HEADER RNA 20-FEB-20 6VWV TITLE TRANSITIONAL UNIT CELL 2 OF ADENINE RIBOSWITCH APTAMER CRYSTAL PHASE TITLE 2 TRANSITION UPON LIGAND BINDING COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENINE RIBOSWITCH APTAMER VARIANT; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 4 ORGANISM_TAXID: 672 KEYWDS RIBOSWITCH, PHASE TRANSITION, TIME-RESOLVED, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.R.STAGNO,Y.-X.WANG REVDAT 4 11-OCT-23 6VWV 1 REMARK REVDAT 3 06-OCT-21 6VWV 1 JRNL REVDAT 2 10-MAR-21 6VWV 1 JRNL REVDAT 1 11-NOV-20 6VWV 0 JRNL AUTH S.RAMAKRISHNAN,J.R.STAGNO,C.E.CONRAD,J.DING,P.YU, JRNL AUTH 2 Y.R.BHANDARI,Y.T.LEE,G.PAULY,O.YEFANOV,M.O.WIEDORN,J.KNOSKA, JRNL AUTH 3 D.OBERTHUR,T.A.WHITE,A.BARTY,V.MARIANI,C.LI,W.BREHM, JRNL AUTH 4 W.F.HEINZ,V.MAGIDSON,S.LOCKETT,M.S.HUNTER,S.BOUTET, JRNL AUTH 5 N.A.ZATSEPIN,X.ZUO,T.D.GRANT,S.PANDEY,M.SCHMIDT, JRNL AUTH 6 J.C.H.SPENCE,H.N.CHAPMAN,Y.X.WANG JRNL TITL SYNCHRONOUS RNA CONFORMATIONAL CHANGES TRIGGER ORDERED PHASE JRNL TITL 2 TRANSITIONS IN CRYSTALS. JRNL REF NAT COMMUN V. 12 1762 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33741910 JRNL DOI 10.1038/S41467-021-21838-5 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18RC5_3822 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7952 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 385 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 27.0000 - 6.4400 1.00 758 36 0.2078 0.2562 REMARK 3 2 6.4400 - 5.1200 1.00 750 30 0.2241 0.2219 REMARK 3 3 5.1200 - 4.4800 1.00 781 33 0.2221 0.2230 REMARK 3 4 4.4800 - 4.0700 1.00 779 37 0.2398 0.2441 REMARK 3 5 4.0700 - 3.7800 1.00 737 31 0.2557 0.2518 REMARK 3 6 3.7800 - 3.5600 1.00 752 40 0.2820 0.2883 REMARK 3 7 3.5600 - 3.3800 1.00 790 46 0.2735 0.3587 REMARK 3 8 3.3800 - 3.2300 0.99 701 42 0.2930 0.3261 REMARK 3 9 3.2300 - 3.1100 1.00 762 46 0.3256 0.3626 REMARK 3 10 3.1100 - 3.0000 0.99 757 44 0.3919 0.4381 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 75.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.05 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 13:83 OR RESID 102:102 OR REMARK 3 RESID 201:201 OR RESID 103:103 OR RESID 101:101 ) ) REMARK 3 OR ( CHAIN B AND ( RESID 13:83 OR RESID 201:201 OR REMARK 3 RESID 102:102 OR RESID 101:101 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.200 -12.062 62.777 REMARK 3 T TENSOR REMARK 3 T11: 0.3591 T22: 0.3936 REMARK 3 T33: 0.4769 T12: -0.0002 REMARK 3 T13: 0.0591 T23: -0.0243 REMARK 3 L TENSOR REMARK 3 L11: 0.4806 L22: 0.6484 REMARK 3 L33: -0.0781 L12: 0.0056 REMARK 3 L13: 0.0526 L23: -0.0194 REMARK 3 S TENSOR REMARK 3 S11: 0.1885 S12: -0.1165 S13: 0.1012 REMARK 3 S21: -0.0659 S22: 0.0509 S23: -0.0620 REMARK 3 S31: -0.0802 S32: 0.0010 S33: 0.0002 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 1503 REMARK 3 RMSD : 0.027 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN X REMARK 3 SELECTION : CHAIN Y REMARK 3 ATOM PAIRS NUMBER : 10 REMARK 3 RMSD : 0.010 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VWV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000247226. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : CXI REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE CXI REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.34 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : CS-PAD CXI-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7980 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 27.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 118.1 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 74.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.570 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: 4TZX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MM SODIUM CACODYLATE, PH 6.5, 80 MM REMARK 280 POTASSIUM CHLORIDE, 100 MM MAGNESIUM CHLORIDE, 12 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE, 65% V/V (+/-)-2-METHYL-2,4-PENTANEDIOL, REMARK 280 BATCH MODE, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 A 13 P G A 13 OP3 -0.125 REMARK 500 G B 13 P G B 13 OP3 -0.125 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 A A 64 O4' - C1' - N9 ANGL. DEV. = -5.8 DEGREES REMARK 500 A B 64 O4' - C1' - N9 ANGL. DEV. = -5.8 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 K A 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 62 O2 REMARK 620 2 U B 62 O2 103.0 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6VWT RELATED DB: PDB REMARK 900 6VWT CONTAINS SAME RNA AT A DIFFERENT STAGE OF THE PHASE TRANSITION REMARK 900 RELATED ID: 5E54 RELATED DB: PDB REMARK 900 5E54 CONTAINS SAME RNA WITHOUT LIGAND, PRIOR TO PHASE TRANSITION DBREF1 6VWV A 13 83 GB CP009262.1 DBREF2 6VWV A 675337566 1106592 1106662 DBREF1 6VWV B 13 83 GB CP009262.1 DBREF2 6VWV B 675337566 1106592 1106662 SEQADV 6VWV G A 13 GB 675337566 C 06592 VARIANT SEQADV 6VWV G A 15 GB 675337566 C 06594 VARIANT SEQADV 6VWV A A 16 GB 675337566 U 06595 VARIANT SEQADV 6VWV A A 17 GB 675337566 U 06596 VARIANT SEQADV 6VWV G A 18 GB 675337566 C 06597 VARIANT SEQADV 6VWV C A 78 GB 675337566 G 06657 VARIANT SEQADV 6VWV U A 79 GB 675337566 A 06658 VARIANT SEQADV 6VWV U A 80 GB 675337566 A 06659 VARIANT SEQADV 6VWV C A 81 GB 675337566 G 06660 VARIANT SEQADV 6VWV C A 82 GB 675337566 U 06661 VARIANT SEQADV 6VWV G B 13 GB 675337566 C 06592 VARIANT SEQADV 6VWV G B 15 GB 675337566 C 06594 VARIANT SEQADV 6VWV A B 16 GB 675337566 U 06595 VARIANT SEQADV 6VWV A B 17 GB 675337566 U 06596 VARIANT SEQADV 6VWV G B 18 GB 675337566 C 06597 VARIANT SEQADV 6VWV C B 78 GB 675337566 G 06657 VARIANT SEQADV 6VWV U B 79 GB 675337566 A 06658 VARIANT SEQADV 6VWV U B 80 GB 675337566 A 06659 VARIANT SEQADV 6VWV C B 81 GB 675337566 G 06660 VARIANT SEQADV 6VWV C B 82 GB 675337566 U 06661 VARIANT SEQRES 1 A 71 G G G A A G A U A U A A U SEQRES 2 A 71 C C U A A U G A U A U G G SEQRES 3 A 71 U U U G G G A G U U U C U SEQRES 4 A 71 A C C A A G A G C C U U A SEQRES 5 A 71 A A C U C U U G A U U A U SEQRES 6 A 71 C U U C C C SEQRES 1 B 71 G G G A A G A U A U A A U SEQRES 2 B 71 C C U A A U G A U A U G G SEQRES 3 B 71 U U U G G G A G U U U C U SEQRES 4 B 71 A C C A A G A G C C U U A SEQRES 5 B 71 A A C U C U U G A U U A U SEQRES 6 B 71 C U U C C C HET ADE A 101 10 HET K A 102 1 HET MG A 103 1 HET ADE B 101 10 HET MG B 102 1 HETNAM ADE ADENINE HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION FORMUL 3 ADE 2(C5 H5 N5) FORMUL 4 K K 1+ FORMUL 5 MG 2(MG 2+) FORMUL 8 HOH *2(H2 O) LINK OP1 A A 24 MG MG A 103 1555 1555 2.09 LINK O2 U A 62 K K A 102 1555 1555 2.71 LINK K K A 102 O2 U B 62 1555 1555 2.82 LINK OP1 A B 24 MG MG B 102 1555 1555 2.09 CRYST1 35.090 25.490 123.960 90.01 84.05 68.89 P 1 2 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 0.028498 -0.011002 -0.003418 0.00000 SCALE2 0.000000 0.042053 0.001701 0.00000 SCALE3 0.000000 0.000000 0.008117 0.00000