HEADER RNA 26-NOV-18 6IA2 TITLE CRYSTAL STRUCTURE OF A SELF-COMPLEMENTARY RNA DUPLEX RECOGNIZED BY COM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*AP*GP*AP*GP*AP*AP*CP*CP*CP*GP*GP*AP*GP*UP*UP*CP*CP*CP*U)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA DUPLEX, COM BINDING MOTIF, RNA EXPDTA X-RAY DIFFRACTION AUTHOR M.NOWACKA,H.FERNANDES,A.KILISZEK,A.BERNAT,G.LACH,J.M.BUJNICKI REVDAT 3 24-JAN-24 6IA2 1 REMARK REVDAT 2 08-MAY-19 6IA2 1 JRNL REVDAT 1 27-MAR-19 6IA2 0 JRNL AUTH M.NOWACKA,H.FERNANDES,A.KILISZEK,A.BERNAT,G.LACH, JRNL AUTH 2 J.M.BUJNICKI JRNL TITL SPECIFIC INTERACTION OF ZINC FINGER PROTEIN COM WITH RNA AND JRNL TITL 2 THE CRYSTAL STRUCTURE OF A SELF-COMPLEMENTARY RNA DUPLEX JRNL TITL 3 RECOGNIZED BY COM. JRNL REF PLOS ONE V. 14 14481 2019 JRNL REFN ESSN 1932-6203 JRNL PMID 31022205 JRNL DOI 10.1371/JOURNAL.PONE.0214481 REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 6176 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 309 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 25.5470 - 2.8587 0.99 3003 158 0.1941 0.2211 REMARK 3 2 2.8587 - 2.2694 1.00 2864 151 0.2774 0.3410 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.65 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 : 0.005 984 REMARK 3 ANGLE : 0.911 1539 REMARK 3 CHIRALITY : 0.032 204 REMARK 3 PLANARITY : 0.005 41 REMARK 3 DIHEDRAL : 10.712 494 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.3586 2.4639 -1.3401 REMARK 3 T TENSOR REMARK 3 T11: 0.3385 T22: 0.3915 REMARK 3 T33: 0.3267 T12: 0.0203 REMARK 3 T13: -0.0531 T23: -0.0136 REMARK 3 L TENSOR REMARK 3 L11: 0.6686 L22: 0.8151 REMARK 3 L33: 1.5273 L12: 0.0049 REMARK 3 L13: -0.1599 L23: 0.9088 REMARK 3 S TENSOR REMARK 3 S11: -0.0133 S12: -0.1960 S13: -0.1852 REMARK 3 S21: 0.1224 S22: 0.3947 S23: -0.0880 REMARK 3 S31: 0.5937 S32: 0.3199 S33: -0.3811 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 12 THROUGH 19 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.4677 -0.6569 24.7696 REMARK 3 T TENSOR REMARK 3 T11: 0.3763 T22: 0.2434 REMARK 3 T33: 0.3498 T12: -0.0457 REMARK 3 T13: -0.0019 T23: 0.0437 REMARK 3 L TENSOR REMARK 3 L11: 0.9836 L22: 2.3172 REMARK 3 L33: 1.3434 L12: -0.3478 REMARK 3 L13: -0.3754 L23: 0.7062 REMARK 3 S TENSOR REMARK 3 S11: -0.0972 S12: 0.1131 S13: 0.1833 REMARK 3 S21: 0.1064 S22: 0.2995 S23: -0.0230 REMARK 3 S31: -0.1514 S32: -0.1576 S33: -0.1865 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.6412 0.5750 14.6469 REMARK 3 T TENSOR REMARK 3 T11: 0.4054 T22: 0.2535 REMARK 3 T33: 0.3352 T12: -0.0023 REMARK 3 T13: 0.0217 T23: 0.0729 REMARK 3 L TENSOR REMARK 3 L11: 0.9460 L22: 1.1471 REMARK 3 L33: 2.6538 L12: -0.4345 REMARK 3 L13: 0.8483 L23: 0.6266 REMARK 3 S TENSOR REMARK 3 S11: 0.2760 S12: 0.2736 S13: 0.1876 REMARK 3 S21: -0.2851 S22: -0.2807 S23: -0.2336 REMARK 3 S31: 0.2029 S32: -0.1944 S33: 0.0269 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 12 THROUGH 19 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.3372 4.7726 -10.1749 REMARK 3 T TENSOR REMARK 3 T11: 0.3032 T22: 0.4296 REMARK 3 T33: 0.3678 T12: -0.1078 REMARK 3 T13: 0.0142 T23: -0.0485 REMARK 3 L TENSOR REMARK 3 L11: 1.0624 L22: 1.1546 REMARK 3 L33: 2.0993 L12: -0.0808 REMARK 3 L13: -0.2439 L23: 0.4124 REMARK 3 S TENSOR REMARK 3 S11: -0.1541 S12: 0.6287 S13: -0.2823 REMARK 3 S21: -0.2029 S22: 0.3884 S23: -0.3942 REMARK 3 S31: 0.3762 S32: -0.3979 S33: -0.2243 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 6IA2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200013027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6194 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 REMARK 200 RESOLUTION RANGE LOW (A) : 25.545 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.832 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.15 REMARK 200 R MERGE FOR SHELL (I) : 0.50300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.550 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.7 REMARK 200 STARTING MODEL: 3GLP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE TRIHYDRATE PH 4.6, REMARK 280 2M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 15.90200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.37950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.95000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.90200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.37950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 2050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 DBREF 6IA2 A 1 19 PDB 6IA2 6IA2 1 19 DBREF 6IA2 B 1 19 PDB 6IA2 6IA2 1 19 SEQRES 1 A 19 A G A G A A C C C G G A G SEQRES 2 A 19 U U C C C U SEQRES 1 B 19 A G A G A A C C C G G A G SEQRES 2 B 19 U U C C C U HET CL B 101 1 HET SO4 B 102 5 HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 3 CL CL 1- FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *10(H2 O) SITE 1 AC1 1 G B 11 SITE 1 AC2 2 C B 9 G B 10 CRYST1 31.804 38.759 101.900 90.00 90.00 90.00 P 21 21 21 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 0.031443 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009814 0.00000