HEADER RNA 21-JAN-24 8XZL TITLE CRYSTAL STRUCTURE OF FOLE RIBOSWITCH WITH DHF 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, DHF, RNA EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.LI,A.M.REN REVDAT 2 21-AUG-24 8XZL 1 JRNL REVDAT 1 24-JUL-24 8XZL 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. 2.13 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) : 2.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 10188 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 537 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 31.4900 - 3.3800 1.00 2539 133 0.1626 0.1742 REMARK 3 2 3.3800 - 2.6900 1.00 2416 134 0.2615 0.2505 REMARK 3 3 2.6900 - 2.3500 0.99 2356 136 0.3042 0.3323 REMARK 3 4 2.3500 - 2.1300 0.98 2340 134 0.3145 0.3968 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.730 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 : 0.005 1312 REMARK 3 ANGLE : 1.180 2029 REMARK 3 CHIRALITY : 0.040 265 REMARK 3 PLANARITY : 0.007 58 REMARK 3 DIHEDRAL : 12.484 655 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 8XZL 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_1300044552. 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 : 10293 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.130 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 : 11.90 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.81400 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 (%): 53.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 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 24.45200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.49450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.49950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.49450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.45200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.49950 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 O HOH A 203 O HOH A 204 2.18 REMARK 500 O3' U A 53 O HOH A 201 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GTP A 1 O3' G A 2 P 0.074 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 G A 2 O3' - P - O5' ANGL. DEV. = -19.2 DEGREES REMARK 500 G A 2 O3' - P - OP1 ANGL. DEV. = 11.2 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 4 O4 REMARK 620 2 HOH A 213 O 149.7 REMARK 620 N 1 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 U A 53 O3' REMARK 620 2 HOH A 201 O 61.6 REMARK 620 3 HOH A 202 O 69.3 71.2 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 HOH A 203 O REMARK 620 2 HOH A 210 O 138.5 REMARK 620 N 1 DBREF 8XZL A 1 53 PDB 8XZL 8XZL 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 DHF A 101 32 HET MG A 102 1 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET SPM A 106 14 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM DHF DIHYDROFOLIC ACID HETNAM MG MAGNESIUM ION HETNAM SPM SPERMINE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 DHF C19 H21 N7 O6 FORMUL 3 MG 4(MG 2+) FORMUL 7 SPM C10 H26 N4 FORMUL 8 HOH *14(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.68 LINK O4 U A 4 MG MG A 103 1555 1555 2.62 LINK O3' U A 53 MG MG A 102 1555 1555 2.09 LINK MG MG A 102 O HOH A 201 1555 1555 2.17 LINK MG MG A 102 O HOH A 202 1555 1555 2.08 LINK MG MG A 103 O HOH A 213 1555 1555 2.46 LINK MG MG A 104 O HOH A 208 1555 1555 2.10 LINK MG MG A 105 O HOH A 203 1555 1555 2.64 LINK MG MG A 105 O HOH A 210 1555 1555 1.97 CRYST1 48.904 56.999 62.989 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 0.020448 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017544 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015876 0.00000 HETATM 1 PG GTP A 1 14.524 33.422 53.315 1.00128.09 P HETATM 2 O1G GTP A 1 15.008 32.177 54.036 1.00122.85 O HETATM 3 O2G GTP A 1 13.012 33.493 53.355 1.00122.17 O HETATM 4 O3G GTP A 1 14.966 33.352 51.867 1.00124.39 O HETATM 5 O3B GTP A 1 15.110 34.762 54.030 1.00125.68 O HETATM 6 PB GTP A 1 16.563 34.921 54.752 1.00126.48 P HETATM 7 O1B GTP A 1 16.974 36.381 54.698 1.00114.89 O HETATM 8 O2B GTP A 1 16.536 34.442 56.191 1.00116.86 O HETATM 9 O3A GTP A 1 17.604 34.021 53.894 1.00117.64 O HETATM 10 PA GTP A 1 18.338 34.581 52.569 1.00117.47 P HETATM 11 O1A GTP A 1 17.345 35.002 51.503 1.00115.33 O HETATM 12 O2A GTP A 1 19.281 33.534 52.011 1.00113.85 O HETATM 13 O5' GTP A 1 19.138 35.863 53.142 1.00110.31 O HETATM 14 C5' GTP A 1 20.482 36.083 52.780 1.00106.30 C HETATM 15 C4' GTP A 1 21.428 36.058 53.973 1.00 99.35 C HETATM 16 O4' GTP A 1 20.792 35.667 55.173 1.00 99.66 O HETATM 17 C3' GTP A 1 22.527 35.032 53.785 1.00 95.76 C HETATM 18 O3' GTP A 1 23.529 35.465 52.887 1.00 95.06 O HETATM 19 C2' GTP A 1 23.000 34.847 55.212 1.00 94.03 C HETATM 20 O2' GTP A 1 23.918 35.865 55.533 1.00 87.70 O HETATM 21 C1' GTP A 1 21.725 35.023 56.031 1.00 96.52 C HETATM 22 N9 GTP A 1 21.169 33.711 56.447 1.00 95.29 N HETATM 23 C8 GTP A 1 19.858 33.324 56.305 1.00 98.10 C HETATM 24 N7 GTP A 1 19.700 32.075 56.802 1.00 91.52 N HETATM 25 C5 GTP A 1 20.890 31.652 57.276 1.00 87.10 C HETATM 26 C6 GTP A 1 21.278 30.461 57.884 1.00 83.43 C HETATM 27 O6 GTP A 1 20.459 29.556 58.073 1.00 81.38 O HETATM 28 N1 GTP A 1 22.594 30.301 58.274 1.00 80.34 N HETATM 29 C2 GTP A 1 23.509 31.317 58.059 1.00 83.44 C HETATM 30 N2 GTP A 1 24.775 31.162 58.434 1.00 81.14 N HETATM 31 N3 GTP A 1 23.115 32.496 57.457 1.00 88.66 N HETATM 32 C4 GTP A 1 21.824 32.669 57.067 1.00 90.13 C