HEADER RNA 26-JUL-18 6E7L TITLE STRUCTURE OF A DIMERIZED UUCG MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*GP*GP*CP*UP*GP*CP*AP*CP*UP*UP*CP*GP*GP*UP*GP*CP*UP*GP*CP*CP*C)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS UUCG TETRALOOP DIMER, RNA EXPDTA X-RAY DIFFRACTION AUTHOR E.J.MONTEMAYOR,S.E.BUTCHER REVDAT 6 03-APR-24 6E7L 1 REMARK REVDAT 5 13-MAR-24 6E7L 1 REMARK REVDAT 4 11-DEC-19 6E7L 1 REMARK REVDAT 3 13-NOV-19 6E7L 1 JRNL REVDAT 2 16-OCT-19 6E7L 1 JRNL REVDAT 1 31-JUL-19 6E7L 0 JRNL AUTH E.J.MONTEMAYOR,J.M.VIRTA,L.D.HAGLER,S.C.ZIMMERMAN, JRNL AUTH 2 S.E.BUTCHER JRNL TITL STRUCTURE OF AN RNA HELIX WITH PYRIMIDINE MISMATCHES AND JRNL TITL 2 CROSS-STRAND STACKING. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 75 652 2019 JRNL REFN ESSN 2053-230X JRNL PMID 31584014 JRNL DOI 10.1107/S2053230X19012172 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.J.MONTEMAYOR,J.M.VIRTA,L.D.HAGLER,S.C.ZIMMERMAN, REMARK 1 AUTH 2 S.E.BUTCHER REMARK 1 TITL STRUCTURE OF AN RNA HELIX WITH PYRIMIDINE MISMATCHES AND REMARK 1 TITL 2 CROSS-STRAND STACKING REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 75 657 2019 REMARK 1 REFN ESSN 2053-230X REMARK 1 DOI 10.1107/S2053230X19012160 REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13-2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4149 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 416 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 36.9965 - 3.7347 1.00 1252 136 0.1284 0.1610 REMARK 3 2 3.7347 - 2.9647 1.00 1222 142 0.2154 0.2482 REMARK 3 3 2.9647 - 2.5901 1.00 1259 138 0.3528 0.4601 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.580 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.012 515 REMARK 3 ANGLE : 1.940 801 REMARK 3 CHIRALITY : 0.086 109 REMARK 3 PLANARITY : 0.015 22 REMARK 3 DIHEDRAL : 9.777 260 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 6E7L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000235861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-18 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20180409 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2473 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.590 REMARK 200 RESOLUTION RANGE LOW (A) : 77.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 23.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 25.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.1 REMARK 200 STARTING MODEL: IDEAL A-FORM RNA, SINGLE STRANDED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM BIS-TRIS PH 6.5 100 MM SODIUM REMARK 280 HEPES PH 7.4 20 % PEG 3,350 20 % GLYCEROL 10 % MPD, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 38.93000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.02050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.02050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.46500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.02050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.02050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.39500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.02050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.02050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.46500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.02050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.02050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 58.39500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 38.93000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 -84.08200 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 84.08200 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 U A 10 C2 U A 10 N3 -0.044 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 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 14 O5' - P - OP1 ANGL. DEV. = -7.2 DEGREES REMARK 500 G A 14 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES REMARK 500 G A 14 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 C A 21 C2 - N3 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 C A 21 N3 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 6E7L A 1 22 PDB 6E7L 6E7L 1 22 SEQRES 1 A 22 G G G C U G C A C U U C G SEQRES 2 A 22 G U G C U G C C C FORMUL 2 HOH *11(H2 O) CRYST1 42.041 42.041 77.860 90.00 90.00 90.00 P 41 21 2 8 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 0.023786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012844 0.00000