HEADER RNA 25-FEB-17 5UZA TITLE ADENINE RIBOSWITCH APTAMER DOMAIN LABELLED WITH IODO-URIDINE BY TITLE 2 POSITION-SELECTIVE LABELLING OF RNA (PLOR) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (71-MER); COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 4 ORGANISM_TAXID: 672 KEYWDS RNA, ADENINE RIBOSWITCH, IODO-URIDINE EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,J.R.STAGNO,Y.-X.WANG REVDAT 4 06-MAR-24 5UZA 1 LINK REVDAT 3 25-APR-18 5UZA 1 JRNL REVDAT 2 18-APR-18 5UZA 1 REMARK REVDAT 1 28-FEB-18 5UZA 0 JRNL AUTH Y.LIU,E.HOLMSTROM,P.YU,K.TAN,X.ZUO,D.J.NESBITT,R.SOUSA, JRNL AUTH 2 J.R.STAGNO,Y.X.WANG JRNL TITL INCORPORATION OF ISOTOPIC, FLUORESCENT, AND JRNL TITL 2 HEAVY-ATOM-MODIFIED NUCLEOTIDES INTO RNAS BY JRNL TITL 3 POSITION-SELECTIVE LABELING OF RNA. JRNL REF NAT PROTOC V. 13 987 2018 JRNL REFN ESSN 1750-2799 JRNL PMID 29651055 JRNL DOI 10.1038/NPROT.2018.002 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2447 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.170 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 17080 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 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 46.6216 - 4.0325 0.99 2763 143 0.1602 0.1755 REMARK 3 2 4.0325 - 3.2010 1.00 2804 140 0.1857 0.2280 REMARK 3 3 3.2010 - 2.7964 1.00 2773 150 0.2436 0.2994 REMARK 3 4 2.7964 - 2.5407 1.00 2792 159 0.2986 0.3244 REMARK 3 5 2.5407 - 2.3586 1.00 2790 152 0.2971 0.3457 REMARK 3 6 2.3586 - 2.2196 0.84 2307 107 0.2912 0.3456 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 25.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.08 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 1705 REMARK 3 ANGLE : 0.386 2630 REMARK 3 CHIRALITY : 0.023 353 REMARK 3 PLANARITY : 0.002 72 REMARK 3 DIHEDRAL : 11.521 833 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): -21.4310 19.2257 -11.1448 REMARK 3 T TENSOR REMARK 3 T11: 0.2233 T22: 0.1851 REMARK 3 T33: 0.1505 T12: -0.0025 REMARK 3 T13: -0.0438 T23: 0.0366 REMARK 3 L TENSOR REMARK 3 L11: 1.6717 L22: 2.2219 REMARK 3 L33: 0.4157 L12: 0.0599 REMARK 3 L13: -0.3413 L23: 0.0333 REMARK 3 S TENSOR REMARK 3 S11: 0.0205 S12: 0.0537 S13: -0.2980 REMARK 3 S21: 0.0224 S22: -0.0226 S23: -0.3009 REMARK 3 S31: -0.0433 S32: -0.0878 S33: 0.0232 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 5UZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226652. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-16 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.55 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17080 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 46.611 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.65800 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: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS-HCL (PH:8.5), 100MM KCL, REMARK 280 10MM MGCL2 AND 30% POLYETHYLENE GLYCOL 400, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 24.49250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.78750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.49250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 75.78750 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: X 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: 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 X 13 P G X 13 OP3 -0.127 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 X 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G X 13 OP1 REMARK 620 2 C X 83 OP2 45.9 REMARK 620 3 HOH X 254 O 57.6 12.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A X 23 OP2 REMARK 620 2 HOH X 217 O 93.3 REMARK 620 3 HOH X 228 O 100.4 100.3 REMARK 620 4 HOH X 245 O 175.6 90.2 76.3 REMARK 620 5 HOH X 250 O 102.8 162.7 83.1 74.0 REMARK 620 6 HOH X 251 O 104.1 85.4 154.5 78.8 84.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A X 24 OP1 REMARK 620 2 HOH X 209 O 89.2 REMARK 620 3 HOH X 218 O 162.1 86.2 REMARK 620 4 HOH X 236 O 88.9 90.5 73.9 REMARK 620 5 HOH X 241 O 94.7 95.4 103.0 173.1 REMARK 620 6 HOH X 244 O 96.0 174.2 88.0 87.2 86.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADE X 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG X 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG X 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG X 104 DBREF 5UZA X 13 83 PDB 5UZA 5UZA 13 83 SEQRES 1 X 71 G G G A A G A U A U A A U SEQRES 2 X 71 C C IU A A IU G A U A U G G SEQRES 3 X 71 U U U G G G A G U U U C U SEQRES 4 X 71 A C C A A G A G C C U U A SEQRES 5 X 71 A A C U C U U G A U U A U SEQRES 6 X 71 C U U C C C HET IU X 28 30 HET IU X 31 30 HET ADE X 101 14 HET MG X 102 1 HET MG X 103 1 HET MG X 104 1 HETNAM IU 5-IODOURIDINE-5'-MONOPHOSPHATE HETNAM ADE ADENINE HETNAM MG MAGNESIUM ION FORMUL 1 IU 2(C9 H12 I N2 O9 P) FORMUL 2 ADE C5 H5 N5 FORMUL 3 MG 3(MG 2+) FORMUL 6 HOH *55(H2 O) LINK O3' C X 27 P IU X 28 1555 1555 1.61 LINK O3' IU X 28 P A X 29 1555 1555 1.61 LINK O3' A X 30 P IU X 31 1555 1555 1.61 LINK O3' IU X 31 P G X 32 1555 1555 1.61 LINK OP1 G X 13 MG MG X 104 1555 2355 2.26 LINK OP2 A X 23 MG MG X 102 1555 1555 2.03 LINK OP1 A X 24 MG MG X 103 1555 1555 1.94 LINK OP2 C X 83 MG MG X 104 1555 1555 2.09 LINK MG MG X 102 O HOH X 217 1555 1555 2.24 LINK MG MG X 102 O HOH X 228 1555 1555 2.17 LINK MG MG X 102 O HOH X 245 1555 1555 2.09 LINK MG MG X 102 O HOH X 250 1555 1555 2.14 LINK MG MG X 102 O HOH X 251 1555 1555 2.12 LINK MG MG X 103 O HOH X 209 1555 1555 2.17 LINK MG MG X 103 O HOH X 218 1555 1555 2.08 LINK MG MG X 103 O HOH X 236 1555 1555 2.19 LINK MG MG X 103 O HOH X 241 1555 1555 2.11 LINK MG MG X 103 O HOH X 244 1555 1555 2.14 LINK MG MG X 104 O HOH X 254 1555 1555 2.14 SITE 1 AC1 9 A X 21 U X 22 U X 47 U X 51 SITE 2 AC1 9 A X 52 A X 73 U X 74 U X 75 SITE 3 AC1 9 HOH X 217 SITE 1 AC2 6 A X 23 HOH X 217 HOH X 228 HOH X 245 SITE 2 AC2 6 HOH X 250 HOH X 251 SITE 1 AC3 6 A X 24 HOH X 209 HOH X 218 HOH X 236 SITE 2 AC3 6 HOH X 241 HOH X 244 SITE 1 AC4 3 G X 13 C X 83 HOH X 254 CRYST1 48.985 151.575 24.735 90.00 90.00 90.00 P 21 21 2 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 0.020414 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006597 0.000000 0.00000 SCALE3 0.000000 0.000000 0.040429 0.00000