HEADER RNA 13-JAN-22 7QSH TITLE 23S RIBOSOMAL RNA SARCIN RICIN LOOP 27-NT FRAGMENT CONTAINING A TITLE 2 XANTHOSINE RESIDUE AT POSITION 2648 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 23S RIBOSOMAL RNA SARCIN RICIN LOOP 27-NUCLEOTIDE FRAGMENT; 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 RNA, MODIFIED BASE EXPDTA X-RAY DIFFRACTION AUTHOR E.ENNIFAR,R.MICURA REVDAT 3 07-FEB-24 7QSH 1 REMARK REVDAT 2 23-AUG-23 7QSH 1 JRNL REVDAT 1 25-JAN-23 7QSH 0 JRNL AUTH S.MAIR,K.ERHARTER,E.RENARD,K.BRILLET,M.BRUNNER,A.LUSSER, JRNL AUTH 2 C.KREUTZ,E.ENNIFAR,R.MICURA JRNL TITL TOWARDS A COMPREHENSIVE UNDERSTANDING OF RNA DEAMINATION: JRNL TITL 2 SYNTHESIS AND PROPERTIES OF XANTHOSINE-MODIFIED RNA. JRNL REF NUCLEIC ACIDS RES. V. 50 6038 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35687141 JRNL DOI 10.1093/NAR/GKAC477 REMARK 2 REMARK 2 RESOLUTION. 0.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 54705 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2736 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 29.5000 - 2.3300 1.00 2661 141 0.1219 0.1598 REMARK 3 2 2.3300 - 1.8500 1.00 2633 138 0.1346 0.1719 REMARK 3 3 1.8500 - 1.6200 1.00 2644 139 0.1220 0.1317 REMARK 3 4 1.6200 - 1.4700 1.00 2609 138 0.1368 0.1464 REMARK 3 5 1.4700 - 1.3700 1.00 2642 139 0.1522 0.1673 REMARK 3 6 1.3700 - 1.2800 1.00 2618 137 0.1510 0.1645 REMARK 3 7 1.2800 - 1.2200 1.00 2621 138 0.1480 0.1466 REMARK 3 8 1.2200 - 1.1700 1.00 2647 140 0.1515 0.1679 REMARK 3 9 1.1700 - 1.1200 1.00 2599 136 0.1571 0.1456 REMARK 3 10 1.1200 - 1.0800 1.00 2633 139 0.1626 0.1582 REMARK 3 11 1.0800 - 1.0500 1.00 2595 137 0.1698 0.1823 REMARK 3 12 1.0500 - 1.0200 1.00 2622 138 0.1806 0.1866 REMARK 3 13 1.0200 - 0.9900 1.00 2637 138 0.1877 0.1831 REMARK 3 14 0.9900 - 0.9700 1.00 2642 140 0.2052 0.2239 REMARK 3 15 0.9700 - 0.9500 1.00 2599 136 0.2128 0.2563 REMARK 3 16 0.9500 - 0.9300 1.00 2610 138 0.2156 0.2181 REMARK 3 17 0.9300 - 0.9100 1.00 2638 139 0.2271 0.2319 REMARK 3 18 0.9100 - 0.8900 0.99 2573 135 0.2593 0.2599 REMARK 3 19 0.8900 - 0.8700 0.96 2544 134 0.2952 0.3070 REMARK 3 20 0.8700 - 0.8600 0.83 2202 116 0.3497 0.3330 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.60 REMARK 3 SHRINKAGE RADIUS : 0.40 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.094 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.288 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.38 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 : 0.005 918 REMARK 3 ANGLE : 1.421 1427 REMARK 3 CHIRALITY : 0.045 186 REMARK 3 PLANARITY : 0.020 40 REMARK 3 DIHEDRAL : 10.954 434 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7QSH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120216. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54707 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.860 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.88 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3DVZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MAGNESIUM ACETATE, REMARK 280 MES PH5.6, VAPOR DIFFUSION, SITTING 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 38.25500 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 57.38250 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 19.12750 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 U A 2647 REMARK 465 XAN A 2648 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 A2655 O5' - P - OP2 ANGL. DEV. = -6.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 7QSH A 2647 2673 PDB 7QSH 7QSH 2647 2673 SEQRES 1 A 27 U XAN C U C C U A G U A C G SEQRES 2 A 27 A G A G G A C C G G A G U SEQRES 3 A 27 G HET URI A2701 56 HET HYJ A2702 49 HET GOL A2703 6 HET SO4 A2704 5 HETNAM URI URIDINE HETNAM HYJ 9-[(2~{R},3~{R},4~{S},5~{R})-3,4-BIS(OXIDANYL)-5- HETNAM 2 HYJ [[TRIS(OXIDANYL)-$L^{5}-PHOSPHANYL]OXYMETHYL]OXOLAN-2- HETNAM 3 HYJ YL]-2-OXIDANYL-1~{H}-PURIN-6-ONE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 URI C9 H12 N2 O6 FORMUL 3 HYJ C10 H13 N4 O9 P FORMUL 4 GOL C3 H8 O3 FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *147(H2 O) LINK P A C A2649 O3'AHYJ A2702 1555 1555 1.60 LINK P B C A2649 O3'BHYJ A2702 1555 1555 1.61 LINK O3'AURI A2701 P AHYJ A2702 1555 1555 1.61 LINK O3'BURI A2701 P BHYJ A2702 1555 1555 1.61 CRYST1 29.500 29.500 76.510 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 0.033898 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033898 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013070 0.00000