HEADER RNA 07-MAR-21 7EAF TITLE CRYSTAL STRUCTURE OF SAM-I RIBOSWITCH WITH THE ACTINOMYCES-1 K-TURN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (94-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: CALDANAEROBACTER SUBTERRANEUS SUBSP. SOURCE 4 TENGCONGENSIS; SOURCE 5 ORGANISM_TAXID: 119072 KEYWDS SAM; RIBOSWITCH, RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.HUANG,D.M.J.LILLEY REVDAT 3 29-NOV-23 7EAF 1 REMARK REVDAT 2 23-JUN-21 7EAF 1 JRNL REVDAT 1 02-JUN-21 7EAF 0 JRNL AUTH L.HUANG,X.LIAO,M.LI,J.WANG,X.PENG,T.J.WILSON,D.M.J.LILLEY JRNL TITL STRUCTURE AND FOLDING OF FOUR PUTATIVE KINK TURNS IDENTIFIED JRNL TITL 2 IN STRUCTURED RNA SPECIES IN A TEST OF STRUCTURAL PREDICTION JRNL TITL 3 RULES. JRNL REF NUCLEIC ACIDS RES. V. 49 5916 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 33978763 JRNL DOI 10.1093/NAR/GKAB333 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 7539 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.264 REMARK 3 R VALUE (WORKING SET) : 0.262 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 367 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 29.2200 - 4.1100 0.99 2496 140 0.2569 0.2912 REMARK 3 2 4.1100 - 3.2600 0.99 2346 121 0.2510 0.2822 REMARK 3 3 3.2600 - 2.8500 0.99 2330 106 0.3025 0.3673 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) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 45.414 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.22 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 2325 REMARK 3 ANGLE : 0.965 3627 REMARK 3 CHIRALITY : 0.044 480 REMARK 3 PLANARITY : 0.007 97 REMARK 3 DIHEDRAL : 15.904 1154 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -9.3268 -9.9577 -23.0867 REMARK 3 T TENSOR REMARK 3 T11: 0.7253 T22: 0.5925 REMARK 3 T33: 0.5132 T12: 0.1408 REMARK 3 T13: 0.0961 T23: 0.0863 REMARK 3 L TENSOR REMARK 3 L11: 1.1441 L22: 1.2149 REMARK 3 L33: 2.2591 L12: 1.4998 REMARK 3 L13: 0.1524 L23: -0.1958 REMARK 3 S TENSOR REMARK 3 S11: -0.0938 S12: -0.1477 S13: 0.2266 REMARK 3 S21: -0.0767 S22: 0.2609 S23: -0.1548 REMARK 3 S31: 0.1352 S32: -0.0019 S33: -0.1470 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 7EAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021069. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7963 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 5FK3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MM NA-CACODYLATE (PH 7.0), 80 MM REMARK 280 KCL, 40 MM BACL2, 12 MM SPERMINE-HCL, 12% (V/V) MPD., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.95500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.73000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.73000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 118.43250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.73000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.73000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.47750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.73000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.73000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 118.43250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.73000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.73000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.47750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 78.95500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 BA BA A 102 LIES ON A SPECIAL POSITION. 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' G A 13 OP2 G A 15 2.13 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 G A 1 P G A 1 OP3 -0.125 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 BA A 104 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 15 O6 REMARK 620 2 G A 16 O6 67.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA A 106 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 50 O6 REMARK 620 2 A A 52 OP1 59.5 REMARK 620 N 1 DBREF 7EAF A 1 94 PDB 7EAF 7EAF 1 94 SEQRES 1 A 94 G G C U U A U C A A G A G SEQRES 2 A 94 A G G G C G A G G G A C U SEQRES 3 A 94 G G C C C G A C G A C C C SEQRES 4 A 94 C C G G C A A C C A G A A SEQRES 5 A 94 A U G G U G C C A A U U C SEQRES 6 A 94 C U G C A G C G G A A A C SEQRES 7 A 94 G U U G A A A G A U G A G SEQRES 8 A 94 C C G HET SAM A 101 27 HET BA A 102 1 HET BA A 103 1 HET BA A 104 1 HET BA A 105 1 HET BA A 106 1 HET BA A 107 1 HET NA A 108 1 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM BA BARIUM ION HETNAM NA SODIUM ION FORMUL 2 SAM C15 H22 N6 O5 S FORMUL 3 BA 6(BA 2+) FORMUL 9 NA NA 1+ FORMUL 10 HOH *5(H2 O) LINK O6 G A 15 BA BA A 104 1555 1555 3.36 LINK O6 G A 16 BA BA A 104 1555 1555 2.97 LINK O6 G A 22 BA BA A 105 1555 1555 2.72 LINK O6 G A 27 BA BA A 103 1555 1555 2.86 LINK O6 G A 42 NA NA A 108 1555 1555 3.11 LINK O6 G A 50 BA BA A 106 1555 1555 3.07 LINK OP1 A A 52 BA BA A 106 1555 1555 3.38 LINK O6 G A 74 BA BA A 107 1555 1555 3.23 CRYST1 61.460 61.460 157.910 90.00 90.00 90.00 P 43 21 2 8 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 0.016271 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006333 0.00000