HEADER TRANSCRIPTION 12-MAY-09 3HFU TITLE CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF E. COLI CYNR WITH TITLE 2 ITS SPECIFIC EFFECTOR AZIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYNR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 63-299; COMPND 5 SYNONYM: CYN OPERON TRANSCRIPTIONAL ACTIVATOR; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B0338, CYNR, JW5894; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON-PLUS RP; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P15TVLIC KEYWDS CYNR, LYSR TRANSCRIPTIONAL ACTIVIATOR, EFFECTOR, AZIDE, ACTIVATOR, KEYWDS 2 CYTOPLASM, DNA-BINDING, REPRESSOR, TRANSCRIPTION, TRANSCRIPTION KEYWDS 3 REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR A.U.SINGER,E.EVDOKIMOVA,O.KAGAN,A.DONG,A.M.EDWARDS,A.SAVCHENKO REVDAT 3 22-NOV-23 3HFU 1 REMARK REVDAT 2 06-SEP-23 3HFU 1 REMARK SEQADV LINK REVDAT 1 09-JUN-09 3HFU 0 JRNL AUTH A.U.SINGER,E.EVDOKIMOVA,O.KAGAN,M.E.CUFF,A.M.EDWARDS, JRNL AUTH 2 A.JOACHIMIAK,A.SAVCHENKO JRNL TITL CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF E. COLI JRNL TITL 2 CYNR WITH ITS SPECIFIC EFFECTOR AZIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 30756 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 SET) : 0.223 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1527 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.63 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3059 REMARK 3 BIN FREE R VALUE : 0.3555 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 47 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6281 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 481 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.45400 REMARK 3 B22 (A**2) : 6.36600 REMARK 3 B33 (A**2) : -18.82000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.67000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HFU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000053081. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : VARIMAX HR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44532 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11100 REMARK 200 FOR THE DATA SET : 17.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.090 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2HXR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG5000 MONOMETHYL ETHER (MME) REMARK 280 PLUS 100 MM TRIS 8.5, CRYOPROTECTED IN 25% ETHYLENE GLYCOL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K, PH 8.5 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 49.18150 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 62 REMARK 465 VAL A 63 REMARK 465 TRP A 64 REMARK 465 ARG A 65 REMARK 465 GLN A 66 REMARK 465 TYR A 67 REMARK 465 ALA A 68 REMARK 465 SER A 69 REMARK 465 ARG A 70 REMARK 465 ALA A 71 REMARK 465 LEU A 72 REMARK 465 GLN A 73 REMARK 465 GLU A 74 REMARK 465 LEU A 75 REMARK 465 GLY A 76 REMARK 465 ALA A 77 REMARK 465 GLY A 78 REMARK 465 LYS A 79 REMARK 465 ARG A 80 REMARK 465 ALA A 81 REMARK 465 ILE A 82 REMARK 465 HIS A 83 REMARK 465 ASP A 84 REMARK 465 VAL A 85 REMARK 465 ALA A 86 REMARK 465 ASP A 87 REMARK 465 LEU A 88 REMARK 465 THR A 89 REMARK 465 ARG A 90 REMARK 465 VAL A 293 REMARK 465 GLY A 294 REMARK 465 GLY A 295 REMARK 465 ASN A 296 REMARK 465 GLU A 297 REMARK 465 SER A 298 REMARK 465 ARG A 299 REMARK 465 GLY B 62 REMARK 465 VAL B 63 REMARK 465 TRP B 64 REMARK 465 ARG B 65 REMARK 465 GLN B 66 REMARK 465 TYR B 67 REMARK 465 ALA B 68 REMARK 465 SER B 69 REMARK 465 ARG B 70 REMARK 465 ALA B 71 REMARK 465 LEU B 72 REMARK 465 GLN B 73 REMARK 465 GLU B 74 REMARK 465 LEU B 75 REMARK 465 GLY B 76 REMARK 465 ALA B 77 REMARK 465 GLY B 78 REMARK 465 LYS B 79 REMARK 465 ARG B 80 REMARK 465 ALA B 81 REMARK 465 ILE B 82 REMARK 465 HIS B 83 REMARK 465 ASP B 84 REMARK 465 VAL B 85 REMARK 465 ALA B 86 REMARK 465 ASP B 87 REMARK 465 LEU B 88 REMARK 465 VAL B 293 REMARK 465 GLY B 294 REMARK 465 GLY B 295 REMARK 465 ASN B 296 REMARK 465 GLU B 297 REMARK 465 SER B 298 REMARK 465 ARG B 299 REMARK 465 GLY C 62 REMARK 465 VAL C 63 REMARK 465 TRP C 64 REMARK 465 ARG C 65 REMARK 465 GLN C 66 REMARK 465 TYR C 67 REMARK 465 ALA C 68 REMARK 465 SER C 69 REMARK 465 ARG C 70 REMARK 465 ALA C 71 REMARK 465 LEU C 72 REMARK 465 GLN C 73 REMARK 465 GLU C 74 REMARK 465 LEU C 75 REMARK 465 GLY C 76 REMARK 465 ALA C 77 REMARK 465 GLY C 78 REMARK 465 LYS C 79 REMARK 465 ARG C 80 REMARK 465 ALA C 81 REMARK 465 ILE C 82 REMARK 465 HIS C 83 REMARK 465 ASP C 84 REMARK 465 VAL C 85 REMARK 465 ALA C 86 REMARK 465 ASP C 87 REMARK 465 LEU C 88 REMARK 465 THR C 89 REMARK 465 VAL C 293 REMARK 465 GLY C 294 REMARK 465 GLY C 295 REMARK 465 ASN C 296 REMARK 465 GLU C 297 REMARK 465 SER C 298 REMARK 465 ARG C 299 REMARK 465 GLY D 62 REMARK 465 VAL D 63 REMARK 465 TRP D 64 REMARK 465 ARG D 65 REMARK 465 GLN D 66 REMARK 465 TYR D 67 REMARK 465 ALA D 68 REMARK 465 SER D 69 REMARK 465 ARG D 70 REMARK 465 ALA D 71 REMARK 465 LEU D 72 REMARK 465 GLN D 73 REMARK 465 GLU D 74 REMARK 465 LEU D 75 REMARK 465 GLY D 76 REMARK 465 ALA D 77 REMARK 465 GLY D 78 REMARK 465 LYS D 79 REMARK 465 ARG D 80 REMARK 465 ALA D 81 REMARK 465 ILE D 82 REMARK 465 HIS D 83 REMARK 465 ASP D 84 REMARK 465 VAL D 85 REMARK 465 ALA D 86 REMARK 465 ASP D 87 REMARK 465 LEU D 88 REMARK 465 THR D 89 REMARK 465 ARG D 90 REMARK 465 VAL D 293 REMARK 465 GLY D 294 REMARK 465 GLY D 295 REMARK 465 ASN D 296 REMARK 465 GLU D 297 REMARK 465 SER D 298 REMARK 465 ARG D 299 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 THR B 89 OG1 CG2 REMARK 470 ARG C 90 CG CD NE CZ NH1 NH2 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 PRO A 99 -56.89 -29.87 REMARK 500 TYR A 104 -26.02 -170.77 REMARK 500 PHE A 105 -64.40 -97.82 REMARK 500 ALA A 146 -153.88 -153.08 REMARK 500 LEU A 160 -60.36 -103.55 REMARK 500 PRO A 174 -19.41 -49.62 REMARK 500 ARG B 90 -79.74 -40.96 REMARK 500 SER B 92 126.95 171.78 REMARK 500 LEU B 93 114.90 -161.41 REMARK 500 TYR B 104 -27.23 -162.50 REMARK 500 PHE B 105 -66.33 -96.51 REMARK 500 ALA B 146 -149.04 -152.61 REMARK 500 THR B 234 -168.00 -128.06 REMARK 500 LEU C 93 109.86 -165.62 REMARK 500 TYR C 104 -33.32 -169.25 REMARK 500 PRO C 118 -18.79 -49.04 REMARK 500 ALA C 146 -153.43 -153.04 REMARK 500 TYR D 104 -32.84 -165.28 REMARK 500 PHE D 105 -72.82 -89.13 REMARK 500 ALA D 146 -154.27 -154.72 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 AZI A 2102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI B 2104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI C 2103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI D 2101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO D 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HXR RELATED DB: PDB REMARK 900 STRUCTURE OF THE LIGAND BINDING DOMAIN OF E. COLI CYNR, A REMARK 900 TRANSCRIPTIONAL REGULATOR CONTROLLING CYANATE METABOLISM DBREF 3HFU A 63 299 UNP P27111 CYNR_ECOLI 63 299 DBREF 3HFU B 63 299 UNP P27111 CYNR_ECOLI 63 299 DBREF 3HFU C 63 299 UNP P27111 CYNR_ECOLI 63 299 DBREF 3HFU D 63 299 UNP P27111 CYNR_ECOLI 63 299 SEQADV 3HFU GLY A 62 UNP P27111 EXPRESSION TAG SEQADV 3HFU GLY B 62 UNP P27111 EXPRESSION TAG SEQADV 3HFU GLY C 62 UNP P27111 EXPRESSION TAG SEQADV 3HFU GLY D 62 UNP P27111 EXPRESSION TAG SEQRES 1 A 238 GLY VAL TRP ARG GLN TYR ALA SER ARG ALA LEU GLN GLU SEQRES 2 A 238 LEU GLY ALA GLY LYS ARG ALA ILE HIS ASP VAL ALA ASP SEQRES 3 A 238 LEU THR ARG GLY SER LEU ARG ILE ALA VAL THR PRO THR SEQRES 4 A 238 PHE THR SER TYR PHE ILE GLY PRO LEU MSE ALA ASP PHE SEQRES 5 A 238 TYR ALA ARG TYR PRO SER ILE THR LEU GLN LEU GLN GLU SEQRES 6 A 238 MSE SER GLN GLU LYS ILE GLU ASP MSE LEU CYS ARG ASP SEQRES 7 A 238 GLU LEU ASP VAL GLY ILE ALA PHE ALA PRO VAL HIS SER SEQRES 8 A 238 PRO GLU LEU GLU ALA ILE PRO LEU LEU THR GLU SER LEU SEQRES 9 A 238 ALA LEU VAL VAL ALA GLN HIS HIS PRO LEU ALA VAL HIS SEQRES 10 A 238 GLU GLN VAL ALA LEU SER ARG LEU HIS ASP GLU LYS LEU SEQRES 11 A 238 VAL LEU LEU SER ALA GLU PHE ALA THR ARG GLU GLN ILE SEQRES 12 A 238 ASP HIS TYR CYS GLU LYS ALA GLY LEU HIS PRO GLN VAL SEQRES 13 A 238 VAL ILE GLU ALA ASN SER ILE SER ALA VAL LEU GLU LEU SEQRES 14 A 238 ILE ARG ARG THR SER LEU SER THR LEU LEU PRO ALA ALA SEQRES 15 A 238 ILE ALA THR GLN HIS ASP GLY LEU LYS ALA ILE SER LEU SEQRES 16 A 238 ALA PRO PRO LEU LEU GLU ARG THR ALA VAL LEU LEU ARG SEQRES 17 A 238 ARG LYS ASN SER TRP GLN THR ALA ALA ALA LYS ALA PHE SEQRES 18 A 238 LEU HIS MSE ALA LEU ASP LYS CYS ALA VAL VAL GLY GLY SEQRES 19 A 238 ASN GLU SER ARG SEQRES 1 B 238 GLY VAL TRP ARG GLN TYR ALA SER ARG ALA LEU GLN GLU SEQRES 2 B 238 LEU GLY ALA GLY LYS ARG ALA ILE HIS ASP VAL ALA ASP SEQRES 3 B 238 LEU THR ARG GLY SER LEU ARG ILE ALA VAL THR PRO THR SEQRES 4 B 238 PHE THR SER TYR PHE ILE GLY PRO LEU MSE ALA ASP PHE SEQRES 5 B 238 TYR ALA ARG TYR PRO SER ILE THR LEU GLN LEU GLN GLU SEQRES 6 B 238 MSE SER GLN GLU LYS ILE GLU ASP MSE LEU CYS ARG ASP SEQRES 7 B 238 GLU LEU ASP VAL GLY ILE ALA PHE ALA PRO VAL HIS SER SEQRES 8 B 238 PRO GLU LEU GLU ALA ILE PRO LEU LEU THR GLU SER LEU SEQRES 9 B 238 ALA LEU VAL VAL ALA GLN HIS HIS PRO LEU ALA VAL HIS SEQRES 10 B 238 GLU GLN VAL ALA LEU SER ARG LEU HIS ASP GLU LYS LEU SEQRES 11 B 238 VAL LEU LEU SER ALA GLU PHE ALA THR ARG GLU GLN ILE SEQRES 12 B 238 ASP HIS TYR CYS GLU LYS ALA GLY LEU HIS PRO GLN VAL SEQRES 13 B 238 VAL ILE GLU ALA ASN SER ILE SER ALA VAL LEU GLU LEU SEQRES 14 B 238 ILE ARG ARG THR SER LEU SER THR LEU LEU PRO ALA ALA SEQRES 15 B 238 ILE ALA THR GLN HIS ASP GLY LEU LYS ALA ILE SER LEU SEQRES 16 B 238 ALA PRO PRO LEU LEU GLU ARG THR ALA VAL LEU LEU ARG SEQRES 17 B 238 ARG LYS ASN SER TRP GLN THR ALA ALA ALA LYS ALA PHE SEQRES 18 B 238 LEU HIS MSE ALA LEU ASP LYS CYS ALA VAL VAL GLY GLY SEQRES 19 B 238 ASN GLU SER ARG SEQRES 1 C 238 GLY VAL TRP ARG GLN TYR ALA SER ARG ALA LEU GLN GLU SEQRES 2 C 238 LEU GLY ALA GLY LYS ARG ALA ILE HIS ASP VAL ALA ASP SEQRES 3 C 238 LEU THR ARG GLY SER LEU ARG ILE ALA VAL THR PRO THR SEQRES 4 C 238 PHE THR SER TYR PHE ILE GLY PRO LEU MSE ALA ASP PHE SEQRES 5 C 238 TYR ALA ARG TYR PRO SER ILE THR LEU GLN LEU GLN GLU SEQRES 6 C 238 MSE SER GLN GLU LYS ILE GLU ASP MSE LEU CYS ARG ASP SEQRES 7 C 238 GLU LEU ASP VAL GLY ILE ALA PHE ALA PRO VAL HIS SER SEQRES 8 C 238 PRO GLU LEU GLU ALA ILE PRO LEU LEU THR GLU SER LEU SEQRES 9 C 238 ALA LEU VAL VAL ALA GLN HIS HIS PRO LEU ALA VAL HIS SEQRES 10 C 238 GLU GLN VAL ALA LEU SER ARG LEU HIS ASP GLU LYS LEU SEQRES 11 C 238 VAL LEU LEU SER ALA GLU PHE ALA THR ARG GLU GLN ILE SEQRES 12 C 238 ASP HIS TYR CYS GLU LYS ALA GLY LEU HIS PRO GLN VAL SEQRES 13 C 238 VAL ILE GLU ALA ASN SER ILE SER ALA VAL LEU GLU LEU SEQRES 14 C 238 ILE ARG ARG THR SER LEU SER THR LEU LEU PRO ALA ALA SEQRES 15 C 238 ILE ALA THR GLN HIS ASP GLY LEU LYS ALA ILE SER LEU SEQRES 16 C 238 ALA PRO PRO LEU LEU GLU ARG THR ALA VAL LEU LEU ARG SEQRES 17 C 238 ARG LYS ASN SER TRP GLN THR ALA ALA ALA LYS ALA PHE SEQRES 18 C 238 LEU HIS MSE ALA LEU ASP LYS CYS ALA VAL VAL GLY GLY SEQRES 19 C 238 ASN GLU SER ARG SEQRES 1 D 238 GLY VAL TRP ARG GLN TYR ALA SER ARG ALA LEU GLN GLU SEQRES 2 D 238 LEU GLY ALA GLY LYS ARG ALA ILE HIS ASP VAL ALA ASP SEQRES 3 D 238 LEU THR ARG GLY SER LEU ARG ILE ALA VAL THR PRO THR SEQRES 4 D 238 PHE THR SER TYR PHE ILE GLY PRO LEU MSE ALA ASP PHE SEQRES 5 D 238 TYR ALA ARG TYR PRO SER ILE THR LEU GLN LEU GLN GLU SEQRES 6 D 238 MSE SER GLN GLU LYS ILE GLU ASP MSE LEU CYS ARG ASP SEQRES 7 D 238 GLU LEU ASP VAL GLY ILE ALA PHE ALA PRO VAL HIS SER SEQRES 8 D 238 PRO GLU LEU GLU ALA ILE PRO LEU LEU THR GLU SER LEU SEQRES 9 D 238 ALA LEU VAL VAL ALA GLN HIS HIS PRO LEU ALA VAL HIS SEQRES 10 D 238 GLU GLN VAL ALA LEU SER ARG LEU HIS ASP GLU LYS LEU SEQRES 11 D 238 VAL LEU LEU SER ALA GLU PHE ALA THR ARG GLU GLN ILE SEQRES 12 D 238 ASP HIS TYR CYS GLU LYS ALA GLY LEU HIS PRO GLN VAL SEQRES 13 D 238 VAL ILE GLU ALA ASN SER ILE SER ALA VAL LEU GLU LEU SEQRES 14 D 238 ILE ARG ARG THR SER LEU SER THR LEU LEU PRO ALA ALA SEQRES 15 D 238 ILE ALA THR GLN HIS ASP GLY LEU LYS ALA ILE SER LEU SEQRES 16 D 238 ALA PRO PRO LEU LEU GLU ARG THR ALA VAL LEU LEU ARG SEQRES 17 D 238 ARG LYS ASN SER TRP GLN THR ALA ALA ALA LYS ALA PHE SEQRES 18 D 238 LEU HIS MSE ALA LEU ASP LYS CYS ALA VAL VAL GLY GLY SEQRES 19 D 238 ASN GLU SER ARG MODRES 3HFU MSE A 110 MET SELENOMETHIONINE MODRES 3HFU MSE A 127 MET SELENOMETHIONINE MODRES 3HFU MSE A 135 MET SELENOMETHIONINE MODRES 3HFU MSE A 285 MET SELENOMETHIONINE MODRES 3HFU MSE B 110 MET SELENOMETHIONINE MODRES 3HFU MSE B 127 MET SELENOMETHIONINE MODRES 3HFU MSE B 135 MET SELENOMETHIONINE MODRES 3HFU MSE B 285 MET SELENOMETHIONINE MODRES 3HFU MSE C 110 MET SELENOMETHIONINE MODRES 3HFU MSE C 127 MET SELENOMETHIONINE MODRES 3HFU MSE C 135 MET SELENOMETHIONINE MODRES 3HFU MSE C 285 MET SELENOMETHIONINE MODRES 3HFU MSE D 110 MET SELENOMETHIONINE MODRES 3HFU MSE D 127 MET SELENOMETHIONINE MODRES 3HFU MSE D 135 MET SELENOMETHIONINE MODRES 3HFU MSE D 285 MET SELENOMETHIONINE HET MSE A 110 8 HET MSE A 127 8 HET MSE A 135 8 HET MSE A 285 8 HET MSE B 110 8 HET MSE B 127 8 HET MSE B 135 8 HET MSE B 285 8 HET MSE C 110 8 HET MSE C 127 8 HET MSE C 135 8 HET MSE C 285 8 HET MSE D 110 8 HET MSE D 127 8 HET MSE D 135 8 HET MSE D 285 8 HET AZI A2102 3 HET AZI B2104 3 HET AZI C2103 3 HET EDO C2002 4 HET AZI D2101 3 HET EDO D2001 4 HETNAM MSE SELENOMETHIONINE HETNAM AZI AZIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 16(C5 H11 N O2 SE) FORMUL 5 AZI 4(N3 1-) FORMUL 8 EDO 2(C2 H6 O2) FORMUL 11 HOH *481(H2 O) HELIX 1 1 THR A 98 SER A 103 1 6 HELIX 2 2 PHE A 105 TYR A 117 1 13 HELIX 3 3 SER A 128 ARG A 138 1 11 HELIX 4 4 SER A 184 ASP A 188 5 5 HELIX 5 5 PHE A 198 ALA A 211 1 14 HELIX 6 6 SER A 223 THR A 234 1 12 HELIX 7 7 ALA A 242 GLN A 247 1 6 HELIX 8 8 THR A 276 CYS A 290 1 15 HELIX 9 9 THR B 98 SER B 103 1 6 HELIX 10 10 PHE B 105 TYR B 117 1 13 HELIX 11 11 SER B 128 ARG B 138 1 11 HELIX 12 12 SER B 184 ASP B 188 5 5 HELIX 13 13 PHE B 198 ALA B 211 1 14 HELIX 14 14 SER B 223 THR B 234 1 12 HELIX 15 15 ALA B 243 HIS B 248 5 6 HELIX 16 16 THR B 276 CYS B 290 1 15 HELIX 17 17 THR C 98 SER C 103 1 6 HELIX 18 18 PHE C 105 TYR C 117 1 13 HELIX 19 19 SER C 128 ARG C 138 1 11 HELIX 20 20 SER C 184 ASP C 188 5 5 HELIX 21 21 PHE C 198 ALA C 211 1 14 HELIX 22 22 SER C 223 ARG C 233 1 11 HELIX 23 23 ALA C 243 HIS C 248 5 6 HELIX 24 24 THR C 276 CYS C 290 1 15 HELIX 25 25 THR D 98 SER D 103 1 6 HELIX 26 26 PHE D 105 TYR D 117 1 13 HELIX 27 27 SER D 128 ARG D 138 1 11 HELIX 28 28 SER D 184 ASP D 188 5 5 HELIX 29 29 PHE D 198 ALA D 211 1 14 HELIX 30 30 SER D 223 THR D 234 1 12 HELIX 31 31 ALA D 243 HIS D 248 5 6 HELIX 32 32 THR D 276 ALA D 291 1 16 SHEET 1 A 4 GLN A 180 ALA A 182 0 SHEET 2 A 4 LEU A 251 ALA A 257 1 O SER A 255 N VAL A 181 SHEET 3 A 4 LEU A 155 ALA A 170 -1 N LEU A 167 O ILE A 254 SHEET 4 A 4 THR A 238 PRO A 241 -1 O THR A 238 N VAL A 168 SHEET 1 B 9 GLN A 180 ALA A 182 0 SHEET 2 B 9 LEU A 251 ALA A 257 1 O SER A 255 N VAL A 181 SHEET 3 B 9 LEU A 155 ALA A 170 -1 N LEU A 167 O ILE A 254 SHEET 4 B 9 GLU A 262 ARG A 270 -1 O ARG A 269 N GLU A 156 SHEET 5 B 9 VAL A 143 PHE A 147 -1 N GLY A 144 O LEU A 268 SHEET 6 B 9 LEU A 93 VAL A 97 1 O ARG A 94 N VAL A 143 SHEET 7 B 9 LEU A 122 GLU A 126 1 O GLN A 123 N ILE A 95 SHEET 8 B 9 GLN C 216 ALA C 221 1 O GLU C 220 N LEU A 122 SHEET 9 B 9 LYS C 190 LEU C 194 1 N LEU C 191 O GLN C 216 SHEET 1 C 9 LYS A 190 LEU A 194 0 SHEET 2 C 9 GLN A 216 ALA A 221 1 O GLN A 216 N LEU A 191 SHEET 3 C 9 THR C 121 GLU C 126 1 O LEU C 124 N GLU A 220 SHEET 4 C 9 SER C 92 VAL C 97 1 N ILE C 95 O GLN C 123 SHEET 5 C 9 VAL C 143 PHE C 147 1 O VAL C 143 N ARG C 94 SHEET 6 C 9 GLU C 262 ARG C 270 -1 O VAL C 266 N ALA C 146 SHEET 7 C 9 LEU C 155 ALA C 170 -1 N GLU C 156 O ARG C 269 SHEET 8 C 9 LEU C 251 ALA C 257 -1 O ILE C 254 N LEU C 167 SHEET 9 C 9 GLN C 180 ALA C 182 1 N VAL C 181 O SER C 255 SHEET 1 D 8 LYS A 190 LEU A 194 0 SHEET 2 D 8 GLN A 216 ALA A 221 1 O GLN A 216 N LEU A 191 SHEET 3 D 8 THR C 121 GLU C 126 1 O LEU C 124 N GLU A 220 SHEET 4 D 8 SER C 92 VAL C 97 1 N ILE C 95 O GLN C 123 SHEET 5 D 8 VAL C 143 PHE C 147 1 O VAL C 143 N ARG C 94 SHEET 6 D 8 GLU C 262 ARG C 270 -1 O VAL C 266 N ALA C 146 SHEET 7 D 8 LEU C 155 ALA C 170 -1 N GLU C 156 O ARG C 269 SHEET 8 D 8 THR C 238 PRO C 241 -1 O LEU C 240 N ALA C 166 SHEET 1 E 4 GLN B 180 ALA B 182 0 SHEET 2 E 4 LEU B 251 ALA B 257 1 O SER B 255 N VAL B 181 SHEET 3 E 4 LEU B 155 ALA B 170 -1 N LEU B 167 O ILE B 254 SHEET 4 E 4 THR B 238 PRO B 241 -1 O LEU B 240 N ALA B 166 SHEET 1 F 9 GLN B 180 ALA B 182 0 SHEET 2 F 9 LEU B 251 ALA B 257 1 O SER B 255 N VAL B 181 SHEET 3 F 9 LEU B 155 ALA B 170 -1 N LEU B 167 O ILE B 254 SHEET 4 F 9 GLU B 262 ARG B 270 -1 O ARG B 269 N GLU B 156 SHEET 5 F 9 VAL B 143 PHE B 147 -1 N ALA B 146 O VAL B 266 SHEET 6 F 9 LEU B 93 VAL B 97 1 O ARG B 94 N VAL B 143 SHEET 7 F 9 LEU B 122 GLU B 126 1 O GLN B 123 N ILE B 95 SHEET 8 F 9 GLN D 216 ALA D 221 1 O VAL D 218 N LEU B 122 SHEET 9 F 9 LYS D 190 LEU D 194 1 N LEU D 191 O GLN D 216 SHEET 1 G 9 LYS B 190 LEU B 194 0 SHEET 2 G 9 GLN B 216 ALA B 221 1 O GLN B 216 N LEU B 191 SHEET 3 G 9 THR D 121 GLU D 126 1 O LEU D 124 N GLU B 220 SHEET 4 G 9 SER D 92 VAL D 97 1 N ILE D 95 O GLN D 123 SHEET 5 G 9 VAL D 143 PHE D 147 1 N VAL D 143 O ARG D 94 SHEET 6 G 9 GLU D 262 ARG D 270 -1 O LEU D 268 N GLY D 144 SHEET 7 G 9 LEU D 155 ALA D 170 -1 N GLU D 156 O ARG D 269 SHEET 8 G 9 LEU D 251 ALA D 257 -1 O ILE D 254 N LEU D 167 SHEET 9 G 9 GLN D 180 ALA D 182 1 N VAL D 181 O SER D 255 SHEET 1 H 8 LYS B 190 LEU B 194 0 SHEET 2 H 8 GLN B 216 ALA B 221 1 O GLN B 216 N LEU B 191 SHEET 3 H 8 THR D 121 GLU D 126 1 O LEU D 124 N GLU B 220 SHEET 4 H 8 SER D 92 VAL D 97 1 N ILE D 95 O GLN D 123 SHEET 5 H 8 VAL D 143 PHE D 147 1 N VAL D 143 O ARG D 94 SHEET 6 H 8 GLU D 262 ARG D 270 -1 O LEU D 268 N GLY D 144 SHEET 7 H 8 LEU D 155 ALA D 170 -1 N GLU D 156 O ARG D 269 SHEET 8 H 8 THR D 238 PRO D 241 -1 O THR D 238 N VAL D 168 LINK C LEU A 109 N MSE A 110 1555 1555 1.33 LINK C MSE A 110 N ALA A 111 1555 1555 1.33 LINK C GLU A 126 N MSE A 127 1555 1555 1.33 LINK C MSE A 127 N SER A 128 1555 1555 1.33 LINK C ASP A 134 N MSE A 135 1555 1555 1.34 LINK C MSE A 135 N LEU A 136 1555 1555 1.33 LINK C HIS A 284 N MSE A 285 1555 1555 1.33 LINK C MSE A 285 N ALA A 286 1555 1555 1.33 LINK C LEU B 109 N MSE B 110 1555 1555 1.33 LINK C MSE B 110 N ALA B 111 1555 1555 1.33 LINK C GLU B 126 N MSE B 127 1555 1555 1.33 LINK C MSE B 127 N SER B 128 1555 1555 1.33 LINK C ASP B 134 N MSE B 135 1555 1555 1.33 LINK C MSE B 135 N LEU B 136 1555 1555 1.33 LINK C HIS B 284 N MSE B 285 1555 1555 1.33 LINK C MSE B 285 N ALA B 286 1555 1555 1.33 LINK C LEU C 109 N MSE C 110 1555 1555 1.32 LINK C MSE C 110 N ALA C 111 1555 1555 1.33 LINK C GLU C 126 N MSE C 127 1555 1555 1.33 LINK C MSE C 127 N SER C 128 1555 1555 1.33 LINK C ASP C 134 N MSE C 135 1555 1555 1.33 LINK C MSE C 135 N LEU C 136 1555 1555 1.33 LINK C HIS C 284 N MSE C 285 1555 1555 1.34 LINK C MSE C 285 N ALA C 286 1555 1555 1.33 LINK C LEU D 109 N MSE D 110 1555 1555 1.33 LINK C MSE D 110 N ALA D 111 1555 1555 1.33 LINK C GLU D 126 N MSE D 127 1555 1555 1.33 LINK C MSE D 127 N SER D 128 1555 1555 1.33 LINK C ASP D 134 N MSE D 135 1555 1555 1.33 LINK C MSE D 135 N LEU D 136 1555 1555 1.33 LINK C HIS D 284 N MSE D 285 1555 1555 1.33 LINK C MSE D 285 N ALA D 286 1555 1555 1.33 CISPEP 1 ALA A 148 PRO A 149 0 0.28 CISPEP 2 ALA A 257 PRO A 258 0 -0.09 CISPEP 3 ALA B 148 PRO B 149 0 0.34 CISPEP 4 ALA B 257 PRO B 258 0 0.30 CISPEP 5 ALA C 148 PRO C 149 0 0.24 CISPEP 6 ALA C 257 PRO C 258 0 0.24 CISPEP 7 ALA D 148 PRO D 149 0 0.08 CISPEP 8 ALA D 257 PRO D 258 0 -0.14 SITE 1 AC1 4 PRO A 99 PHE A 198 THR A 200 HOH A1881 SITE 1 AC2 4 PRO B 99 PHE B 198 ALA B 199 THR B 200 SITE 1 AC3 5 PRO C 99 PHE C 198 ALA C 199 THR C 200 SITE 2 AC3 5 HOH C1882 SITE 1 AC4 5 PRO C 99 GLU C 126 SER C 223 ILE C 224 SITE 2 AC4 5 HOH C1858 SITE 1 AC5 6 PRO D 99 THR D 100 PHE D 198 ALA D 199 SITE 2 AC5 6 THR D 200 HOH D1450 SITE 1 AC6 6 GLU B 126 SER B 223 SER B 225 GLU D 126 SITE 2 AC6 6 SER D 223 HOH D1668 CRYST1 62.176 98.363 86.272 90.00 103.77 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 0.016083 0.000000 0.003941 0.00000 SCALE2 0.000000 0.010166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011934 0.00000