HEADER RNA 05-JUN-18 6DN1 TITLE CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1151 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 (57-MER); COMPND 7 CHAIN: Z; 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 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: FUSOBACTERIUM NUCLEATUM; SOURCE 8 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 5 11-OCT-23 6DN1 1 REMARK REVDAT 4 21-OCT-20 6DN1 1 REMARK REVDAT 3 31-OCT-18 6DN1 1 JRNL REVDAT 2 03-OCT-18 6DN1 1 JRNL REVDAT 1 05-SEP-18 6DN1 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. 3.03 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) : 3.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 8941 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 471 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) : 3.03 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.39 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.95 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2541 REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2395 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.75 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 146 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 : 2384 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 28 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 80.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.06530 REMARK 3 B22 (A**2) : 4.06530 REMARK 3 B33 (A**2) : -8.13060 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) : 0.430 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.404 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL 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 : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2733 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4275 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 564 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 143 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2733 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 10 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 444 ; 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 : 2740 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.77 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : 26.69 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 6DN1 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_1000234920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36651 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 140.711 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 67.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 15.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 7.63100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.020 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 (%): 60.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 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 46.90333 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 93.80667 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 93.80667 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 46.90333 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: 6400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Z 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 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 U X 6 O5' U X 6 C5' -0.106 REMARK 500 U Z 111 O5' U Z 111 C5' -0.071 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 Z 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U Z 89 O4 REMARK 620 2 A Z 92 OP2 95.8 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 GZ7 Z 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG Z 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG Z 204 DBREF 6DN1 X 1 54 PDB 6DN1 6DN1 1 54 DBREF 6DN1 Z 57 113 PDB 6DN1 6DN1 57 113 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 U C C SEQRES 5 X 54 A U SEQRES 1 Z 57 G G A U U G A U U U G G U SEQRES 2 Z 57 G A A A U U C C A A A A C SEQRES 3 Z 57 C G A C A G U A G A G U C SEQRES 4 Z 57 U G G A U G A G A G A A G SEQRES 5 Z 57 A U U C G HET MG X 101 1 HET MG X 102 1 HET MG X 103 1 HET MG X 104 1 HET GZ7 Z 201 61 HET K Z 202 1 HET MG Z 203 1 HET MG Z 204 1 HETNAM MG MAGNESIUM ION HETNAM GZ7 10-(6-CARBOXYHEXYL)-8-(CYCLOPENTYLAMINO)-2,4-DIHYDROXY- HETNAM 2 GZ7 7-METHYLBENZO[G]PTERIDIN-10-IUM HETNAM K POTASSIUM ION FORMUL 3 MG 6(MG 2+) FORMUL 7 GZ7 C23 H30 N5 O4 1+ FORMUL 8 K K 1+ FORMUL 11 HOH *28(H2 O) LINK O4 U Z 89 MG MG Z 204 1555 1555 2.41 LINK OP2 A Z 92 MG MG Z 204 1555 1555 2.08 SITE 1 AC1 11 G X 10 G X 11 G X 32 A X 48 SITE 2 AC1 11 A X 49 U Z 61 G Z 62 G Z 84 SITE 3 AC1 11 A Z 85 G Z 98 A Z 99 SITE 1 AC2 1 G Z 93 SITE 1 AC3 2 U Z 89 A Z 92 CRYST1 74.440 74.440 140.710 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 0.013434 0.007756 0.000000 0.00000 SCALE2 0.000000 0.015512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007107 0.00000