HEADER RNA 21-JAN-24 8XZK TITLE CRYSTAL STRUCTURE OF FOLE RIBOSWITCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (53-MER); COMPND 3 CHAIN: A; COMPND 4 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, RNA EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.LI,A.M.REN REVDAT 2 21-AUG-24 8XZK 1 JRNL REVDAT 1 24-JUL-24 8XZK 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. 2.58 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) : 2.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.6 REMARK 3 NUMBER OF REFLECTIONS : 4609 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 461 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 36.5500 - 3.7200 0.98 1615 181 0.1648 0.2140 REMARK 3 2 3.7200 - 2.9500 0.97 1492 167 0.2341 0.3235 REMARK 3 3 2.9500 - 2.5800 0.67 1041 113 0.3193 0.3947 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.020 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 1261 REMARK 3 ANGLE : 1.100 1963 REMARK 3 CHIRALITY : 0.044 264 REMARK 3 PLANARITY : 0.006 53 REMARK 3 DIHEDRAL : 13.958 632 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 8XZK 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_1300044550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-22 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4721 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.580 REMARK 200 RESOLUTION RANGE LOW (A) : 41.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 1.53000 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 (%): 47.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 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 22.64100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.95150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.81200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.95150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.64100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.81200 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 O2' C A 28 OP2 U A 30 2.15 REMARK 500 O6 G A 3 O HOH A 101 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 GDP A 1 C3' - O3' - P ANGL. DEV. = -10.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 8XZK A 1 53 PDB 8XZK 8XZK 1 53 SEQRES 1 A 53 GDP 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 GDP A 1 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 1 GDP C10 H15 N5 O11 P2 FORMUL 2 HOH *4(H2 O) LINK O3' GDP A 1 P G A 2 1555 1555 1.56 CRYST1 45.282 55.624 61.903 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 0.022084 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016154 0.00000 HETATM 1 PB GDP A 1 30.583 9.477 -22.503 1.00122.80 P HETATM 2 O1B GDP A 1 29.383 9.702 -23.401 1.00110.93 O HETATM 3 O2B GDP A 1 31.351 10.776 -22.397 1.00118.09 O HETATM 4 O3B GDP A 1 31.471 8.390 -23.084 1.00110.22 O HETATM 5 O3A GDP A 1 30.067 9.050 -21.029 1.00118.79 O HETATM 6 PA GDP A 1 29.294 7.650 -20.797 1.00119.19 P HETATM 7 O1A GDP A 1 29.709 6.648 -21.858 1.00116.04 O HETATM 8 O2A GDP A 1 29.504 7.098 -19.402 1.00103.32 O HETATM 9 O5' GDP A 1 27.750 8.078 -21.003 1.00108.91 O HETATM 10 C5' GDP A 1 27.308 9.420 -20.786 1.00104.10 C HETATM 11 C4' GDP A 1 26.047 9.689 -21.600 1.00 98.04 C HETATM 12 O4' GDP A 1 26.329 9.645 -23.005 1.00 93.71 O HETATM 13 C3' GDP A 1 24.975 8.640 -21.356 1.00 90.17 C HETATM 14 O3' GDP A 1 24.091 9.011 -20.294 1.00 88.46 O HETATM 15 C2' GDP A 1 24.247 8.567 -22.678 1.00 87.53 C HETATM 16 O2' GDP A 1 23.219 9.558 -22.724 1.00 79.52 O HETATM 17 C1' GDP A 1 25.320 8.895 -23.694 1.00 91.59 C HETATM 18 N9 GDP A 1 25.896 7.603 -24.148 1.00 94.09 N HETATM 19 C8 GDP A 1 27.174 7.221 -23.951 1.00 96.39 C HETATM 20 N7 GDP A 1 27.400 5.980 -24.458 1.00 96.99 N HETATM 21 C5 GDP A 1 26.245 5.525 -24.991 1.00 92.00 C HETATM 22 C6 GDP A 1 25.796 4.280 -25.685 1.00 85.06 C HETATM 23 O6 GDP A 1 26.581 3.325 -25.906 1.00 81.39 O HETATM 24 N1 GDP A 1 24.510 4.210 -26.074 1.00 83.82 N HETATM 25 C2 GDP A 1 23.634 5.221 -25.859 1.00 84.60 C HETATM 26 N2 GDP A 1 22.355 5.061 -26.284 1.00 79.78 N HETATM 27 N3 GDP A 1 23.977 6.388 -25.232 1.00 86.36 N HETATM 28 C4 GDP A 1 25.247 6.600 -24.778 1.00 91.82 C