HEADER RNA 03-MAY-20 6WTR TITLE STRUCTURE OF HUMAN PIR-MIRNA-300 APICAL LOOP FUSED TO THE YDAO TITLE 2 RIBOSWITCH SCAFFOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (125-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS MICRORNA, RNA PROCESSING, PROTEIN-RNA INTERACTION, RNA EXPDTA X-RAY DIFFRACTION AUTHOR G.M.SHOFFNER,Z.PENG,F.GUO REVDAT 2 18-OCT-23 6WTR 1 REMARK REVDAT 1 05-MAY-21 6WTR 0 SPRSDE 05-MAY-21 6WTR 6N5R JRNL AUTH G.M.SHOFFNER,Z.PENG,F.GUO JRNL TITL STRUCTURES OF MICRORNA-PRECURSOR APICAL JUNCTIONS AND LOOPS JRNL TITL 2 REVEALED BY SCAFFOLD-DIRECTED CRYSTALLOGRAPHY: IMPORTANCE OF JRNL TITL 3 NON-CANONICAL BASE PAIRS IN PROCESSING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 15789 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1582 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 74.2950 - 6.8531 1.00 1399 156 0.1353 0.1493 REMARK 3 2 6.8531 - 5.4401 1.00 1323 147 0.1411 0.1519 REMARK 3 3 5.4401 - 4.7525 1.00 1316 146 0.1458 0.1760 REMARK 3 4 4.7525 - 4.3181 1.00 1306 146 0.1529 0.1852 REMARK 3 5 4.3181 - 4.0086 0.99 1289 143 0.1636 0.2191 REMARK 3 6 4.0086 - 3.7723 0.99 1283 144 0.1864 0.2384 REMARK 3 7 3.7723 - 3.5833 0.99 1279 142 0.1996 0.2434 REMARK 3 8 3.5833 - 3.4274 0.99 1276 142 0.2072 0.2303 REMARK 3 9 3.4274 - 3.2954 0.99 1287 144 0.2205 0.2822 REMARK 3 10 3.2954 - 3.1817 1.00 1281 143 0.2757 0.3011 REMARK 3 11 3.1817 - 3.0822 0.91 1168 129 0.4196 0.4584 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 100.5 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 128.3 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 : 0.003 3096 REMARK 3 ANGLE : 0.754 4823 REMARK 3 CHIRALITY : 0.034 640 REMARK 3 PLANARITY : 0.003 129 REMARK 3 DIHEDRAL : 18.126 1541 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 6WTR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000248987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.116 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15789 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.080 REMARK 200 RESOLUTION RANGE LOW (A) : 74.295 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 18.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 15.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4QK8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.90 M (NH4)2SO4, 0.158 M LI2SO4, AND REMARK 280 0.1 M NAHEPES PH 7.4, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.01667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.03333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 76.03333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.01667 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 28 OP1 REMARK 620 2 U A 46 OP1 74.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 30 OP2 REMARK 620 2 G A 97 OP1 81.4 REMARK 620 3 C A 98 OP2 158.6 79.4 REMARK 620 4 U A 99 O4 80.1 77.2 86.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2BA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2BA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 207 DBREF 6WTR A 1 125 PDB 6WTR 6WTR 1 125 SEQRES 1 A 125 GDP G U U G C C G A A U C C SEQRES 2 A 125 U U U A C U U G G U A C G SEQRES 3 A 125 G A G G A A C C G C U U U SEQRES 4 A 125 U U G G G G U U A A U C U SEQRES 5 A 125 G C A G U G A A G C U G C SEQRES 6 A 125 A G U A G G G A U A C C U SEQRES 7 A 125 U C U G U C C C G C A C C SEQRES 8 A 125 C G A C A G C U A A C U C SEQRES 9 A 125 C G G A G G C A A U A A A SEQRES 10 A 125 G G A A G G A G HET GDP A 1 28 HET 2BA A 201 44 HET 2BA A 202 44 HET MG A 203 1 HET MG A 204 1 HET K A 205 1 HET MG A 206 1 HET SO4 A 207 5 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM 2BA (2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6- HETNAM 2 2BA AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3', HETNAM 3 2BA 2'-J][1,3,7,9,2,8 ]TETRAOXADIPHOSPHACYCLODODECINE-3,5, HETNAM 4 2BA 10,12-TETROL 5,12-DIOXIDE HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM SO4 SULFATE ION HETSYN 2BA BIS-(3',5')-CYCLIC-DIMERIC-ADENOSINE-MONOPHOSPHATE FORMUL 1 GDP C10 H15 N5 O11 P2 FORMUL 2 2BA 2(C20 H24 N10 O12 P2) FORMUL 4 MG 3(MG 2+) FORMUL 6 K K 1+ FORMUL 8 SO4 O4 S 2- FORMUL 9 HOH *4(H2 O) LINK O3' GDP A 1 P G A 2 1555 1555 1.56 LINK OP1 A A 28 MG MG A 204 1555 1555 2.46 LINK OP2 G A 30 MG MG A 203 1555 1555 2.07 LINK OP1 U A 46 MG MG A 204 1555 1555 2.28 LINK OP1 G A 97 MG MG A 203 1555 1555 2.47 LINK OP2 G A 97 MG MG A 206 1555 1555 2.22 LINK OP2 C A 98 MG MG A 203 1555 1555 2.03 LINK O4 U A 99 MG MG A 203 1555 1555 2.41 SITE 1 AC1 15 G A 5 C A 6 C A 7 G A 8 SITE 2 AC1 15 A A 48 G A 71 G A 72 A A 73 SITE 3 AC1 15 U A 74 A A 75 C A 85 C A 86 SITE 4 AC1 15 G A 110 C A 111 A A 112 SITE 1 AC2 14 A A 9 G A 26 G A 27 A A 28 SITE 2 AC2 14 G A 29 G A 44 G A 45 U A 46 SITE 3 AC2 14 U A 47 C A 91 C A 92 A A 96 SITE 4 AC2 14 C A 105 G A 106 SITE 1 AC3 5 G A 30 A A 96 G A 97 C A 98 SITE 2 AC3 5 U A 99 SITE 1 AC4 2 A A 28 U A 46 SITE 1 AC5 1 GDP A 1 SITE 1 AC6 1 G A 97 SITE 1 AC7 3 A A 32 C A 98 U A 99 CRYST1 113.070 113.070 114.050 90.00 90.00 120.00 P 31 2 1 6 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 0.008844 0.005106 0.000000 0.00000 SCALE2 0.000000 0.010212 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008768 0.00000 HETATM 1 PB GDP A 1 -55.961 2.373 -28.916 1.00137.77 P HETATM 2 O1B GDP A 1 -55.349 3.408 -29.830 1.00143.11 O HETATM 3 O2B GDP A 1 -56.353 2.984 -27.591 1.00135.17 O HETATM 4 O3B GDP A 1 -54.918 1.169 -28.679 1.00135.94 O HETATM 5 O3A GDP A 1 -57.201 1.672 -29.672 1.00135.21 O HETATM 6 PA GDP A 1 -58.636 2.384 -29.866 1.00120.54 P HETATM 7 O1A GDP A 1 -58.713 2.987 -31.247 1.00133.63 O HETATM 8 O2A GDP A 1 -59.746 1.382 -29.649 1.00115.40 O HETATM 9 O5' GDP A 1 -58.727 3.548 -28.759 1.00 99.12 O HETATM 10 C5' GDP A 1 -59.588 3.376 -27.655 1.00100.44 C HETATM 11 C4' GDP A 1 -60.146 4.704 -27.148 1.00 93.21 C HETATM 12 O4' GDP A 1 -59.090 5.584 -26.812 1.00102.35 O HETATM 13 C3' GDP A 1 -61.005 5.466 -28.143 1.00 91.58 C HETATM 14 O3' GDP A 1 -62.352 5.058 -28.119 1.00 71.82 O HETATM 15 C2' GDP A 1 -60.858 6.890 -27.653 1.00100.67 C HETATM 16 O2' GDP A 1 -61.800 7.154 -26.639 1.00 86.63 O HETATM 17 C1' GDP A 1 -59.455 6.927 -27.074 1.00103.52 C HETATM 18 N9 GDP A 1 -58.579 7.458 -28.130 1.00105.96 N HETATM 19 C8 GDP A 1 -57.587 6.762 -28.770 1.00107.09 C HETATM 20 N7 GDP A 1 -57.006 7.577 -29.678 1.00103.75 N HETATM 21 C5 GDP A 1 -57.610 8.783 -29.623 1.00 95.20 C HETATM 22 C6 GDP A 1 -57.397 9.957 -30.330 1.00 94.15 C HETATM 23 O6 GDP A 1 -56.517 10.009 -31.189 1.00104.43 O HETATM 24 N1 GDP A 1 -58.176 11.061 -30.062 1.00 95.09 N HETATM 25 C2 GDP A 1 -59.160 10.992 -29.096 1.00 89.23 C HETATM 26 N2 GDP A 1 -59.909 12.063 -28.844 1.00 87.58 N HETATM 27 N3 GDP A 1 -59.365 9.818 -28.397 1.00 84.80 N HETATM 28 C4 GDP A 1 -58.602 8.728 -28.654 1.00 94.45 C