HEADER RNA 08-APR-20 6YML TITLE CRYSTAL STRUCTURE OF THE SAM-SAH RIBOSWITCH WITH DECARBOXYLATED SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAINS: A,C; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CHAINS: B,D; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ROSEOBACTER SP.; SOURCE 4 ORGANISM_TAXID: 1907202; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: ROSEOBACTER SP.; SOURCE 8 ORGANISM_TAXID: 1907202 KEYWDS PSEUDOKNOT; SAM; RIBOSWITCH, RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.HUANG,D.M.J.LILLEY REVDAT 3 24-JAN-24 6YML 1 REMARK REVDAT 2 29-JUL-20 6YML 1 JRNL REVDAT 1 22-JUL-20 6YML 0 JRNL AUTH L.HUANG,T.W.LIAO,J.WANG,T.HA,D.M.J.LILLEY JRNL TITL CRYSTAL STRUCTURE AND LIGAND-INDUCED FOLDING OF THE SAM/SAH JRNL TITL 2 RIBOSWITCH. JRNL REF NUCLEIC ACIDS RES. V. 48 7545 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32520325 JRNL DOI 10.1093/NAR/GKAA493 REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 17121 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.230 REMARK 3 FREE R VALUE TEST SET COUNT : 725 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 53.0500 - 3.7000 1.00 3375 156 0.1475 0.1730 REMARK 3 2 3.7000 - 2.9400 1.00 3317 130 0.2243 0.2864 REMARK 3 3 2.9400 - 2.5700 1.00 3318 141 0.3347 0.3678 REMARK 3 4 2.5700 - 2.3300 1.00 3230 172 0.3192 0.3989 REMARK 3 5 2.3300 - 2.1700 0.96 3156 126 0.2990 0.3536 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.345 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.187 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1731 REMARK 3 ANGLE : 1.489 2683 REMARK 3 CHIRALITY : 0.126 356 REMARK 3 PLANARITY : 0.011 73 REMARK 3 DIHEDRAL : 17.548 857 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 20.5269 -28.5434 17.9665 REMARK 3 T TENSOR REMARK 3 T11: 0.7926 T22: 0.6120 REMARK 3 T33: 0.7594 T12: -0.0282 REMARK 3 T13: -0.0031 T23: 0.0300 REMARK 3 L TENSOR REMARK 3 L11: -0.6020 L22: 0.2640 REMARK 3 L33: -0.2334 L12: 0.1816 REMARK 3 L13: 0.1597 L23: 0.0682 REMARK 3 S TENSOR REMARK 3 S11: 0.0259 S12: -0.0313 S13: 0.0060 REMARK 3 S21: -0.1111 S22: -0.1605 S23: 0.0823 REMARK 3 S31: -0.0300 S32: 0.0430 S33: -0.0022 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YML COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9188 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17121 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.170 REMARK 200 RESOLUTION RANGE LOW (A) : 75.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 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: 6YL5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M MAGNESIUM SULFATE, 0.05 M REMARK 280 SODIUM CACODYLATE PH 6.0, 1.8 M LITHIUM SULFATE MONOHYDRATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -Y,-X,-Z REMARK 290 5555 -X+Y,Y,-Z REMARK 290 6555 X,X-Y,-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 -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 0.00000 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 0.00000 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 0.00000 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 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, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2' C A 22 O HOH A 201 2.17 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 G A 24 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 24 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 A C 11 O3' - P - OP2 ANGL. DEV. = -16.9 DEGREES REMARK 500 A C 11 O3' - P - OP1 ANGL. DEV. = -25.3 DEGREES REMARK 500 A C 11 OP1 - P - OP2 ANGL. DEV. = 10.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 AMP A 101 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DSH A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DSH C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide CBV C 10 and A C REMARK 800 11 DBREF 6YML A 7 32 PDB 6YML 6YML 7 32 DBREF 6YML B 43 51 PDB 6YML 6YML 43 51 DBREF 6YML C 7 32 PDB 6YML 6YML 7 32 DBREF 6YML D 43 51 PDB 6YML 6YML 43 51 SEQRES 1 A 26 G G U CBV A C A A C G G C U SEQRES 2 A 26 U C C U G G C G U G A C C SEQRES 1 B 9 A U U G G A G C A SEQRES 1 C 26 G G U CBV A C A A C G G C U SEQRES 2 C 26 U C C U G G C G U G A C C SEQRES 1 D 9 A U U G G A G C A HET CBV A 10 21 HET CBV C 10 21 HET AMP A 101 31 HET DSH A 102 42 HET SO4 A 103 5 HET DSH C 101 42 HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM DSH 5'-S-(3-AMINOPROPYL)-5'-THIOADENOSINE HETNAM SO4 SULFATE ION FORMUL 1 CBV 2(C9 H13 BR N3 O8 P) FORMUL 5 AMP C10 H14 N5 O7 P FORMUL 6 DSH 2(C13 H20 N6 O3 S) FORMUL 7 SO4 O4 S 2- FORMUL 9 HOH *5(H2 O) LINK O3' U A 9 P CBV A 10 1555 1555 1.60 LINK O3' CBV A 10 P A A 11 1555 1555 1.61 LINK O3' U C 9 P CBV C 10 1555 1555 1.61 LINK O3' CBV C 10 P A C 11 1555 1555 1.62 SITE 1 AC1 7 A A 14 G A 24 G A 25 C A 26 SITE 2 AC1 7 U B 44 C C 22 U C 23 SITE 1 AC2 8 C A 15 G A 16 U A 23 G A 24 SITE 2 AC2 8 G A 25 U B 44 U B 45 G B 46 SITE 1 AC3 2 C A 31 C A 32 SITE 1 AC4 8 A B 43 C C 15 G C 16 U C 23 SITE 2 AC4 8 G C 24 U D 44 U D 45 G D 46 SITE 1 AC5 6 U C 9 C C 12 U C 28 G C 29 SITE 2 AC5 6 A C 30 HOH C 201 CRYST1 86.218 86.218 75.395 90.00 90.00 120.00 P 3 1 2 12 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 0.011599 0.006696 0.000000 0.00000 SCALE2 0.000000 0.013393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013263 0.00000