HEADER RNA 09-JAN-23 8HZM TITLE A NEW FLUORESCENT RNA APTAMER BOUND WITH N, MANGANESE SOAK COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (36-MER); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS FLUORESCENT RNA APTAMER, RNA EXPDTA X-RAY DIFFRACTION AUTHOR K.Y.HUANG,A.M.REN REVDAT 1 19-JUN-24 8HZM 0 JRNL AUTH K.HUANG,Q.SONG,M.FANG,D.YAO,X.SHEN,X.XU,X.CHEN,L.ZHU,Y.YANG, JRNL AUTH 2 A.REN JRNL TITL STRUCTURAL BASIS OF A SMALL MONOMERIC CLIVIA FLUOROGENIC RNA JRNL TITL 2 WITH A LARGE STOKES SHIFT. JRNL REF NAT.CHEM.BIOL. 2024 JRNL REFN ESSN 1552-4469 JRNL PMID 38816645 JRNL DOI 10.1038/S41589-024-01633-1 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 6390 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 328 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 39.1400 - 3.1500 1.00 3159 158 0.1852 0.2221 REMARK 3 2 3.1500 - 2.5000 0.94 2903 170 0.2772 0.3676 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.360 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 : 0.006 1806 REMARK 3 ANGLE : 1.142 2800 REMARK 3 CHIRALITY : 0.046 358 REMARK 3 PLANARITY : 0.006 82 REMARK 3 DIHEDRAL : 15.728 874 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 8HZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034653. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-20 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.240 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6395 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.56100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 8HZE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M MAGNESIUM CHLORIDE, 0.1 M HEPES REMARK 280 PH7.5, 30%POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, 0.6% 1,6- REMARK 280 DIAMINOHEXANE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 38.84700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.43550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.84700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.43550 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: 4100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 MN MN B 102 O HOH B 203 1.58 REMARK 500 OP1 G B 2 O3' GTP B 101 2.02 REMARK 500 OP1 G B 24 O HOH B 201 2.03 REMARK 500 OP2 G A 24 O HOH A 201 2.09 REMARK 500 N7 GTP A 101 O HOH A 202 2.10 REMARK 500 OP1 U B 7 O HOH B 202 2.11 REMARK 500 O HOH A 208 O HOH A 216 2.14 REMARK 500 OP2 C A 30 O HOH A 203 2.15 REMARK 500 OP1 G A 2 O3' GTP A 101 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 A 108 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 8 OP1 REMARK 620 2 U A 8 OP2 53.8 REMARK 620 3 HOH A 210 O 104.1 52.9 REMARK 620 4 G B 20 O3' 148.7 148.1 105.9 REMARK 620 5 A B 21 OP1 133.7 150.0 103.1 45.5 REMARK 620 6 HOH B 206 O 134.2 108.6 61.2 70.3 42.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 105 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 20 OP2 REMARK 620 2 HOH A 214 O 92.3 REMARK 620 3 HOH B 223 O 174.3 84.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 109 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 20 O3' REMARK 620 2 U B 8 OP1 165.1 REMARK 620 3 U B 8 OP2 143.6 48.8 REMARK 620 4 HOH B 216 O 86.8 100.1 60.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 103 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 24 N7 REMARK 620 2 HOH A 201 O 102.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 111 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 30 OP2 REMARK 620 2 A A 31 OP2 89.4 REMARK 620 3 HOH A 203 O 48.3 66.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 110 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 36 O3' REMARK 620 2 C A 36 O2' 88.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 102 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 215 O REMARK 620 2 HOH B 210 O 78.8 REMARK 620 3 HOH B 212 O 87.4 92.7 REMARK 620 4 HOH B 221 O 76.1 82.1 163.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 102 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 206 O REMARK 620 2 C B 30 OP2 91.0 REMARK 620 3 A B 31 OP2 85.3 92.3 REMARK 620 4 HOH B 215 O 167.2 85.2 82.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 108 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 12 OP1 REMARK 620 2 HOH B 201 O 104.2 REMARK 620 3 HOH B 209 O 85.0 160.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 103 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 213 O REMARK 620 2 HOH B 217 O 92.4 REMARK 620 3 HOH B 218 O 67.7 105.0 REMARK 620 N 1 2 DBREF 8HZM A 2 36 PDB 8HZM 8HZM 2 36 DBREF 8HZM B 2 36 PDB 8HZM 8HZM 2 36 SEQRES 1 A 35 G A A G A U U G U A A A C SEQRES 2 A 35 A U G C C G A A A G G C A SEQRES 3 A 35 G A C A C U U C C SEQRES 1 B 35 G A A G A U U G U A A A C SEQRES 2 B 35 A U G C C G A A A G G C A SEQRES 3 B 35 G A C A C U U C C HET GTP A 101 32 HET MN A 102 1 HET MN A 103 1 HET MN A 104 1 HET MN A 105 1 HET MN A 106 1 HET MN A 107 1 HET K A 108 1 HET K A 109 1 HET MG A 110 1 HET MG A 111 1 HET NI4 A 112 27 HET GTP B 101 32 HET MN B 102 1 HET MN B 103 1 HET MN B 104 1 HET MN B 105 1 HET MN B 106 1 HET MG B 107 1 HET MG B 108 1 HET MG B 109 1 HET NI4 B 110 27 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM NI4 (5~{Z})-5-[[4-[2-HYDROXYETHYL(METHYL) HETNAM 2 NI4 AMINO]PHENYL]METHYLIDENE]-3-METHYL-2-[(~{E})-2- HETNAM 3 NI4 PHENYLETHENYL]IMIDAZOL-4-ONE FORMUL 3 GTP 2(C10 H16 N5 O14 P3) FORMUL 4 MN 11(MN 2+) FORMUL 10 K 2(K 1+) FORMUL 12 MG 5(MG 2+) FORMUL 14 NI4 2(C22 H23 N3 O2) FORMUL 25 HOH *42(H2 O) LINK P G A 2 O3' GTP A 101 1555 1555 1.56 LINK P G B 2 O3' GTP B 101 1555 1555 1.57 LINK OP1 U A 8 K K A 108 1555 1555 2.90 LINK OP2 U A 8 K K A 108 1555 1555 2.85 LINK OP1 U A 10 MN MN A 107 1555 1555 2.18 LINK OP1 C A 18 MN MN A 104 1555 1555 2.32 LINK OP2 G A 20 MN MN A 105 1555 1555 2.04 LINK O3' G A 20 K K A 109 1555 1555 3.44 LINK N7 G A 24 MN MN A 103 1555 1555 2.39 LINK OP1 G A 25 MG MG B 107 1555 1555 2.94 LINK OP2 A A 27 MN MN A 106 1555 1555 2.74 LINK OP2 C A 30 MG MG A 111 1555 1555 2.63 LINK OP2 A A 31 MG MG A 111 1555 1555 2.20 LINK O3' C A 36 MG MG A 110 1555 1555 1.75 LINK O2' C A 36 MG MG A 110 1555 1555 2.05 LINK MN MN A 102 O HOH A 215 1555 1555 2.20 LINK MN MN A 102 O HOH B 210 1555 1555 2.26 LINK MN MN A 102 O HOH B 212 1555 1555 2.25 LINK MN MN A 102 O HOH B 221 1555 2555 1.73 LINK MN MN A 103 O HOH A 201 1555 1555 2.41 LINK MN MN A 105 O HOH A 214 1555 1555 2.27 LINK MN MN A 105 O HOH B 223 1555 4455 2.41 LINK K K A 108 O HOH A 210 1555 1555 2.56 LINK K K A 108 O3' G B 20 1555 1555 3.27 LINK K K A 108 OP1 A B 21 1555 1555 3.22 LINK K K A 108 O HOH B 206 1555 1555 3.38 LINK K K A 109 OP1 U B 8 1555 1555 3.08 LINK K K A 109 OP2 U B 8 1555 1555 3.11 LINK K K A 109 O HOH B 216 1555 1555 2.56 LINK MG MG A 111 O HOH A 203 1555 1555 2.62 LINK O HOH A 206 MN MN B 102 1556 1555 2.19 LINK OP1 U B 10 MN MN B 104 1555 1555 1.88 LINK OP1 A B 12 MG MG B 108 1555 1555 2.02 LINK OP2 G B 20 MN MN B 105 1555 1555 2.25 LINK OP2 C B 30 MN MN B 102 1555 1555 2.25 LINK OP2 A B 31 MN MN B 102 1555 1555 2.20 LINK MN MN B 102 O HOH B 215 1555 1555 2.32 LINK MN MN B 103 O HOH B 213 1555 1555 2.43 LINK MN MN B 103 O HOH B 217 1555 1555 2.66 LINK MN MN B 103 O HOH B 218 1555 1555 1.92 LINK MG MG B 108 O HOH B 201 1555 2555 1.79 LINK MG MG B 108 O HOH B 209 1555 1555 1.80 CRYST1 77.694 46.871 56.722 90.00 113.70 90.00 C 1 2 1 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 0.012871 0.000000 0.005651 0.00000 SCALE2 0.000000 0.021335 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019254 0.00000