HEADER RNA 21-JAN-24 8XZN TITLE CRYSTAL STRUCTURE OF FOLE RIBOSWITCH WITH BH4 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, BH4, RNA EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.LI,A.M.REN REVDAT 1 24-JUL-24 8XZN 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. 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38769061 JRNL DOI 10.1093/NAR/GKAE377 REMARK 2 REMARK 2 RESOLUTION. 1.82 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16502 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 851 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 31.4600 - 3.3100 0.99 2734 152 0.1678 0.2078 REMARK 3 2 3.3100 - 2.6300 1.00 2617 151 0.2583 0.2774 REMARK 3 3 2.6300 - 2.2900 1.00 2584 144 0.2875 0.2761 REMARK 3 4 2.2900 - 2.0800 1.00 2596 143 0.2903 0.3186 REMARK 3 5 2.0800 - 1.9400 1.00 2578 119 0.2875 0.3374 REMARK 3 6 1.9400 - 1.8200 0.99 2542 142 0.3151 0.3402 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) : 32.330 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 1296 REMARK 3 ANGLE : 1.187 2008 REMARK 3 CHIRALITY : 0.047 267 REMARK 3 PLANARITY : 0.007 54 REMARK 3 DIHEDRAL : 15.192 653 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 8XZN 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_1300044556. 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 : 16566 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 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 : 12.70 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 11.80 REMARK 200 R MERGE FOR SHELL (I) : 1.11100 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 (%): 53.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 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 24.63850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.45700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.74500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.45700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.63850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.74500 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 216 O HOH A 227 1.99 REMARK 500 O HOH A 203 O HOH A 228 2.00 REMARK 500 N7 A A 33 O HOH A 201 2.03 REMARK 500 O HOH A 202 O HOH A 204 2.09 REMARK 500 O3' U A 53 O HOH A 202 2.10 REMARK 500 O HOH A 222 O HOH A 224 2.17 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. = -10.4 DEGREES REMARK 500 A A 33 N9 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 A A 33 N1 - C6 - N6 ANGL. DEV. = 4.2 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 22 O4 REMARK 620 2 HOH A 214 O 79.5 REMARK 620 3 HOH A 219 O 108.6 75.2 REMARK 620 4 HOH A 228 O 123.9 102.3 126.3 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 U A 53 O3' REMARK 620 2 U A 53 O2' 86.2 REMARK 620 3 HOH A 202 O 67.5 140.6 REMARK 620 4 HOH A 204 O 78.2 83.1 63.7 REMARK 620 N 1 2 3 DBREF 8XZN A 1 53 PDB 8XZN 8XZN 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 H4B A 101 17 HET MG A 102 1 HET MG A 103 1 HET SPM A 104 14 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM H4B 5,6,7,8-TETRAHYDROBIOPTERIN HETNAM MG MAGNESIUM ION HETNAM SPM SPERMINE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 H4B C9 H15 N5 O3 FORMUL 3 MG 2(MG 2+) FORMUL 5 SPM C10 H26 N4 FORMUL 6 HOH *29(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.64 LINK O4 U A 22 MG MG A 103 1555 1555 2.57 LINK O3' U A 53 MG MG A 102 1555 1555 1.88 LINK O2' U A 53 MG MG A 102 1555 1555 2.03 LINK MG MG A 102 O HOH A 202 1555 1555 1.89 LINK MG MG A 102 O HOH A 204 1555 1555 2.07 LINK MG MG A 103 O HOH A 214 1555 1555 2.94 LINK MG MG A 103 O HOH A 219 1555 1555 2.74 LINK MG MG A 103 O HOH A 228 1555 1555 2.84 CRYST1 49.277 57.490 62.914 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 0.020293 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017394 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015895 0.00000 HETATM 1 PG GTP A 1 15.283 35.633 54.764 1.00124.88 P HETATM 2 O1G GTP A 1 14.561 36.595 53.850 1.00123.34 O HETATM 3 O2G GTP A 1 14.555 35.547 56.084 1.00126.16 O HETATM 4 O3G GTP A 1 16.703 36.111 54.984 1.00112.87 O HETATM 5 O3B GTP A 1 15.273 34.183 54.061 1.00123.78 O HETATM 6 PB GTP A 1 16.279 33.887 52.840 1.00125.15 P HETATM 7 O1B GTP A 1 16.036 32.492 52.309 1.00121.41 O HETATM 8 O2B GTP A 1 16.106 34.928 51.755 1.00119.58 O HETATM 9 O3A GTP A 1 17.725 33.959 53.556 1.00110.01 O HETATM 10 PA GTP A 1 19.027 34.572 52.832 1.00100.34 P HETATM 11 O1A GTP A 1 20.151 33.568 52.932 1.00 92.81 O HETATM 12 O2A GTP A 1 18.767 34.931 51.386 1.00105.26 O HETATM 13 O5' GTP A 1 19.391 35.879 53.702 1.00 96.44 O HETATM 14 C5' GTP A 1 20.582 36.583 53.426 1.00 88.60 C HETATM 15 C4' GTP A 1 21.702 36.298 54.425 1.00 84.32 C HETATM 16 O4' GTP A 1 21.220 35.811 55.661 1.00 84.04 O HETATM 17 C3' GTP A 1 22.685 35.241 53.955 1.00 80.55 C HETATM 18 O3' GTP A 1 23.649 35.755 53.066 1.00 78.59 O HETATM 19 C2' GTP A 1 23.307 34.801 55.261 1.00 78.94 C HETATM 20 O2' GTP A 1 24.409 35.630 55.544 1.00 76.91 O HETATM 21 C1' GTP A 1 22.207 35.012 56.293 1.00 78.12 C HETATM 22 N9 GTP A 1 21.608 33.708 56.650 1.00 76.63 N HETATM 23 C8 GTP A 1 20.293 33.354 56.476 1.00 77.01 C HETATM 24 N7 GTP A 1 20.111 32.091 56.921 1.00 69.36 N HETATM 25 C5 GTP A 1 21.290 31.631 57.393 1.00 69.89 C HETATM 26 C6 GTP A 1 21.658 30.416 57.962 1.00 64.52 C HETATM 27 O6 GTP A 1 20.832 29.515 58.108 1.00 62.78 O HETATM 28 N1 GTP A 1 22.964 30.222 58.354 1.00 64.81 N HETATM 29 C2 GTP A 1 23.894 31.229 58.191 1.00 67.62 C HETATM 30 N2 GTP A 1 25.151 31.034 58.574 1.00 64.26 N HETATM 31 N3 GTP A 1 23.524 32.433 57.628 1.00 70.21 N HETATM 32 C4 GTP A 1 22.242 32.635 57.232 1.00 72.34 C