HEADER RNA 30-MAR-21 7EI8 TITLE RNA KINK-TURN MOTIF WITH 2-AMINOPURINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))- COMPND 3 R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3'); COMPND 4 CHAIN: A, B, C, D; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS KINK-TURN MOTIF, 2-AMINOPURINE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,S.SAISU REVDAT 2 29-NOV-23 7EI8 1 REMARK REVDAT 1 30-MAR-22 7EI8 0 JRNL AUTH J.KONDO,S.SAISU JRNL TITL RNA KINK-TURN MOTIF WITH 2-AMINOPURINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 4486 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.140 REMARK 3 FREE R VALUE TEST SET COUNT : 455 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 48.2600 - 4.4700 0.98 1381 157 0.1706 0.2191 REMARK 3 2 4.4700 - 3.5500 0.97 1320 156 0.2152 0.2917 REMARK 3 3 3.5500 - 3.1000 0.96 1330 142 0.2458 0.3429 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 73.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.14 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 7EI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-19 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-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.60499 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 : 4510 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 48.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 6.499 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.61 REMARK 200 R MERGE FOR SHELL (I) : 0.33400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.480 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 (%): 51.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, HEXAMMINE COBALT, REMARK 280 MPD, POTASSIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 57.56200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.44750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.56200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.44750 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 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: 6180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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: 6270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CO CO C 101 LIES ON A SPECIAL POSITION. REMARK 375 CO CO D 101 LIES ON A SPECIAL POSITION. REMARK 375 CO CO D 103 LIES ON A SPECIAL POSITION. DBREF 7EI8 A 1 19 PDB 7EI8 7EI8 1 19 DBREF 7EI8 B 1 19 PDB 7EI8 7EI8 1 19 DBREF 7EI8 C 1 19 PDB 7EI8 7EI8 1 19 DBREF 7EI8 D 1 19 PDB 7EI8 7EI8 1 19 SEQRES 1 A 19 G G C 2PR 2PR 2PR 2PR A A C C G G SEQRES 2 A 19 G G A G C C SEQRES 1 B 19 G G C 2PR 2PR 2PR 2PR A A C C G G SEQRES 2 B 19 G G A G C C SEQRES 1 C 19 G G C 2PR 2PR 2PR 2PR A A C C G G SEQRES 2 C 19 G G A G C C SEQRES 1 D 19 G G C 2PR 2PR 2PR 2PR A A C C G G SEQRES 2 D 19 G G A G C C HET 2PR A 4 21 HET 2PR A 5 21 HET 2PR A 6 21 HET 2PR A 7 21 HET 2PR B 4 21 HET 2PR B 5 21 HET 2PR B 6 21 HET 2PR B 7 21 HET 2PR C 4 21 HET 2PR C 5 21 HET 2PR C 6 21 HET 2PR C 7 21 HET 2PR D 4 21 HET 2PR D 5 21 HET 2PR D 6 21 HET 2PR D 7 21 HET CO A 101 1 HET CO A 102 1 HET CO B 101 1 HET CO B 102 1 HET CO B 103 1 HET CO C 101 1 HET CO C 102 1 HET CO C 103 1 HET CO C 104 1 HET CO C 105 1 HET CO D 101 1 HET CO D 102 1 HET CO D 103 1 HET CO D 104 1 HETNAM 2PR 2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'- HETNAM 2 2PR MONOPHOSPHATE HETNAM CO COBALT (II) ION HETSYN 2PR 2-AMINOPURINE-2'-DEOXYRIBO-5'-MONOPHOSPHATE FORMUL 1 2PR 16(C10 H14 N5 O6 P) FORMUL 5 CO 14(CO 2+) LINK O3' C A 3 P 2PR A 4 1555 1555 1.60 LINK O3' 2PR A 4 P 2PR A 5 1555 1555 1.60 LINK O3' 2PR A 5 P 2PR A 6 1555 1555 1.61 LINK O3' 2PR A 6 P 2PR A 7 1555 1555 1.61 LINK O3' 2PR A 7 P A A 8 1555 1555 1.61 LINK O3' C B 3 P 2PR B 4 1555 1555 1.60 LINK O3' 2PR B 4 P 2PR B 5 1555 1555 1.61 LINK O3' 2PR B 5 P 2PR B 6 1555 1555 1.60 LINK O3' 2PR B 6 P 2PR B 7 1555 1555 1.61 LINK O3' 2PR B 7 P A B 8 1555 1555 1.60 LINK O3' C C 3 P 2PR C 4 1555 1555 1.60 LINK O3' 2PR C 4 P 2PR C 5 1555 1555 1.60 LINK O3' 2PR C 5 P 2PR C 6 1555 1555 1.61 LINK O3' 2PR C 6 P 2PR C 7 1555 1555 1.61 LINK O3' 2PR C 7 P A C 8 1555 1555 1.61 LINK O3' C D 3 P 2PR D 4 1555 1555 1.61 LINK O3' 2PR D 4 P 2PR D 5 1555 1555 1.61 LINK O3' 2PR D 5 P 2PR D 6 1555 1555 1.61 LINK O3' 2PR D 6 P 2PR D 7 1555 1555 1.61 LINK O3' 2PR D 7 P A D 8 1555 1555 1.59 CRYST1 115.124 42.895 56.269 90.00 116.04 90.00 C 1 2 1 16 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 0.008686 0.000000 0.004245 0.00000 SCALE2 0.000000 0.023313 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019780 0.00000