HEADER RNA 25-JUL-20 7JJD TITLE SARCIN-RICIN LOOP WITH GUANOSINE MONOTHIOPHOSPHATE RESIDUE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (27-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS SARCIN-RICIN LOOP, RNA CRYSTAL STRUCTURE, RNA TETRALOOPS, RNA EXPDTA X-RAY DIFFRACTION AUTHOR P.S.PALLAN,M.EGLI,J.M.HARP REVDAT 2 18-OCT-23 7JJD 1 REMARK REVDAT 1 23-DEC-20 7JJD 0 JRNL AUTH P.S.PALLAN,T.P.LYBRAND,M.K.SCHLEGEL,J.M.HARP,H.JAHNS, JRNL AUTH 2 M.MANOHARAN,M.EGLI JRNL TITL INCORPORATING A THIOPHOSPHATE MODIFICATION INTO A COMMON RNA JRNL TITL 2 TETRALOOP MOTIF CAUSES AN UNANTICIPATED STABILITY BOOST. JRNL REF BIOCHEMISTRY V. 59 4627 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 33275419 JRNL DOI 10.1021/ACS.BIOCHEM.0C00685 REMARK 2 REMARK 2 RESOLUTION. 1.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 579 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7JJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000250942. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19854 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.53800 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ID: 3S7C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION SET-UPS WERE MADE BY REMARK 280 MIXING 4 UL OF 350 UM RNA SOLUTION [1 MM NA 2 EDTA (PH 8.0) AND REMARK 280 10 MM TRIS-HCL (PH 8.0)] WITH 2 UL OF A CRYSTALLIZATION BUFFER REMARK 280 COMPOSED OF 3.0 M AMMONIUM SULFATE, 10 MM MAGNESIUM CHLORIDE, 10 REMARK 280 MM MANGANESE CHLORIDE, AND 50 MM POTASSIUM 3-(N-MORPHOLINO) REMARK 280 PROPANESULFONIC ACID (MOPS), PH 7.0 AT 18 C., VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.32900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.49350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.16450 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 U A2647 C6 - N1 - C2 ANGL. DEV. = 4.2 DEGREES REMARK 500 G A2648 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 U A2650 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 U A2650 C5' - C4' - O4' ANGL. DEV. = 6.2 DEGREES REMARK 500 U A2650 N1 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 G A2655 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES REMARK 500 G A2655 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 U A2656 C4 - C5 - C6 ANGL. DEV. = -4.2 DEGREES REMARK 500 U A2656 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 C A2658 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 C A2658 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 G A2659 N9 - C1' - C2' ANGL. DEV. = -7.5 DEGREES REMARK 500 G A2659 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 A A2662 N1 - C2 - N3 ANGL. DEV. = -3.6 DEGREES REMARK 500 A A2662 C4 - C5 - N7 ANGL. DEV. = 3.1 DEGREES REMARK 500 A A2662 N1 - C6 - N6 ANGL. DEV. = 4.9 DEGREES REMARK 500 G A2663 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 G A2664 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 G A2664 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 C A2666 C2 - N3 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 C A2666 N1 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 G A2669 C6 - N1 - C2 ANGL. DEV. = -4.5 DEGREES REMARK 500 G A2669 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 G A2671 O5' - C5' - C4' ANGL. DEV. = -5.5 DEGREES REMARK 500 G A2671 O4' - C4' - C3' ANGL. DEV. = 5.5 DEGREES REMARK 500 G A2671 C5' - C4' - C3' ANGL. DEV. = -9.1 DEGREES REMARK 500 G A2671 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 G A2671 N3 - C4 - C5 ANGL. DEV. = 3.6 DEGREES REMARK 500 G A2671 N3 - C4 - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 U A2672 N1 - C2 - N3 ANGL. DEV. = 3.8 DEGREES REMARK 500 U A2672 C2 - N3 - C4 ANGL. DEV. = -4.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 7JJD A 2647 2673 PDB 7JJD 7JJD 2647 2673 SEQRES 1 A 27 U G C U C C U A G U A C G SEQRES 2 A 27 A G46 A G G A C C G G A G U SEQRES 3 A 27 G HET G46 A2661 26 HETNAM G46 GUANOSINE-5'-MONOTHIOPHOSPHATE HETSYN G46 5'-O-THIOPHOSPHONOGUANOSINE FORMUL 1 G46 C10 H14 N5 O7 P S FORMUL 2 HOH *113(H2 O) LINK O3' A A2660 P AG46 A2661 1555 1555 1.61 LINK O3' A A2660 P BG46 A2661 1555 1555 1.60 LINK O3' G46 A2661 P A A2662 1555 1555 1.60 CRYST1 29.639 29.639 76.658 90.00 90.00 90.00 P 43 4 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 0.033739 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033739 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013045 0.00000