HEADER RNA 07-AUG-18 6HAG TITLE THE STRUCTURE OF THE SAM/SAH-BINDING RIBOSWITCH. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAM RIBOSWITCH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PROTEOBACTERIA; SOURCE 3 ORGANISM_TAXID: 1224; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBOSWITCH, SAM, SAH, PSEUDOKNOT, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.K.WEICKHMANN REVDAT 4 29-JAN-20 6HAG 1 REMARK REVDAT 3 08-MAY-19 6HAG 1 REMARK REVDAT 2 20-MAR-19 6HAG 1 JRNL REVDAT 1 09-JAN-19 6HAG 0 JRNL AUTH A.K.WEICKHMANN,H.KELLER,J.P.WURM,E.STREBITZER,M.A.JUEN, JRNL AUTH 2 J.KREMSER,Z.WEINBERG,C.KREUTZ,E.DUCHARDT-FERNER,J.WOHNERT JRNL TITL THE STRUCTURE OF THE SAM/SAH-BINDING RIBOSWITCH. JRNL REF NUCLEIC ACIDS RES. V. 47 2654 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 30590743 JRNL DOI 10.1093/NAR/GKY1283 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.97 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HAG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011078. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 298; 271 REMARK 210 PH : 6.2; 6.2; 6.2 REMARK 210 IONIC STRENGTH : 50; 50; 50 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 710 UM [U-13C; U-15N] ENV9B, 2 REMARK 210 MM S-ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 90% H2O/10% REMARK 210 D2O; 910 UM [U-15N] ENV9B, 2.5 REMARK 210 MM S-ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 90% H2O/10% REMARK 210 D2O; 800 UM [U-13C; U-15N]-URA REMARK 210 ENV9B, 1.6 MM S- REMARK 210 ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 90% H2O/10% REMARK 210 D2O; 750 SATURATED [U-5-D1/ REMARK 210 RIBOSE-3 ,4 ,5 ,5 -D4] ENV9B, 3 REMARK 210 MM S-ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 90% H2O/10% REMARK 210 D2O; 700 UM ENV9B, 0.5 MM [U-13C; REMARK 210 U-15N] S-ADENOSYLHOMOCYSTEINE, REMARK 210 25 MM POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 90% H2O/10% REMARK 210 D2O; 800 UM [U-13C; U-15N]-CYT, REMARK 210 [U-13C; U-15N]-ADE ENV9B, 2 MM S- REMARK 210 ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 90% H2O/10% REMARK 210 D2O; 850 UM [U-13C; U-15N]-GUA REMARK 210 ENV9B, 2 MM S- REMARK 210 ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 50% H2O/50% REMARK 210 D2O; 1.2 MM ENV9B, 4 MM S- REMARK 210 ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 90% H2O/10% REMARK 210 D2O; 800 UM [U-13C; U-15N]-CYT, REMARK 210 [U-13C; U-15N]-ADE ENV9B, 2 MM S- REMARK 210 ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 100% D2O; 800 REMARK 210 UM [U-13C; U-15N]-URA ENV9B, 1.6 REMARK 210 MM S-ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 100% D2O; 850 REMARK 210 UM [U-13C; U-15N]-GUA ENV9B, 2 REMARK 210 MM S-ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 100% D2O; 480 REMARK 210 UM [U-13C; U-15N]-URA ENV9B, 750 REMARK 210 UM [U-13C; U-15N] S- REMARK 210 ADENOSYLHOMOCYSTEINE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 MAGNESIUM ACETATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N HSQC REMARK 210 NH2 ONLY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-1H NOESY; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-13C REMARK 210 NOESY ALIPHATIC3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D HCCH-TOCSY; 3D REMARK 210 HCCH-COSY; 1D 1H-HS11ECHO; 2D 1H- REMARK 210 15N HNN-COSY; 2D 1H-13C HNCO; 2D REMARK 210 1H-13C H5C5(C4N)H; 2D 1H-15N HCN REMARK 210 AROMATIC; 2D 1H-15N HCN REMARK 210 ALIPHATIC; 2D 1H-15N 2BOND-HSQC; REMARK 210 TROSY RELAYED HCCH-COSY; 2D 1H- REMARK 210 13C LONG-RANGEH8(C8)C5(N1)H1; 2D REMARK 210 LR-1H,15N-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 900 MHZ; 800 MHZ; 700 REMARK 210 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.97, TOPSPIN, CARA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 2 U A 34 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 3 G A 9 C1' - O4' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 4 G A 9 C1' - O4' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 5 G A 9 C1' - O4' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 6 G A 9 C1' - O4' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 7 G A 9 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 8 G A 9 C1' - O4' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 8 U A 28 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 9 G A 9 C1' - O4' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 9 U A 28 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 10 G A 9 C1' - O4' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAH A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27452 RELATED DB: BMRB DBREF 6HAG A 1 43 PDB 6HAG 6HAG 1 43 SEQRES 1 A 43 G U C A C A A C G G C U U SEQRES 2 A 43 C C U G A C G U G G C A G SEQRES 3 A 43 A U U G A A U U A U U G G SEQRES 4 A 43 A G C A HET SAH A 101 46 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S SITE 1 AC1 8 C A 8 G A 9 C A 15 U A 16 SITE 2 AC1 8 G A 17 U A 36 U A 37 G A 38 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1