HEADER RNA 20-FEB-20 6VWT TITLE TRANSITIONAL UNIT CELL 1 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 6VWT 1 REMARK REVDAT 3 06-OCT-21 6VWT 1 JRNL REVDAT 2 10-MAR-21 6VWT 1 JRNL REVDAT 1 11-NOV-20 6VWT 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. 3.03 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) : 3.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 7285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.960 REMARK 3 FREE R VALUE TEST SET COUNT : 434 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 25.1700 - 6.5100 1.00 701 38 0.1725 0.2013 REMARK 3 2 6.5000 - 5.1800 0.99 691 36 0.1816 0.2429 REMARK 3 3 5.1800 - 4.5300 0.98 678 55 0.2267 0.1852 REMARK 3 4 4.5300 - 4.1100 1.00 682 57 0.2574 0.3440 REMARK 3 5 4.1100 - 3.8200 0.99 718 34 0.2288 0.2346 REMARK 3 6 3.8200 - 3.6000 0.99 650 34 0.2624 0.2973 REMARK 3 7 3.6000 - 3.4200 0.98 707 56 0.3019 0.2930 REMARK 3 8 3.4200 - 3.2700 0.98 674 54 0.2821 0.2999 REMARK 3 9 3.2700 - 3.1400 0.98 643 30 0.3114 0.2743 REMARK 3 10 3.1400 - 3.0300 0.96 707 40 0.3895 0.3265 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 82.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.29 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 101:101 OR REMARK 3 RESID 102:105 ) ) OR ( CHAIN B AND ( RESID 102:105 REMARK 3 OR RESID 13:83 OR RESID 101:101 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.983 -11.544 -0.177 REMARK 3 T TENSOR REMARK 3 T11: 0.4551 T22: 0.5763 REMARK 3 T33: 0.7094 T12: 0.0010 REMARK 3 T13: 0.0019 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: -0.5502 L22: 1.0658 REMARK 3 L33: 5.0676 L12: -0.0178 REMARK 3 L13: 0.3020 L23: -0.0210 REMARK 3 S TENSOR REMARK 3 S11: -0.0777 S12: 0.0038 S13: -0.0986 REMARK 3 S21: -0.0163 S22: -0.0059 S23: 0.0032 REMARK 3 S31: -0.0520 S32: 0.0032 S33: 0.0642 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 : 0.095 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 : 0.006 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VWT 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_1000247220. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-17 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 : BERYLLIUM LENS 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 0.9.0 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7656 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 751.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4900 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 : 207.7 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.580 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: PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 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 -0.126 REMARK 500 G B 13 P G B 13 OP3 -0.126 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 G A 13 OP2 REMARK 620 2 C B 83 OP2 31.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 83 OP2 REMARK 620 2 G B 13 OP2 42.8 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5E54 RELATED DB: PDB REMARK 900 5E54 CONTAINS SAME RNA WITHOUT LIGAND, PRIOR TO PHASE TRANSITION DBREF1 6VWT A 13 83 GB CP009262.1 DBREF2 6VWT A 675337566 1106592 1106662 DBREF1 6VWT B 13 83 GB CP009262.1 DBREF2 6VWT B 675337566 1106592 1106662 SEQADV 6VWT G A 13 GB 675337566 C 06592 VARIANT SEQADV 6VWT G A 15 GB 675337566 C 06594 VARIANT SEQADV 6VWT A A 16 GB 675337566 U 06595 VARIANT SEQADV 6VWT A A 17 GB 675337566 U 06596 VARIANT SEQADV 6VWT G A 18 GB 675337566 C 06597 VARIANT SEQADV 6VWT C A 78 GB 675337566 G 06657 VARIANT SEQADV 6VWT U A 79 GB 675337566 A 06658 VARIANT SEQADV 6VWT U A 80 GB 675337566 A 06659 VARIANT SEQADV 6VWT C A 81 GB 675337566 G 06660 VARIANT SEQADV 6VWT C A 82 GB 675337566 U 06661 VARIANT SEQADV 6VWT G B 13 GB 675337566 C 06592 VARIANT SEQADV 6VWT G B 15 GB 675337566 C 06594 VARIANT SEQADV 6VWT A B 16 GB 675337566 U 06595 VARIANT SEQADV 6VWT A B 17 GB 675337566 U 06596 VARIANT SEQADV 6VWT G B 18 GB 675337566 C 06597 VARIANT SEQADV 6VWT C B 78 GB 675337566 G 06657 VARIANT SEQADV 6VWT U B 79 GB 675337566 A 06658 VARIANT SEQADV 6VWT U B 80 GB 675337566 A 06659 VARIANT SEQADV 6VWT C B 81 GB 675337566 G 06660 VARIANT SEQADV 6VWT 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 MG A 102 1 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET ADE B 101 10 HET MG B 102 1 HET MG B 103 1 HET MG B 104 1 HET MG B 105 1 HETNAM ADE ADENINE HETNAM MG MAGNESIUM ION FORMUL 3 ADE 2(C5 H5 N5) FORMUL 4 MG 8(MG 2+) LINK OP1 G A 13 MG MG A 102 1555 1555 2.14 LINK OP2 G A 13 MG MG A 103 1555 1555 1.97 LINK OP2 A A 23 MG MG A 104 1555 1555 2.09 LINK OP1 A A 24 MG MG A 105 1555 1555 2.06 LINK OP2 C A 83 MG MG B 103 1555 1655 2.67 LINK MG MG A 103 OP2 C B 83 1455 1555 2.82 LINK OP1 G B 13 MG MG B 102 1555 1555 2.08 LINK OP2 G B 13 MG MG B 103 1555 1555 1.93 LINK OP2 A B 23 MG MG B 104 1555 1555 2.13 LINK OP1 A B 24 MG MG B 105 1555 1555 2.01 CRYST1 50.340 25.200 78.740 99.29 90.55 90.21 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 0.019865 0.000073 0.000205 0.00000 SCALE2 0.000000 0.039683 0.006493 0.00000 SCALE3 0.000000 0.000000 0.012870 0.00000