HEADER RNA 10-DEC-13 4NYA TITLE CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH 5- TITLE 2 (AZIDOMETHYL)-2-METHYLPYRIMIDIN-4-AMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIM TPP RIBOSWITCH; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562 KEYWDS FRAGMENT-BASED DRUG DISCOVERY, RIBOSWITCH, RNA EXPDTA X-RAY DIFFRACTION AUTHOR K.D.WARNER,P.HOMAN,K.M.WEEKS,A.G.SMITH,C.ABELL,A.R.FERRE-D'AMARE REVDAT 2 20-SEP-23 4NYA 1 REMARK LINK REVDAT 1 04-JUN-14 4NYA 0 JRNL AUTH K.D.WARNER,P.HOMAN,K.M.WEEKS,A.G.SMITH,C.ABELL, JRNL AUTH 2 A.R.FERRE-D'AMARE JRNL TITL VALIDATING FRAGMENT-BASED DRUG DISCOVERY FOR BIOLOGICAL JRNL TITL 2 RNAS: LEAD FRAGMENTS BIND AND REMODEL THE TPP RIBOSWITCH JRNL TITL 3 SPECIFICALLY. JRNL REF CHEM.BIOL. V. 21 591 2014 JRNL REFN ISSN 1074-5521 JRNL PMID 24768306 JRNL DOI 10.1016/J.CHEMBIOL.2014.03.007 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 11499 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1193 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 0 REMARK 3 NUCLEIC ACID ATOMS : 3410 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.39200 REMARK 3 B22 (A**2) : 13.36600 REMARK 3 B33 (A**2) : -5.97300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -6.25700 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) : 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.000 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.563 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.524 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 26.63 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CYCP-DNA-RNA_REP-13.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : CCC.PARAM REMARK 3 PARAMETER FILE 6 : AZMPDRGCNS.PAR REMARK 3 PARAMETER FILE 7 : GTP.PARAM REMARK 3 PARAMETER FILE 8 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 TOPOLOGY FILE 7 : NULL REMARK 3 TOPOLOGY FILE 8 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4NYA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083807. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : CRYO-COOLED DOUBLE CRYSTAL REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11991 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.57100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 2GDI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4000, 0.1 M SODIUM ACETATE, PH REMARK 280 5.1, 0.3 M AMMONIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 74.86500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.94500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.86500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.94500 REMARK 290 SMTRY3 4 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GTP A 10 PG O1G O2G O3G REMARK 470 U A 46 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U A 46 C6 REMARK 470 C A 55 N1 C2 O2 N3 C4 N4 C5 REMARK 470 C A 55 C6 REMARK 470 U B 54 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U B 54 C6 REMARK 470 C B 55 N1 C2 O2 N3 C4 N4 C5 REMARK 470 C B 55 C6 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 G A 11 O3' A A 12 P 0.083 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 C A 23 N1 - C1' - C2' ANGL. DEV. = 8.0 DEGREES REMARK 500 A A 61 C2' - C3' - O3' ANGL. DEV. = 12.8 DEGREES REMARK 500 A A 85 C2' - C3' - O3' ANGL. DEV. = 10.2 DEGREES REMARK 500 G B 11 O3' - P - OP2 ANGL. DEV. = 19.0 DEGREES REMARK 500 G B 11 O3' - P - OP1 ANGL. DEV. = -15.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 U A 28 0.07 SIDE CHAIN REMARK 500 G A 40 0.06 SIDE CHAIN REMARK 500 G B 78 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 A 108 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 77 O2' REMARK 620 2 G A 78 OP1 94.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 61 OP1 REMARK 620 2 C B 63 O4' 118.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 64 O5' REMARK 620 2 U B 64 OP2 61.6 REMARK 620 3 G B 65 OP2 142.0 136.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2QB A 110 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2QB B 107 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NYB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH (4- REMARK 900 (1,2,3-THIADIAZOL-4-YL)PHENYL)METHANAMINE REMARK 900 RELATED ID: 4NYC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH REMARK 900 THIENO[2,3-B]PYRAZIN-7-AMINE REMARK 900 RELATED ID: 4NYD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH REMARK 900 HYPOXANTHINE REMARK 900 RELATED ID: 4NYG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH REMARK 900 THIAMINE DBREF 4NYA A 10 89 PDB 4NYA 4NYA 10 89 DBREF 4NYA B 10 89 PDB 4NYA 4NYA 10 89 SEQRES 1 A 80 GTP G A C U C G G G G U G C SEQRES 2 A 80 C C U U C U G C G U G A A SEQRES 3 A 80 G G C U G A G A A A U A C SEQRES 4 A 80 C C G U A U C A C C U G A SEQRES 5 A 80 U C U G G A U A A U G C C SEQRES 6 A 80 A G C G U A G G G A A G U SEQRES 7 A 80 U CCC SEQRES 1 B 80 GTP G A C U C G G G G U G C SEQRES 2 B 80 C C U U C U G C G U G A A SEQRES 3 B 80 G G C U G A G A A A U A C SEQRES 4 B 80 C C G U A U C A C C U G A SEQRES 5 B 80 U C U G G A U A A U G C C SEQRES 6 B 80 A G C G U A G G G A A G U SEQRES 7 B 80 U CCC MODRES 4NYA GTP A 10 G GUANOSINE-5'-TRIPHOSPHATE MODRES 4NYA CCC A 89 C MODRES 4NYA GTP B 10 G GUANOSINE-5'-TRIPHOSPHATE MODRES 4NYA CCC B 89 C HET GTP A 10 28 HET CCC A 89 23 HET GTP B 10 32 HET CCC B 89 23 HET MG A 101 1 HET MG A 102 1 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET MG A 106 1 HET MG A 107 1 HET MG A 108 1 HET MG A 109 1 HET 2QB A 110 12 HET MG B 101 1 HET MG B 102 1 HET MG B 103 1 HET MG B 104 1 HET MG B 105 1 HET MG B 106 1 HET 2QB B 107 12 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM 2QB 5-(AZIDOMETHYL)-2-METHYLPYRIMIDIN-4-AMINE FORMUL 1 GTP 2(C10 H16 N5 O14 P3) FORMUL 1 CCC 2(C9 H13 N3 O10 P2) FORMUL 3 MG 15(MG 2+) FORMUL 12 2QB 2(C6 H8 N6) FORMUL 20 HOH *3(H2 O) LINK O3' GTP A 10 P G A 11 1555 1555 1.61 LINK O3' U A 88 P CCC A 89 1555 1555 1.60 LINK O3' GTP B 10 P G B 11 1555 1555 1.58 LINK O3' U B 88 P CCC B 89 1555 1555 1.60 LINK O2' G A 40 MG MG A 109 1555 1555 2.37 LINK O3' C A 55 MG MG A 101 1555 1555 2.44 LINK O6 G A 60 MG MG A 107 1555 1555 2.65 LINK OP1 C A 63 MG MG A 102 1555 1555 2.01 LINK OP1 C A 77 MG MG A 103 1555 1555 2.88 LINK O2' C A 77 MG MG A 108 1555 1555 2.22 LINK OP1 G A 78 MG MG A 108 1555 1555 2.91 LINK MG MG A 104 O HOH A 201 1555 1555 2.28 LINK OP1 A B 61 MG MG B 105 1555 1555 2.03 LINK O4' C B 63 MG MG B 105 1555 1555 2.26 LINK O5' U B 64 MG MG B 104 1555 1555 2.09 LINK OP2 U B 64 MG MG B 104 1555 1555 2.72 LINK OP2 G B 65 MG MG B 104 1555 1555 2.44 LINK O4 U B 68 MG MG B 103 1555 1555 2.81 LINK O4 U B 87 MG MG B 106 1555 1555 2.80 SITE 1 AC1 2 C A 55 A A 56 SITE 1 AC2 3 U A 62 C A 63 U A 64 SITE 1 AC3 3 C A 77 G A 78 U A 79 SITE 1 AC4 3 G A 37 G A 40 HOH A 201 SITE 1 AC5 2 G A 81 G A 82 SITE 1 AC6 1 GTP A 10 SITE 1 AC7 4 U A 59 G A 60 G A 72 G A 78 SITE 1 AC8 3 G A 60 C A 77 G A 78 SITE 1 AC9 1 G A 40 SITE 1 BC1 4 G A 19 G A 40 G A 42 A A 43 SITE 1 BC2 2 C B 58 G B 82 SITE 1 BC3 2 U B 79 A B 80 SITE 1 BC4 1 U B 68 SITE 1 BC5 2 U B 64 G B 65 SITE 1 BC6 2 A B 61 C B 63 SITE 1 BC7 2 U B 87 U B 88 SITE 1 BC8 5 G B 19 G B 40 G B 42 A B 43 SITE 2 BC8 5 G B 72 CRYST1 149.730 29.890 95.430 90.00 93.94 90.00 C 1 2 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 0.006679 0.000000 0.000460 0.00000 SCALE2 0.000000 0.033456 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010504 0.00000 HETATM 1 O3B GTP A 10 -32.538 -8.828 73.291 1.00 91.11 O HETATM 2 PB GTP A 10 -31.459 -9.851 73.560 1.00 92.65 P HETATM 3 O1B GTP A 10 -31.605 -11.010 72.603 1.00 90.95 O HETATM 4 O2B GTP A 10 -31.583 -10.357 74.980 1.00 91.41 O HETATM 5 O3A GTP A 10 -30.105 -9.210 73.369 1.00 89.40 O HETATM 6 PA GTP A 10 -28.895 -8.354 73.942 1.00 89.17 P HETATM 7 O1A GTP A 10 -29.604 -7.079 74.196 1.00 89.46 O HETATM 8 O2A GTP A 10 -28.194 -9.050 75.044 1.00 89.35 O HETATM 9 O5' GTP A 10 -27.851 -8.135 72.751 1.00 86.62 O HETATM 10 C5' GTP A 10 -27.085 -9.237 72.278 1.00 81.89 C HETATM 11 C4' GTP A 10 -26.505 -8.934 70.910 1.00 78.90 C HETATM 12 O4' GTP A 10 -27.519 -9.162 69.895 1.00 76.97 O HETATM 13 C3' GTP A 10 -26.082 -7.487 70.689 1.00 77.95 C HETATM 14 O3' GTP A 10 -24.777 -7.249 71.211 1.00 77.28 O HETATM 15 C2' GTP A 10 -26.110 -7.437 69.169 1.00 76.29 C HETATM 16 O2' GTP A 10 -25.037 -8.163 68.602 1.00 74.01 O HETATM 17 C1' GTP A 10 -27.426 -8.158 68.900 1.00 74.62 C HETATM 18 N9 GTP A 10 -28.594 -7.281 68.987 1.00 72.40 N HETATM 19 C8 GTP A 10 -29.595 -7.319 69.930 1.00 72.62 C HETATM 20 N7 GTP A 10 -30.508 -6.402 69.757 1.00 71.37 N HETATM 21 C5 GTP A 10 -30.086 -5.706 68.629 1.00 70.88 C HETATM 22 C6 GTP A 10 -30.670 -4.601 67.958 1.00 69.28 C HETATM 23 O6 GTP A 10 -31.713 -3.994 68.237 1.00 69.85 O HETATM 24 N1 GTP A 10 -29.919 -4.204 66.854 1.00 68.61 N HETATM 25 C2 GTP A 10 -28.749 -4.803 66.447 1.00 69.07 C HETATM 26 N2 GTP A 10 -28.160 -4.285 65.358 1.00 68.08 N HETATM 27 N3 GTP A 10 -28.193 -5.837 67.064 1.00 70.36 N HETATM 28 C4 GTP A 10 -28.910 -6.236 68.144 1.00 71.31 C