HEADER RNA 04-FEB-09 3G4M TITLE CRYSTAL STRUCTURE OF GUANINE RIBOSWITCH BOUND TO 2-AMINOPURINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANINE RIBOSWITCH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS ENGINEERED BASED ON THE GUANINE SOURCE 4 RIBOSWITCH IN THE 5'UTR OF THE XPT-PBUX GENE IN BACILLUS SUBTILIS. KEYWDS RIBOSWITCH, MRNA, 2-AMINOPURINE, GUANINE, THREE-WAY JUNCTION, RNA- KEYWDS 2 LIGAND COMPLEX, DOUBLE HELIX, BASE-TRIPLE., RNA EXPDTA X-RAY DIFFRACTION AUTHOR S.D.GILBERT,R.T.BATEY REVDAT 2 06-SEP-23 3G4M 1 REMARK REVDAT 1 23-JUN-09 3G4M 0 JRNL AUTH S.D.GILBERT,F.E.REYES,A.L.EDWARDS,R.T.BATEY JRNL TITL ADAPTIVE LIGAND BINDING BY THE PURINE RIBOSWITCH IN THE JRNL TITL 2 RECOGNITION OF GUANINE AND ADENINE ANALOGS. JRNL REF STRUCTURE V. 17 857 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19523903 JRNL DOI 10.1016/J.STR.2009.04.009 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 320880.120 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 13374 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1296 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1876 REMARK 3 BIN R VALUE (WORKING SET) : 0.3820 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 188 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1422 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.97000 REMARK 3 B22 (A**2) : -11.53000 REMARK 3 B33 (A**2) : 4.57000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 8.80000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.60 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.71 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.003 REMARK 3 BOND ANGLES (DEGREES) : 0.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.200 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 26.06 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP_REVISE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : COHEX_REP.PARAM REMARK 3 PARAMETER FILE 5 : HPA5.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : COHEX_REP.TOP REMARK 3 TOPOLOGY FILE 5 : HPA5.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3G4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051416. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NICKEL FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13481 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 19.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 1.830 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.64 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28400 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1U8D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3K, 12.5 MM COBALT HEXAMMINE, REMARK 280 600MM AMMONIUM ACETATE, 10 MM K-HEPES., PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 63.71500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.58000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.71500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.58000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2BP A 91 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 96 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 110 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 111 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 112 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U8D RELATED DB: PDB REMARK 900 GUANINE RIBOSWITCH BOUND TO COGNATE LIGAND HYPOXANTHINE REMARK 900 RELATED ID: 3GAO RELATED DB: PDB REMARK 900 RELATED ID: 3GER RELATED DB: PDB REMARK 900 RELATED ID: 3GES RELATED DB: PDB DBREF 3G4M A 15 81 PDB 3G4M 3G4M 15 81 SEQRES 1 A 67 G G A C A U A U A A U C G SEQRES 2 A 67 C G U G G A U A U G G C A SEQRES 3 A 67 C G C A A G U U U C U A C SEQRES 4 A 67 C G G G C A C C G U A A A SEQRES 5 A 67 U G U C C G A C U A U G U SEQRES 6 A 67 C C HET 2BP A 91 10 HET ACT A 96 4 HET NCO A 101 7 HET NCO A 102 7 HET NCO A 103 7 HET NCO A 104 7 HET NCO A 105 7 HET NCO A 107 7 HET NCO A 108 7 HET NCO A 109 7 HET NCO A 110 7 HET NCO A 111 7 HET NCO A 112 7 HETNAM 2BP 9H-PURIN-2-AMINE HETNAM ACT ACETATE ION HETNAM NCO COBALT HEXAMMINE(III) HETSYN 2BP 2-AMINOPURINE FORMUL 2 2BP C5 H5 N5 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 NCO 11(CO H18 N6 3+) FORMUL 15 HOH *64(H2 O) SITE 1 AC1 8 A A 21 U A 22 U A 47 U A 51 SITE 2 AC1 8 A A 52 A A 73 C A 74 U A 75 SITE 1 AC2 6 G A 32 A A 33 G A 38 C A 39 SITE 2 AC2 6 A A 66 HOH A 523 SITE 1 AC3 6 G A 29 U A 30 A A 66 U A 67 SITE 2 AC3 6 HOH A 530 HOH A 542 SITE 1 AC4 7 G A 38 C A 39 G A 56 G A 57 SITE 2 AC4 7 C A 58 HOH A 510 HOH A 554 SITE 1 AC5 9 C A 39 G A 55 G A 56 G A 57 SITE 2 AC5 9 G A 68 U A 69 HOH A 506 HOH A 508 SITE 3 AC5 9 HOH A 514 SITE 1 AC6 7 U A 30 G A 31 G A 32 A A 65 SITE 2 AC6 7 A A 66 HOH A 501 HOH A 503 SITE 1 AC7 3 G A 37 G A 38 HOH A 539 SITE 1 AC8 5 C A 41 G A 42 C A 53 C A 54 SITE 2 AC8 5 HOH A 562 SITE 1 AC9 5 G A 46 U A 47 C A 50 U A 51 SITE 2 AC9 5 HOH A 553 SITE 1 BC1 4 A A 24 C A 71 HOH A 507 HOH A 522 SITE 1 BC2 4 A A 21 U A 22 G A 78 HOH A 531 SITE 1 BC3 5 G A 32 A A 33 U A 34 A A 65 SITE 2 BC3 5 HOH A 543 SITE 1 BC4 7 C A 18 U A 36 G A 42 C A 43 SITE 2 BC4 7 G A 72 A A 73 HOH A 532 CRYST1 127.430 35.160 42.240 90.00 91.18 90.00 C 1 2 1 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 0.007847 0.000000 0.000162 0.00000 SCALE2 0.000000 0.028441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023679 0.00000