HEADER RNA 21-JAN-24 8XZM TITLE CRYSTAL STRUCTURE OF FOLE RIBOSWITCH WITH DHN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (53-MER); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENV6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNIDENTIFIED EUBACTERIUM CLONE A70; SOURCE 3 ORGANISM_TAXID: 41312; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS RIBOSWITCH, DHN, RNA EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.LI,A.M.REN REVDAT 2 21-AUG-24 8XZM 1 JRNL REVDAT 1 24-JUL-24 8XZM 0 JRNL AUTH C.LI,X.XU,Z.GENG,L.ZHENG,Q.SONG,X.SHEN,J.WU,J.ZHAO,H.LI, JRNL AUTH 2 M.HE,X.TAI,L.ZHANG,J.MA,Y.DONG,A.REN JRNL TITL STRUCTURE-BASED CHARACTERIZATION AND COMPOUND IDENTIFICATION JRNL TITL 2 OF THE WILD-TYPE THF CLASS-II RIBOSWITCH. JRNL REF NUCLEIC ACIDS RES. V. 52 8454 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38769061 JRNL DOI 10.1093/NAR/GKAE377 REMARK 2 REMARK 2 RESOLUTION. 1.98 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 12861 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 638 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 28.5400 - 3.3800 1.00 2580 123 0.1650 0.1838 REMARK 3 2 3.3800 - 2.6800 1.00 2448 119 0.2499 0.2546 REMARK 3 3 2.6800 - 2.3400 1.00 2428 121 0.2865 0.3586 REMARK 3 4 2.3400 - 2.1300 1.00 2396 142 0.2744 0.3520 REMARK 3 5 2.1300 - 1.9800 0.99 2371 133 0.2719 0.3144 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.850 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 : 0.004 1297 REMARK 3 ANGLE : 1.088 2009 REMARK 3 CHIRALITY : 0.043 266 REMARK 3 PLANARITY : 0.007 54 REMARK 3 DIHEDRAL : 12.615 649 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 8XZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300044555. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 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-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12927 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 0.67300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M SODIUM CHLORIDE, 0.04 M SODIUM REMARK 280 CACODYLATE TRIHYDRATE PH 7.0, 30% V/V MPD, 0.012 M SPERMINE REMARK 280 TETRAHYDROCHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.40400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.71100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.54250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.71100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.40400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.54250 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: MONOMERIC 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 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 N7 A A 33 O HOH A 201 2.03 REMARK 500 O HOH A 223 O HOH A 234 2.12 REMARK 500 O3' U A 53 O HOH A 202 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GTP A 1 C3' - O3' - P ANGL. DEV. = -13.0 DEGREES REMARK 500 G A 2 O3' - P - OP2 ANGL. DEV. = 18.3 DEGREES REMARK 500 G A 2 O3' - P - OP1 ANGL. DEV. = -13.8 DEGREES 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 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 6 O4 REMARK 620 2 G A 7 O6 69.8 REMARK 620 3 HOH A 221 O 82.9 147.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 22 O4 REMARK 620 2 HOH A 218 O 83.7 REMARK 620 3 HOH A 224 O 104.4 60.9 REMARK 620 4 HOH A 231 O 109.8 101.5 139.4 REMARK 620 N 1 2 3 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 U A 53 O3' REMARK 620 2 U A 53 O2' 83.6 REMARK 620 3 HOH A 202 O 64.3 111.4 REMARK 620 N 1 2 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 214 O REMARK 620 2 HOH A 229 O 74.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 219 O REMARK 620 2 HOH A 226 O 90.2 REMARK 620 3 HOH A 227 O 69.6 89.2 REMARK 620 N 1 2 DBREF 8XZM A 1 53 PDB 8XZM 8XZM 1 53 SEQRES 1 A 53 GTP G G U G U G U A C C G U SEQRES 2 A 53 U C A A C U C G U C C C A SEQRES 3 A 53 G C U U C G A C U G G G A SEQRES 4 A 53 C U A C G G G A G C G C C SEQRES 5 A 53 U HET GTP A 1 32 HET MG A 101 1 HET MG A 102 1 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET NPR A 106 18 HET SPM A 107 14 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NPR 2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)- HETNAM 2 NPR PTERIDINONE HETNAM SPM SPERMINE HETSYN NPR 7,8-DIHYDRONEOPTERIN FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 MG 5(MG 2+) FORMUL 7 NPR C9 H13 N5 O4 FORMUL 8 SPM C10 H26 N4 FORMUL 9 HOH *34(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.56 LINK O4 U A 6 MG MG A 103 1555 1555 2.78 LINK O6 G A 7 MG MG A 103 1555 1555 2.69 LINK O4 U A 22 MG MG A 105 1555 1555 2.63 LINK O3' U A 53 MG MG A 101 1555 1555 1.95 LINK O2' U A 53 MG MG A 101 1555 1555 2.05 LINK MG MG A 101 O HOH A 202 1555 1555 2.09 LINK MG MG A 102 O HOH A 214 1555 1555 2.48 LINK MG MG A 102 O HOH A 229 1555 1555 1.94 LINK MG MG A 103 O HOH A 221 1555 1555 2.61 LINK MG MG A 104 O HOH A 219 1555 1555 2.30 LINK MG MG A 104 O HOH A 226 1555 1555 2.35 LINK MG MG A 104 O HOH A 227 1555 1555 2.07 LINK MG MG A 105 O HOH A 218 1555 1555 2.73 LINK MG MG A 105 O HOH A 224 1555 1555 2.59 LINK MG MG A 105 O HOH A 231 1555 1555 2.80 CRYST1 48.808 57.085 63.422 90.00 90.00 90.00 P 21 21 21 4 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 0.020488 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015767 0.00000 HETATM 1 PG GTP A 1 14.330 33.720 54.273 1.00122.22 P HETATM 2 O1G GTP A 1 14.678 32.740 55.375 1.00115.64 O HETATM 3 O2G GTP A 1 12.828 33.845 54.159 1.00111.75 O HETATM 4 O3G GTP A 1 14.866 33.205 52.953 1.00111.77 O HETATM 5 O3B GTP A 1 14.962 35.178 54.621 1.00118.08 O HETATM 6 PB GTP A 1 16.464 35.418 55.190 1.00113.09 P HETATM 7 O1B GTP A 1 16.938 36.821 54.871 1.00102.99 O HETATM 8 O2B GTP A 1 16.536 35.165 56.679 1.00108.72 O HETATM 9 O3A GTP A 1 17.370 34.335 54.405 1.00108.87 O HETATM 10 PA GTP A 1 17.815 34.508 52.865 1.00103.66 P HETATM 11 O1A GTP A 1 18.203 33.153 52.316 1.00100.23 O HETATM 12 O2A GTP A 1 16.749 35.165 52.015 1.00105.25 O HETATM 13 O5' GTP A 1 19.131 35.419 52.996 1.00 97.11 O HETATM 14 C5' GTP A 1 20.288 34.773 53.454 1.00 90.18 C HETATM 15 C4' GTP A 1 21.231 35.678 54.228 1.00 85.87 C HETATM 16 O4' GTP A 1 20.805 35.754 55.571 1.00 86.56 O HETATM 17 C3' GTP A 1 22.596 35.014 54.224 1.00 82.47 C HETATM 18 O3' GTP A 1 23.484 35.635 53.318 1.00 82.70 O HETATM 19 C2' GTP A 1 23.061 35.049 55.670 1.00 82.29 C HETATM 20 O2' GTP A 1 23.961 36.109 55.898 1.00 77.38 O HETATM 21 C1' GTP A 1 21.771 35.217 56.464 1.00 83.83 C HETATM 22 N9 GTP A 1 21.267 33.882 56.862 1.00 81.30 N HETATM 23 C8 GTP A 1 19.969 33.467 56.702 1.00 82.58 C HETATM 24 N7 GTP A 1 19.842 32.203 57.157 1.00 75.33 N HETATM 25 C5 GTP A 1 21.043 31.794 57.617 1.00 74.58 C HETATM 26 C6 GTP A 1 21.451 30.593 58.188 1.00 69.17 C HETATM 27 O6 GTP A 1 20.649 29.669 58.341 1.00 66.09 O HETATM 28 N1 GTP A 1 22.765 30.441 58.574 1.00 68.44 N HETATM 29 C2 GTP A 1 23.659 31.477 58.394 1.00 71.75 C HETATM 30 N2 GTP A 1 24.923 31.321 58.769 1.00 72.89 N HETATM 31 N3 GTP A 1 23.249 32.669 57.829 1.00 75.13 N HETATM 32 C4 GTP A 1 21.955 32.834 57.441 1.00 77.54 C