HEADER RNA 03-JUL-21 7F8Z TITLE RNA KINK-TURN MOTIF WITH 2-AMINOPURINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))- COMPND 3 R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3'); COMPND 4 CHAIN: A, B, C, D, E, F, G, H, I, J; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS 2-AMINOPURINE, KINK-TURN MOTIF, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,T.MIYAUCHI REVDAT 2 29-NOV-23 7F8Z 1 REMARK REVDAT 1 06-JUL-22 7F8Z 0 JRNL AUTH J.KONDO,T.MIYAUCHI JRNL TITL RNA KINK-TURN MOTIF WITH 2-AMINOPURINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 14856 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1485 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 35.0400 - 6.6400 0.95 1271 142 0.1626 0.1827 REMARK 3 2 6.6400 - 5.2800 0.99 1262 140 0.1397 0.1786 REMARK 3 3 5.2800 - 4.6100 0.99 1229 136 0.1660 0.2121 REMARK 3 4 4.6100 - 4.1900 0.99 1228 138 0.1540 0.2151 REMARK 3 5 4.1900 - 3.8900 1.00 1223 136 0.1655 0.2335 REMARK 3 6 3.8900 - 3.6600 0.99 1193 131 0.1752 0.2534 REMARK 3 7 3.6600 - 3.4800 0.98 1219 135 0.1967 0.2733 REMARK 3 8 3.4800 - 3.3300 0.98 1199 133 0.1981 0.2481 REMARK 3 9 3.3300 - 3.2000 0.99 1200 132 0.2039 0.2902 REMARK 3 10 3.2000 - 3.0900 0.99 1217 136 0.2166 0.2699 REMARK 3 11 3.0900 - 2.9900 0.95 1130 126 0.2518 0.2901 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.22 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7F8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023054. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14856 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.796 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.85 REMARK 200 R MERGE FOR SHELL (I) : 0.39600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.230 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: 4C40 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SPERMINE TETRAHYDROCHLORIDE, REMARK 280 POTASSIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 32.98100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.86300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.98100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.86300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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: 3450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 3190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 REMARK 350 BIOMOLECULE: 3 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: 3470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 REMARK 350 BIOMOLECULE: 4 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: 3490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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 REMARK 350 BIOMOLECULE: 5 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: 3350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, J 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 K G 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G G 12 O6 REMARK 620 2 G G 13 O6 61.6 REMARK 620 N 1 DBREF 7F8Z A 1 19 PDB 7F8Z 7F8Z 1 19 DBREF 7F8Z B 1 19 PDB 7F8Z 7F8Z 1 19 DBREF 7F8Z C 1 19 PDB 7F8Z 7F8Z 1 19 DBREF 7F8Z D 1 19 PDB 7F8Z 7F8Z 1 19 DBREF 7F8Z E 1 19 PDB 7F8Z 7F8Z 1 19 DBREF 7F8Z F 1 19 PDB 7F8Z 7F8Z 1 19 DBREF 7F8Z G 1 19 PDB 7F8Z 7F8Z 1 19 DBREF 7F8Z H 1 19 PDB 7F8Z 7F8Z 1 19 DBREF 7F8Z I 1 19 PDB 7F8Z 7F8Z 1 19 DBREF 7F8Z J 1 19 PDB 7F8Z 7F8Z 1 19 SEQRES 1 A 19 G G C G A 2PR G A A C C G G SEQRES 2 A 19 G G A G C C SEQRES 1 B 19 G G C G A 2PR G A A C C G G SEQRES 2 B 19 G G A G C C SEQRES 1 C 19 G G C G A 2PR G A A C C G G SEQRES 2 C 19 G G A G C C SEQRES 1 D 19 G G C G A 2PR G A A C C G G SEQRES 2 D 19 G G A G C C SEQRES 1 E 19 G G C G A 2PR G A A C C G G SEQRES 2 E 19 G G A G C C SEQRES 1 F 19 G G C G A 2PR G A A C C G G SEQRES 2 F 19 G G A G C C SEQRES 1 G 19 G G C G A 2PR G A A C C G G SEQRES 2 G 19 G G A G C C SEQRES 1 H 19 G G C G A 2PR G A A C C G G SEQRES 2 H 19 G G A G C C SEQRES 1 I 19 G G C G A 2PR G A A C C G G SEQRES 2 I 19 G G A G C C SEQRES 1 J 19 G G C G A 2PR G A A C C G G SEQRES 2 J 19 G G A G C C HET 2PR A 6 21 HET 2PR B 6 21 HET 2PR C 6 21 HET 2PR D 6 21 HET 2PR E 6 21 HET 2PR F 6 21 HET 2PR G 6 21 HET 2PR H 6 21 HET 2PR I 6 21 HET 2PR J 6 21 HET K A 101 1 HET K C 101 1 HET K F 101 1 HET K G 101 1 HET K J 101 1 HETNAM 2PR 2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'- HETNAM 2 2PR MONOPHOSPHATE HETNAM K POTASSIUM ION HETSYN 2PR 2-AMINOPURINE-2'-DEOXYRIBO-5'-MONOPHOSPHATE FORMUL 1 2PR 10(C10 H14 N5 O6 P) FORMUL 11 K 5(K 1+) FORMUL 16 HOH *11(H2 O) LINK O3' A A 5 P 2PR A 6 1555 1555 1.60 LINK O3' 2PR A 6 P G A 7 1555 1555 1.61 LINK O3' A B 5 P 2PR B 6 1555 1555 1.60 LINK O3' 2PR B 6 P G B 7 1555 1555 1.61 LINK O3' A C 5 P 2PR C 6 1555 1555 1.60 LINK O3' 2PR C 6 P G C 7 1555 1555 1.61 LINK O3' A D 5 P 2PR D 6 1555 1555 1.60 LINK O3' 2PR D 6 P G D 7 1555 1555 1.61 LINK O3' A E 5 P 2PR E 6 1555 1555 1.61 LINK O3' 2PR E 6 P G E 7 1555 1555 1.60 LINK O3' A F 5 P 2PR F 6 1555 1555 1.61 LINK O3' 2PR F 6 P G F 7 1555 1555 1.60 LINK O3' A G 5 P 2PR G 6 1555 1555 1.61 LINK O3' 2PR G 6 P G G 7 1555 1555 1.62 LINK O3' A H 5 P 2PR H 6 1555 1555 1.60 LINK O3' 2PR H 6 P G H 7 1555 1555 1.60 LINK O3' A I 5 P 2PR I 6 1555 1555 1.61 LINK O3' 2PR I 6 P G I 7 1555 1555 1.61 LINK O3' A J 5 P 2PR J 6 1555 1555 1.60 LINK O3' 2PR J 6 P G J 7 1555 1555 1.62 LINK O6 G A 14 K K A 101 1555 1555 3.10 LINK OP2 A C 5 K K C 101 1555 1555 3.45 LINK O6 G F 14 K K F 101 1555 1555 3.10 LINK O6 G G 12 K K G 101 1555 1555 3.43 LINK O6 G G 13 K K G 101 1555 1555 3.40 CRYST1 65.962 87.726 124.273 90.00 90.00 90.00 P 21 21 2 40 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 0.015160 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011399 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008047 0.00000