HEADER RNA 23-SEP-19 6UET TITLE SAM-BOUND SAM-IV RIBOSWITCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (119-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SP. MCS; SOURCE 4 ORGANISM_TAXID: 164756; SOURCE 5 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 SOURCE 6 RNA POLYMERASE KEYWDS SAM-IV RIBOSWITCH, CRYO-EM, SMALL RNA, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR K.ZHANG,S.LI,K.KAPPEL,G.PINTILIE,Z.SU,T.MOU,M.SCHMID,R.DAS,W.CHIU REVDAT 2 20-MAR-24 6UET 1 REMARK REVDAT 1 18-DEC-19 6UET 0 JRNL AUTH K.ZHANG,S.LI,K.KAPPEL,G.PINTILIE,Z.SU,T.C.MOU,M.F.SCHMID, JRNL AUTH 2 R.DAS,W.CHIU JRNL TITL CRYO-EM STRUCTURE OF A 40 KDA SAM-IV RIBOSWITCH RNA AT 3.7 JRNL TITL 2 ANGSTROM RESOLUTION. JRNL REF NAT COMMUN V. 10 5511 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31796736 JRNL DOI 10.1038/S41467-019-13494-7 REMARK 2 REMARK 2 RESOLUTION. 4.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EMAN2, EPU, CTFFIND, UCSF CHIMERA, REMARK 3 PHENIX, RELION, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : BACKBONE TRACE REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.100 REMARK 3 NUMBER OF PARTICLES : 588580 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6UET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000244496. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SAM-BOUND SAM-IV RIBOSWITCH; REMARK 245 SAM-BOUND SAM-IV RIBOSWITCH REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.20 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.20 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 6030 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 760.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 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: 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' A A 74 O6 G A 76 1.98 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 C A 4 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 4 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 G A 9 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 C A 24 O5' - P - OP1 ANGL. DEV. = 9.3 DEGREES REMARK 500 C A 41 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 C A 41 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 C A 41 N3 - C2 - O2 ANGL. DEV. = -5.9 DEGREES REMARK 500 C A 45 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 C A 48 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 48 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 C A 66 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 G A 69 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 G A 69 N3 - C4 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A 69 C6 - C5 - N7 ANGL. DEV. = -3.7 DEGREES REMARK 500 G A 69 N1 - C2 - N2 ANGL. DEV. = -6.3 DEGREES REMARK 500 G A 69 N3 - C2 - N2 ANGL. DEV. = 5.2 DEGREES REMARK 500 G A 69 C8 - N9 - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 G A 69 C4 - N9 - C1' ANGL. DEV. = 9.4 DEGREES REMARK 500 G A 85 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 A A 86 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 A A 86 O5' - P - OP1 ANGL. DEV. = 12.8 DEGREES REMARK 500 A A 86 O5' - P - OP2 ANGL. DEV. = -6.7 DEGREES REMARK 500 C A 92 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 G A 93 N9 - C1' - C2' ANGL. DEV. = -9.4 DEGREES REMARK 500 G A 95 C6 - C5 - N7 ANGL. DEV. = -3.7 DEGREES REMARK 500 G A 95 C8 - N9 - C1' ANGL. DEV. = -8.4 DEGREES REMARK 500 G A 95 C4 - N9 - C1' ANGL. DEV. = 10.2 DEGREES REMARK 500 C A 97 C6 - N1 - C2 ANGL. DEV. = -3.6 DEGREES REMARK 500 C A 97 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 C A 97 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 C A 100 N1 - C2 - O2 ANGL. DEV. = 4.9 DEGREES REMARK 500 C A 105 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 111 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 G A 111 C8 - N9 - C1' ANGL. DEV. = -10.5 DEGREES REMARK 500 G A 111 C4 - N9 - C1' ANGL. DEV. = 11.4 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 SAM A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-20755 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-20756 RELATED DB: EMDB REMARK 900 SAM-BOUND SAM-IV RIBOSWITCH DBREF1 6UET A 1 119 GB CP000384.1 DBREF2 6UET A 108767400 1307439 1307321 SEQRES 1 A 119 G G U C A U G A G U G C C SEQRES 2 A 119 A G C G U C A A G C C C C SEQRES 3 A 119 G G C U U G C U G G C C G SEQRES 4 A 119 G C A A C C C U C C A A C SEQRES 5 A 119 C G C G G U G G G G U G C SEQRES 6 A 119 C C C G G G U G A U G A C SEQRES 7 A 119 C A G G U U G A G U A G C SEQRES 8 A 119 C G U G A C G G C U A C G SEQRES 9 A 119 C G G C A A G C G C G G G SEQRES 10 A 119 U C HET SAM A 301 27 HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 2 SAM C15 H22 N6 O5 S SITE 1 AC1 6 G A 2 U A 3 G A 7 A A 42 SITE 2 AC1 6 C A 44 U A 63 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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