10 20 30 40 50 60 70 80 4LVY - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 26-JUL-13 4LVY
TITLE STRUCTURE OF THE THF RIBOSWITCH BOUND TO PEMETREXED
COMPND MOL_ID: 1; COMPND 2 MOLECULE: THF RIBOSWITCH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: T7 IN VITRO TRANSCRIBED
KEYWDS APTAMERS, NUCLEOTIDE, BACILLUS SUBTILIS, BACTERIAL PROTEINS, BASE KEYWDS 2 SEQUENCE, BINDING SITES, CALORIMETRY, FOLIC ACID, GENE EXPRESSION KEYWDS 3 REGULATION, BACTERIAL, GUANINE, LEUCOVORIN, LIGANDS, MAGNESIUM, KEYWDS 4 MOLECULAR SEQUENCE DATA, NUCLEIC ACID CONFORMATION, POINT MUTATION, KEYWDS 5 PROTEIN BINDING, PROTEIN STRUCTURE, SECONDARY, RNA, RIBOSWITCH, S- KEYWDS 6 ADENOSYLMETHIONINE, STREPTOCOCCUS MUTANS, TERMINATOR REGIONS, KEYWDS 7 GENETIC, TETRAHYDROFOLATES, THERMODYNAMICS, TRANSCRIPTION, THREE-WAY KEYWDS 8 JUNCTION, PSEUDOKNOT, REGULATION, NCRNA, PEMETREXED BINDING, MRNA
EXPDTA X-RAY DIFFRACTION
AUTHOR J.J.TRAUSCH,R.T.BATEY
REVDAT 1 19-MAR-14 4LVY 0
JRNL AUTH J.J.TRAUSCH,R.T.BATEY JRNL TITL A DISCONNECT BETWEEN HIGH-AFFINITY BINDING AND EFFICIENT JRNL TITL 2 REGULATION BY ANTIFOLATES AND PURINES IN THE JRNL TITL 3 TETRAHYDROFOLATE RIBOSWITCH. JRNL REF CHEM.BIOL. V. 21 205 2014 JRNL REFN ISSN 1074-5521 JRNL PMID 24388757 JRNL DOI 10.1016/J.CHEMBIOL.2013.11.012
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.J.TRAUSCH,P.CERES,F.E.REYES,R.T.BATEY REMARK 1 TITL THE STRUCTURE OF A TETRAHYDROFOLATE-SENSING RIBOSWITCH REMARK 1 TITL 2 REVEALS TWO LIGAND BINDING SITES IN A SINGLE APTAMER. REMARK 1 REF STRUCTURE V. 19 1413 2011 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 21906956 REMARK 1 DOI 10.1016/J.STR.2011.06.019
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 20628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1032 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 34.2250 - 3.8244 0.98 2951 156 0.1600 0.1888 REMARK 3 2 3.8244 - 3.0361 0.99 2809 147 0.1851 0.2212 REMARK 3 3 3.0361 - 2.6525 1.00 2820 148 0.2672 0.2823 REMARK 3 4 2.6525 - 2.4101 1.00 2781 148 0.2799 0.3091 REMARK 3 5 2.4101 - 2.2373 1.00 2748 145 0.2811 0.3445 REMARK 3 6 2.2373 - 2.1055 1.00 2719 142 0.2961 0.3070 REMARK 3 7 2.1055 - 2.0000 1.00 2768 146 0.2953 0.3610 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 2190 REMARK 3 ANGLE : 0.953 3408 REMARK 3 CHIRALITY : 0.042 445 REMARK 3 PLANARITY : 0.007 95 REMARK 3 DIHEDRAL : 13.653 1083 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4LVY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-13. REMARK 100 THE RCSB ID CODE IS RCSB081153.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1051 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 51.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.26300 REMARK 200 R SYM FOR SHELL (I) : 0.15400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400 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: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2,4-METHYL-PENTANEDIOL, SPERMINE, REMARK 280 SODIUM CACODYLATE, SODIUM CHLORIDE, DITHIOTHREITOL, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 303K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 13.68500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.91500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.22000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.91500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.68500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.22000 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 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 O6 G A 24 N2 G A 54 2.05 REMARK 500 O HOH A 201 O HOH A 310 2.09 REMARK 500 O4' A A 62 O HOH A 309 2.16 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 C A 79 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 LYA A 101 REMARK 610 LYA A 102
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LYA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LYA A 102
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SD3 RELATED DB: PDB REMARK 900 RELATED ID: 4LVV RELATED DB: PDB REMARK 900 RELATED ID: 4LVW RELATED DB: PDB REMARK 900 RELATED ID: 4LVY RELATED DB: PDB REMARK 900 RELATED ID: 4LVZ RELATED DB: PDB REMARK 900 RELATED ID: 4LW0 RELATED DB: PDB
DBREF 4LVY A 1 89 PDB 4LVY 4LVY 1 89
SEQRES 1 A 89 G G A G A G U A G A U G A SEQRES 2 A 89 U U C G C G U U A A G U G SEQRES 3 A 89 U G U G U G A A U G G G A SEQRES 4 A 89 U G U C G U C A C A C A A SEQRES 5 A 89 C G A A G C G A G A G C G SEQRES 6 A 89 C G G U G A A U C A U U G SEQRES 7 A 89 C A U C C G C U C C A
HET LYA A 101 22 HET LYA A 102 22
HETNAM LYA 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3- HETNAM 2 LYA D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC HETNAM 3 LYA ACID
HETSYN LYA LY231514
FORMUL 2 LYA 2(C20 H21 N5 O6) FORMUL 4 HOH *139(H2 O)
SITE 1 AC1 7 C A 18 U A 25 G A 26 C A 53 SITE 2 AC1 7 G A 54 G A 68 HOH A 300 SITE 1 AC2 8 U A 7 A A 8 U A 35 U A 42 SITE 2 AC2 8 C A 43 G A 44 G A 78 C A 79
CRYST1 27.370 68.440 155.830 90.00 90.00 90.00 P 21 21 21 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 0.036536 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014611 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006417 0.00000