HEADER RNA 26-OCT-17 6BFB TITLE CRYSTAL STRUCTURE OF A F. NUCLEATUM FMN RIBOSWITCH BOUND TO WG-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (54-MER); 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 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: FUSOBACTERIUM NUCLEATUM; SOURCE 8 ORGANISM_TAXID: 851 KEYWDS RNA, TRANSLATION, RNA-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.F.RIZVI,T.O.FISCHMANN REVDAT 3 06-MAR-24 6BFB 1 REMARK REVDAT 2 28-MAR-18 6BFB 1 JRNL REVDAT 1 21-FEB-18 6BFB 0 JRNL AUTH N.F.RIZVI,J.A.HOWE,A.NAHVI,D.J.KLEIN,T.O.FISCHMANN,H.Y.KIM, JRNL AUTH 2 M.A.MCCOY,S.S.WALKER,A.HRUZA,M.P.RICHARDS,C.CHAMBERLIN, JRNL AUTH 3 P.SARADJIAN,M.T.BUTKO,G.MERCADO,J.BURCHARD,C.STRICKLAND, JRNL AUTH 4 P.J.DANDLIKER,G.F.SMITH,E.B.NICKBARG JRNL TITL DISCOVERY OF SELECTIVE RNA-BINDING SMALL MOLECULES BY JRNL TITL 2 AFFINITY-SELECTION MASS SPECTROMETRY. JRNL REF ACS CHEM. BIOL. V. 13 820 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 29412640 JRNL DOI 10.1021/ACSCHEMBIO.7B01013 REMARK 2 REMARK 2 RESOLUTION. 2.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AUTOBUSTER 2.11.7 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) : 2.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 9842 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 481 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 : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.82 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.15 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2902 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2300 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2755 REMARK 3 BIN R VALUE (WORKING SET) : 0.2259 REMARK 3 BIN FREE R VALUE : 0.3172 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.07 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 147 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 : 2340 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 107.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 104.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.53430 REMARK 3 B22 (A**2) : 0.53430 REMARK 3 B33 (A**2) : -1.06870 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) : 0.340 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.357 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 1.852 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.336 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 : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2674 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4181 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 549 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 140 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2674 ; 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 : 2629 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.78 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : 22.60 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { X|* } REMARK 3 ORIGIN FOR THE GROUP (A): 26.5663 40.3519 15.7745 REMARK 3 T TENSOR REMARK 3 T11: -0.3330 T22: -0.2070 REMARK 3 T33: -0.2562 T12: 0.0460 REMARK 3 T13: -0.0264 T23: 0.0330 REMARK 3 L TENSOR REMARK 3 L11: 5.4604 L22: 2.4945 REMARK 3 L33: 2.3067 L12: -0.9686 REMARK 3 L13: -0.2539 L23: -0.2980 REMARK 3 S TENSOR REMARK 3 S11: 0.2351 S12: -0.0941 S13: -0.8363 REMARK 3 S21: 0.2436 S22: 0.1166 S23: 0.3704 REMARK 3 S31: -0.2646 S32: -0.1301 S33: -0.3517 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { Y|* } REMARK 3 ORIGIN FOR THE GROUP (A): 22.9560 43.9106 17.0999 REMARK 3 T TENSOR REMARK 3 T11: -0.3940 T22: -0.2372 REMARK 3 T33: -0.3299 T12: 0.0350 REMARK 3 T13: 0.0389 T23: -0.0259 REMARK 3 L TENSOR REMARK 3 L11: 4.5424 L22: 2.4574 REMARK 3 L33: 2.4314 L12: -0.9479 REMARK 3 L13: 0.8391 L23: -0.7895 REMARK 3 S TENSOR REMARK 3 S11: 0.1724 S12: -0.1819 S13: -0.6270 REMARK 3 S21: 0.5007 S22: -0.0076 S23: 0.3916 REMARK 3 S31: -0.3327 S32: -0.2465 S33: -0.1649 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BFB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230807. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5-6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9904 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.820 REMARK 200 RESOLUTION RANGE LOW (A) : 56.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: AUTOBUSTER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 5.5-6.5, 0.2 M REMARK 280 MGCL2, 7-11% V/V PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 300K 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 47.06333 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 94.12667 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 94.12667 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 47.06333 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: 5810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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: 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 G Y 57 OP1 - P - OP2 ANGL. DEV. = -9.7 DEGREES 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 X 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DKM X 500 O3 REMARK 620 2 DKM X 500 O1 65.3 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 DKM X 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG X 501 DBREF 6BFB X 1 54 PDB 6BFB 6BFB 1 54 DBREF 6BFB Y 57 112 PDB 6BFB 6BFB 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 DKM X 500 51 HET MG X 501 1 HETNAM DKM 5-[(3S,4S)-3-(DIMETHYLAMINO)-4-HYDROXYPYRROLIDIN-1-YL]- HETNAM 2 DKM 6-FLUORO-4-METHYL-8-OXO-3,4-DIHYDRO-8H-1-THIA-4,9B- HETNAM 3 DKM DIAZACYCLOPENTA[CD]PHENALENE-9-CARBOXYLIC ACID HETNAM MG MAGNESIUM ION FORMUL 3 DKM C20 H21 F N4 O4 S FORMUL 4 MG MG 2+ FORMUL 5 HOH *12(H2 O) LINK O3 DKM X 500 MG MG X 501 1555 1555 2.36 LINK O1 DKM X 500 MG MG X 501 1555 1555 2.45 SITE 1 AC1 9 G X 10 G X 11 G X 47 A X 48 SITE 2 AC1 9 MG X 501 U Y 61 G Y 62 G Y 84 SITE 3 AC1 9 A Y 85 SITE 1 AC2 1 DKM X 500 CRYST1 71.130 71.130 141.190 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 0.014059 0.008117 0.000000 0.00000 SCALE2 0.000000 0.016234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007083 0.00000