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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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