HEADER RNA 05-JUN-18 6DN3 TITLE CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA RIBOSWITCH; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (56-MER); COMPND 7 CHAIN: Y; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: FUSOBACTERIUM NUCLEATUM; SOURCE 4 ORGANISM_TAXID: 851; SOURCE 5 OTHER_DETAILS: IN VITRO TRANSCRIBED RNA FROM FUSOBACTERIUM NUCLEATUM SOURCE 6 IMPX GENE; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: FUSOBACTERIUM NUCLEATUM; SOURCE 10 ORGANISM_TAXID: 851 KEYWDS FMN, RIBOSWITCH, TRANSCRIPTION, RNA EXPDTA X-RAY DIFFRACTION AUTHOR Q.VICENS,E.MONDRAGON,F.E.REYES,J.BERMAN,H.KAUR,K.KELLS,P.WICKENS, AUTHOR 2 J.WILSON,R.GADWOOD,H.SCHOSTAREZ,R.K.SUTO,P.COISH,K.F.BLOUNT, AUTHOR 3 R.T.BATEY REVDAT 4 11-OCT-23 6DN3 1 REMARK REVDAT 3 31-OCT-18 6DN3 1 JRNL REVDAT 2 03-OCT-18 6DN3 1 JRNL REVDAT 1 05-SEP-18 6DN3 0 JRNL AUTH Q.VICENS,E.MONDRAGON,F.E.REYES,P.COISH,P.ARISTOFF,J.BERMAN, JRNL AUTH 2 H.KAUR,K.W.KELLS,P.WICKENS,J.WILSON,R.C.GADWOOD, JRNL AUTH 3 H.J.SCHOSTAREZ,R.K.SUTO,K.F.BLOUNT,R.T.BATEY JRNL TITL STRUCTURE-ACTIVITY RELATIONSHIP OF FLAVIN ANALOGUES THAT JRNL TITL 2 TARGET THE FLAVIN MONONUCLEOTIDE RIBOSWITCH. JRNL REF ACS CHEM. BIOL. V. 13 2908 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 30107111 JRNL DOI 10.1021/ACSCHEMBIO.8B00533 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 10388 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 501 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.34 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2764 REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2619 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.25 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 145 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 : 2337 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.46180 REMARK 3 B22 (A**2) : 1.46180 REMARK 3 B33 (A**2) : -2.92370 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.370 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.320 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.920 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.302 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2667 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4166 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 550 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 149 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2667 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 436 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2682 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.74 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : 23.06 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DN3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234866. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10406 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.37800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: 3F4E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 6.5, EVAPORATION, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 46.75667 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 93.51333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 93.51333 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 46.75667 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: 6630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Y 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 U X 54 C5' C4' O4' C3' O3' C2' O2' REMARK 470 U X 54 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U X 54 C5 C6 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 G X 11 0.07 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 Y 205 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U Y 89 O4 REMARK 620 2 A Y 92 OP2 96.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL X 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG X 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG X 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GZ4 Y 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K Y 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG Y 205 DBREF 6DN3 X 1 54 PDB 6DN3 6DN3 1 54 DBREF 6DN3 Y 57 112 PDB 6DN3 6DN3 57 112 SEQRES 1 X 54 G G A U C U U C G G G G C SEQRES 2 X 54 A G G G U G A A A U U C C SEQRES 3 X 54 C G A C C G G U G G U A U SEQRES 4 X 54 A G U C C A C G A A A G C SEQRES 5 X 54 U U SEQRES 1 Y 56 G C U U U G A U U U G G U SEQRES 2 Y 56 G A A A U U C C A A A A C SEQRES 3 Y 56 C G A C A G U A G A G U C SEQRES 4 Y 56 U G G A U G A G A G A A G SEQRES 5 Y 56 A U U C HET CL X 101 1 HET MG X 102 1 HET MG X 103 1 HET MG X 104 1 HET MG X 105 1 HET GZ4 Y 201 48 HET K Y 202 1 HET MG Y 203 1 HET MG Y 204 1 HET MG Y 205 1 HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM GZ4 7,8-DIMETHYL-2,4-DIOXO-10-(3-PHENYLPROPYL)-1,2,3,4- HETNAM 2 GZ4 TETRAHYDROBENZO[G]PTERIDIN-10-IUM HETNAM K POTASSIUM ION FORMUL 3 CL CL 1- FORMUL 4 MG 7(MG 2+) FORMUL 8 GZ4 C21 H21 N4 O2 1+ FORMUL 9 K K 1+ FORMUL 13 HOH *4(H2 O) LINK OP2 A X 49 MG MG X 105 1555 1555 2.52 LINK O4 U Y 89 MG MG Y 205 1555 1555 2.49 LINK OP2 A Y 92 MG MG Y 205 1555 1555 2.08 LINK O6 G Y 97 K K Y 202 1555 1555 3.07 SITE 1 AC1 5 G X 11 G X 32 G Y 62 G Y 84 SITE 2 AC1 5 GZ4 Y 201 SITE 1 AC2 2 U X 37 A X 40 SITE 1 AC3 1 A X 49 SITE 1 AC4 10 G X 10 G X 11 A X 48 A X 49 SITE 2 AC4 10 CL X 101 U Y 61 G Y 62 G Y 84 SITE 3 AC4 10 A Y 85 A Y 99 SITE 1 AC5 1 G Y 97 SITE 1 AC6 2 U Y 89 A Y 92 CRYST1 71.550 71.550 140.270 90.00 90.00 120.00 P 31 2 1 6 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 0.013976 0.008069 0.000000 0.00000 SCALE2 0.000000 0.016138 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007129 0.00000