92.77903 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -49.64067 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2037 LIES ON A SPECIAL POSITION. 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 LEU A 30 REMARK 465 GLY A 31 REMARK 465 LEU A 32 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 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 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 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 ASP A 5 CG OD1 OD2 REMARK 470 ASN A 15 CG OD1 ND2 REMARK 470 GLN A 16 CG CD OE1 NE2 REMARK 470 LEU A 17 CG CD1 CD2 REMARK 470 LEU A 18 CG CD1 CD2 REMARK 470 GLU A 28 CG CD OE1 OE2 REMARK 470 LYS A 29 CG CD CE NZ REMARK 470 GLN A 34 CG CD OE1 NE2 REMARK 470 VAL A 37 CG1 CG2 REMARK 470 SER A 38 OG REMARK 470 SER A 40 OG REMARK 470 LYS A 42 CG CD CE NZ REMARK 470 ARG A 43 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 45 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 ALA A 66 CB REMARK 470 LEU A 69 CG CD1 CD2 REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 TYR A 75 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 77 CG CD1 CD2 REMARK 470 LEU A 80 CG CD1 CD2 REMARK 470 LEU A 84 CG CD1 CD2 REMARK 470 THR A 85 OG1 CG2 REMARK 470 ARG A 87 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 88 CG OD1 OD2 REMARK 470 LYS A 219 CG CD CE NZ REMARK 470 LYS A 267 CD CE NZ REMARK 470 ASP B 5 CG OD1 OD2 REMARK 470 ILE B 6 CG1 CG2 CD1 REMARK 470 LEU B 10 CG CD1 CD2 REMARK 470 LEU B 17 CG CD1 CD2 REMARK 470 LEU B 19 CG CD1 CD2 REMARK 470 ARG B 21 CG CD NE CZ NH1 NH2 REMARK 470 SER B 24 OG REMARK 470 LYS B 29 CG CD CE NZ REMARK 470 LEU B 30 CG CD1 CD2 REMARK 470 LEU B 32 CG CD1 CD2 REMARK 470 THR B 33 OG1 CG2 REMARK 470 SER B 40 OG REMARK 470 LEU B 41 CG CD1 CD2 REMARK 470 LYS B 42 CG CD CE NZ REMARK 470 GLU B 61 CG CD OE1 OE2 REMARK 470 ALA B 66 CB REMARK 470 ILE B 74 CG1 CG2 CD1 REMARK 470 TYR B 75 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU B 77 CG CD1 CD2 REMARK 470 ASN B 78 CG OD1 ND2 REMARK 470 LEU B 80 CG CD1 CD2 REMARK 470 LEU B 84 CG CD1 CD2 REMARK 470 ARG B 87 O REMARK 470 ASN B 134 CG OD1 ND2 REMARK 470 LYS B 139 CD CE NZ REMARK 470 GLU B 143 OE1 OE2 REMARK 470 ARG B 170 NE CZ NH1 NH2 REMARK 470 LYS B 183 CD CE NZ REMARK 470 LYS B 189 CG CD CE NZ REMARK 470 LYS B 219 CG CD CE NZ REMARK 470 LYS B 267 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O THR A 96 O HOH A 2007 1.96 REMARK 500 O HOH A 2003 O HOH A 2028 2.11 REMARK 500 O THR A 159 O2 GOL A 1304 2.14 REMARK 500 NH1 ARG B 220 O HOH B 2017 2.16 REMARK 500 NH2 ARG A 223 O ALA B 123 2.19 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 ILE A 6 -140.11 43.35 REMARK 500 ARG A 21 -122.46 57.11 REMARK 500 ASN A 49 -38.15 -34.29 REMARK 500 PRO A 133 24.08 -64.04 REMARK 500 ASN A 134 22.84 -148.55 REMARK 500 GLN A 158 -83.91 -126.28 REMARK 500 SER A 181 -26.11 -142.46 REMARK 500 ARG A 302 36.31 -95.46 REMARK 500 SER B 22 -6.97 -53.59 REMARK 500 ASN B 49 18.40 58.67 REMARK 500 PRO B 64 -127.55 -104.10 REMARK 500 GLN B 158 -50.80 -132.17 REMARK 500 ASP B 178 37.35 -83.02 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 GOL A 1304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AE4 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 5AE5 A 1 301 UNP Q7WT50 Q7WT50_9BURK 1 301 DBREF 5AE5 B 1 301 UNP Q7WT50 Q7WT50_9BURK 1 301 SEQADV 5AE5 ARG A 302 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS A 303 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS A 304 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS A 305 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS A 306 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS A 307 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS A 308 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 SER A 192 UNP Q7WT50 THR 192 CONFLICT SEQADV 5AE5 ARG B 302 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS B 303 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS B 304 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS B 305 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS B 306 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS B 307 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 HIS B 308 UNP Q7WT50 EXPRESSION TAG SEQADV 5AE5 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 HIS 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 HIS 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 GOL A1304 6 HET GOL A1305 6 HET GOL A1306 6 HET GOL A1307 6 HET GOL A1308 6 HET GOL B1301 6 HET GOL B1302 6 HET GOL B1303 6 HET GOL B1304 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 9(C3 H8 O3) FORMUL 12 HOH *81(H2 O) HELIX 1 1 MET A 1 ILE A 6 1 6 HELIX 2 2 LEU A 8 PHE A 14 1 7 HELIX 3 3 SER A 22 LYS A 29 1 8 HELIX 4 4 THR A 33 LEU A 48 1 16 HELIX 5 5 THR A 63 THR A 82 1 20 HELIX 6 6 ALA A 83 THR A 85 5 3 HELIX 7 7 THR A 104 ALA A 123 1 20 HELIX 8 8 ASN A 137 SER A 144 1 8 HELIX 9 9 SER A 187 LEU A 194 1 8 HELIX 10 10 THR A 204 GLY A 207 5 4 HELIX 11 11 GLU A 208 ARG A 215 1 8 HELIX 12 12 ALA A 231 THR A 239 1 9 HELIX 13 13 GLN A 247 GLY A 258 1 12 HELIX 14 14 LYS A 280 ASN A 282 5 3 HELIX 15 15 ASP A 284 SER A 299 1 16 HELIX 16 16 LEU B 8 ASP B 20 1 13 HELIX 17 17 ALA B 26 GLY B 31 1 6 HELIX 18 18 THR B 33 ASN B 49 1 17 HELIX 19 19 TYR B 65 THR B 85 1 21 HELIX 20 20 THR B 104 ALA B 123 1 20 HELIX 21 21 ASN B 137 SER B 144 1 8 HELIX 22 22 SER B 187 LEU B 194 1 8 HELIX 23 23 THR B 204 GLY B 207 5 4 HELIX 24 24 GLU B 208 ALA B 216 1 9 HELIX 25 25 ALA B 231 THR B 239 1 9 HELIX 26 26 GLN B 247 GLY B 258 1 12 HELIX 27 27 LYS B 280 ASN B 282 5 3 HELIX 28 28 ASP B 284 SER B 299 1 16 SHEET 1 AA10 PHE A 161 HIS A 169 0 SHEET 2 AA10 ILE A 271 HIS A 278 -1 O ILE A 271 N HIS 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 AB 3 ALA A 243 PRO A 246 0 SHEET 2 AB 3 TYR A 171 ARG A 176 -1 O VAL A 172 N VAL A 245 SHEET 3 AB 3 LEU A 259 PRO A 263 -1 O THR A 260 N PHE A 175 SHEET 1 AC 7 GLU A 195 VAL A 199 0 SHEET 2 AC 7 ARG A 221 VAL A 226 1 O ARG A 221 N HIS A 196 SHEET 3 AC 7 GLN B 127 LEU B 131 1 O ILE B 128 N VAL A 225 SHEET 4 AC 7 THR B 98 ALA B 102 1 O PHE B 99 N SER B 129 SHEET 5 AC 7 LEU B 149 GLY B 152 1 O LEU B 149 N ALA B 102 SHEET 6 AC 7 ILE B 271 HIS B 278 -1 O ASN B 274 N GLY B 152 SHEET 7 AC 7 PHE B 161 HIS B 169 -1 O PHE B 162 N TRP B 277 CISPEP 1 SER A 184 PRO A 185 0 4.79 CISPEP 2 SER B 24 THR B 25 0 14.04 CISPEP 3 ASN B 134 ALA B 135 0 0.58 CISPEP 4 GLY B 136 ASN B 137 0 4.68 CISPEP 5 SER B 184 PRO B 185 0 2.99 SITE 1 AC1 7 THR A 159 PHE A 161 PHE A 162 ARG B 164 SITE 2 AC1 7 GLN B 292 VAL B 295 GOL B1303 SITE 1 AC2 4 ALA A 279 ASN A 282 ARG A 283 SER B 299 SITE 1 AC3 7 ASP A 105 ARG A 132 HIS A 228 HOH A2055 SITE 2 AC3 7 ASP B 105 ARG B 132 HIS B 228 SITE 1 AC4 4 VAL A 199 ASP A 210 ARG A 220 THR A 244 SITE 1 AC5 1 ARG A 252 SITE 1 AC6 8 MET A 116 ALA A 120 GLU B 195 ARG B 223 SITE 2 AC6 8 THR B 239 ASP B 240 LEU B 241 HOH B2022 SITE 1 AC7 9 MET A 109 ILE A 230 PHE A 257 MET B 109 SITE 2 AC7 9 PHE B 229 ILE B 230 GLY B 233 PHE B 249 SITE 3 AC7 9 PHE B 257 SITE 1 AC8 4 GOL A1304 TRP B 277 ASN B 282 ARG B 291 SITE 1 AC9 2 SER B 89 PHE B 90 CRYST1 107.132 107.132 297.844 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 0.009334 0.005389 0.000000 0.00000 SCALE2 0.000000 0.010778 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003357 0.00000