HEADER RNA 16-JUN-23 8PFQ TITLE RNA STRUCTURE WITH 1-METHYLPSEUDOURIDINE, P1 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAINS: A,B; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS SARS-COV-2, COVID-19, CORONAVIRUS, MRNA VACCINE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR B.SPINGLER,K.MCAULEY,P.NIEVERGELT,A.THORN REVDAT 4 06-NOV-24 8PFQ 1 TITLE REVDAT 3 01-MAY-24 8PFQ 1 JRNL REVDAT 2 24-APR-24 8PFQ 1 JRNL REVDAT 1 31-JAN-24 8PFQ 0 JRNL AUTH P.NIEVERGELT,F.BERLIAT,K.E.MCAULEY,C.R.DORGAN,R.M.VAN WELL, JRNL AUTH 2 A.THORN,B.SPINGLER JRNL TITL RNA OLIGOMERS AT ATOMIC RESOLUTION CONTAINING JRNL TITL 2 1-METHYLPSEUDOURIDINE, AN ESSENTIAL BUILDING BLOCK OF MRNA JRNL TITL 3 VACCINES. JRNL REF CHEMMEDCHEM V. 19 00600 2024 JRNL REFN ESSN 1860-7187 JRNL PMID 38235959 JRNL DOI 10.1002/CMDC.202300600 REMARK 2 REMARK 2 RESOLUTION. 1.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.6 REMARK 3 NUMBER OF REFLECTIONS : 27256 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1364 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 23.3800 - 2.1700 0.97 3091 163 0.1433 0.1607 REMARK 3 2 2.1700 - 1.7200 0.96 3034 160 0.1467 0.1673 REMARK 3 3 1.7200 - 1.5100 0.94 2988 157 0.1376 0.1614 REMARK 3 4 1.5100 - 1.3700 0.93 2965 157 0.1563 0.1716 REMARK 3 5 1.3700 - 1.2700 0.92 2886 151 0.1589 0.1995 REMARK 3 6 1.2700 - 1.2000 0.91 2934 155 0.1551 0.1850 REMARK 3 7 1.2000 - 1.1400 0.89 2807 148 0.1791 0.1955 REMARK 3 8 1.1400 - 1.0900 0.84 2656 139 0.2130 0.2457 REMARK 3 9 1.0900 - 1.0400 0.55 1733 92 0.2794 0.2852 REMARK 3 10 1.0400 - 1.0100 0.25 798 42 0.3999 0.5002 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.103 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.581 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.78 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 : 0.004 572 REMARK 3 ANGLE : 0.953 890 REMARK 3 CHIRALITY : 0.027 116 REMARK 3 PLANARITY : 0.010 24 REMARK 3 DIHEDRAL : 6.645 268 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 8PFQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131264. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27271 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.010 REMARK 200 RESOLUTION RANGE LOW (A) : 23.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05207 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 26.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.80880 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 % V/V MPD, 40 MM SODIUM CACODYLATE, REMARK 280 12 MM SPERMINE AND 80 MM POTASSIUM CHLORIDE, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 O HOH A 213 O HOH A 266 2.10 REMARK 500 O HOH A 203 O HOH A 243 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 223 O HOH B 227 1565 2.08 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 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 247 O REMARK 620 2 HOH A 260 O 75.8 REMARK 620 3 HOH B 249 O 79.0 151.2 REMARK 620 4 HOH B 281 O 172.0 96.7 107.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 230 O REMARK 620 2 HOH A 232 O 86.2 REMARK 620 3 HOH A 276 O 80.3 165.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 281 O REMARK 620 2 HOH B 230 O 172.6 REMARK 620 3 HOH B 235 O 81.6 91.2 REMARK 620 4 HOH B 243 O 89.2 92.4 90.4 REMARK 620 5 HOH B 282 O 82.3 105.0 162.9 83.8 REMARK 620 6 HOH B 283 O 87.5 90.8 88.9 176.7 95.9 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8PFK RELATED DB: PDB REMARK 900 8PFK CONTAINS THE SAME SEQUENCE IN SPACE GROUP C2 DBREF 8PFQ A 1 12 PDB 8PFQ 8PFQ 1 12 DBREF 8PFQ B 21 32 PDB 8PFQ 8PFQ 21 32 SEQRES 1 A 12 C G C G A A B8H U A G C G SEQRES 1 B 12 C G C G A A B8H U A G C G HET B8H A 7 33 HET B8H B 27 33 HET MG A 101 1 HET MG A 102 1 HET MG B 101 1 HETNAM B8H [(2~{R},3~{S},4~{R},5~{S})-5-[1-METHYL-2,4- HETNAM 2 B8H BIS(OXIDANYLIDENE)PYRIMIDIN-5-YL]-3,4-BIS(OXIDANYL) HETNAM 3 B8H OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 B8H 2(C10 H15 N2 O9 P) FORMUL 3 MG 3(MG 2+) FORMUL 6 HOH *167(H2 O) LINK O3' A A 6 P B8H A 7 1555 1555 1.62 LINK O3' B8H A 7 P U A 8 1555 1555 1.60 LINK O3' A B 26 P B8H B 27 1555 1555 1.61 LINK O3' B8H B 27 P U B 28 1555 1555 1.61 LINK MG MG A 101 O HOH A 247 1555 1555 2.29 LINK MG MG A 101 O HOH A 260 1555 1555 2.36 LINK MG MG A 101 O HOH B 249 1555 1555 2.09 LINK MG MG A 101 O HOH B 281 1555 1555 2.17 LINK MG MG A 102 O HOH A 230 1555 1555 2.32 LINK MG MG A 102 O HOH A 232 1555 1555 2.09 LINK MG MG A 102 O HOH A 276 1555 1555 2.15 LINK O HOH A 281 MG MG B 101 1555 1555 2.24 LINK MG MG B 101 O HOH B 230 1555 1555 2.06 LINK MG MG B 101 O HOH B 235 1555 1555 2.05 LINK MG MG B 101 O HOH B 243 1555 1555 2.01 LINK MG MG B 101 O HOH B 282 1555 1555 2.03 LINK MG MG B 101 O HOH B 283 1555 1555 2.03 CRYST1 26.763 27.037 29.141 62.59 63.80 88.70 P 1 2 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 0.037365 -0.000848 -0.020767 0.00000 SCALE2 0.000000 0.036996 -0.021476 0.00000 SCALE3 0.000000 0.000000 0.044222 0.00000 CONECT 170 215 CONECT 195 196 204 205 CONECT 196 195 206 207 CONECT 197 202 206 210 CONECT 198 199 202 211 216 CONECT 199 198 200 208 217 CONECT 200 199 201 209 218 CONECT 201 200 203 211 219 CONECT 202 197 198 204 CONECT 203 201 212 220 221 CONECT 204 195 202 222 CONECT 205 195 223 224 225 CONECT 206 196 197 226 CONECT 207 196 CONECT 208 199 227 CONECT 209 200 228 CONECT 210 197 CONECT 211 198 201 CONECT 212 203 215 CONECT 213 215 CONECT 214 215 CONECT 215 170 212 213 214 CONECT 216 198 CONECT 217 199 CONECT 218 200 CONECT 219 201 CONECT 220 203 CONECT 221 203 CONECT 222 204 CONECT 223 205 CONECT 224 205 CONECT 225 205 CONECT 226 206 CONECT 227 208 CONECT 228 209 CONECT 561 606 CONECT 586 587 595 596 CONECT 587 586 597 598 CONECT 588 593 597 601 CONECT 589 590 593 602 607 CONECT 590 589 591 599 608 CONECT 591 590 592 600 609 CONECT 592 591 594 602 610 CONECT 593 588 589 595 CONECT 594 592 603 611 612 CONECT 595 586 593 613 CONECT 596 586 614 615 616 CONECT 597 587 588 617 CONECT 598 587 CONECT 599 590 618 CONECT 600 591 619 CONECT 601 588 CONECT 602 589 592 CONECT 603 594 606 CONECT 604 606 CONECT 605 606 CONECT 606 561 603 604 605 CONECT 607 589 CONECT 608 590 CONECT 609 591 CONECT 610 592 CONECT 611 594 CONECT 612 594 CONECT 613 595 CONECT 614 596 CONECT 615 596 CONECT 616 596 CONECT 617 597 CONECT 618 599 CONECT 619 600 CONECT 783 832 845 918 950 CONECT 784 815 817 861 CONECT 785 866 899 904 912 CONECT 785 951 952 CONECT 815 784 CONECT 817 784 CONECT 832 783 CONECT 845 783 CONECT 861 784 CONECT 866 785 CONECT 899 785 CONECT 904 785 CONECT 912 785 CONECT 918 783 CONECT 950 783 CONECT 951 785 CONECT 952 785 MASTER 251 0 5 0 0 0 0 6 682 2 87 2 END