HEADER RNA 08-JUN-11 3SD1 OBSLTE 19-MAR-14 3SD1 4LVV TITLE THE STRUCTURE OF A TETRAHYDROFOLATE RIBOSWITCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETRAHYDROFOLATE RIBOSWITCH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED WITH T7 RNA POLYMERASE FROM A RECOMBINANT SOURCE 4 PCR TEMPLATE KEYWDS TETRAHYDROFOLATE RNA RIBOSWITCH, RNA EXPDTA X-RAY DIFFRACTION AUTHOR F.E.REYES,J.J.TRAUSCH,P.CERES,R.T.BATEY REVDAT 4 19-MAR-14 3SD1 1 OBSLTE REVDAT 3 02-NOV-11 3SD1 1 JRNL REVDAT 2 28-SEP-11 3SD1 1 JRNL REVDAT 1 21-SEP-11 3SD1 0 JRNL AUTH J.J.TRAUSCH,P.CERES,F.E.REYES,R.T.BATEY JRNL TITL THE STRUCTURE OF A TETRAHYDROFOLATE-SENSING RIBOSWITCH JRNL TITL 2 REVEALS TWO LIGAND BINDING SITES IN A SINGLE APTAMER. JRNL REF STRUCTURE V. 19 1413 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 21906956 JRNL DOI 10.1016/J.STR.2011.06.019 REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_572) 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.3 REMARK 3 NUMBER OF REFLECTIONS : 13840 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 2293 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 28.5991 - 5.7136 0.89 1326 140 0.1631 0.2019 REMARK 3 2 5.7136 - 4.5410 0.89 1318 145 0.1550 0.2049 REMARK 3 3 4.5410 - 3.9687 0.89 1300 156 0.1689 0.1854 REMARK 3 4 3.9687 - 3.6066 0.91 1389 150 0.2011 0.2475 REMARK 3 5 3.6066 - 3.3485 0.90 1320 140 0.2276 0.2634 REMARK 3 6 3.3485 - 3.1513 0.90 1336 157 0.2677 0.3145 REMARK 3 7 3.1513 - 2.9937 0.90 1360 149 0.2648 0.2639 REMARK 3 8 2.9937 - 2.8635 0.90 1356 150 0.2949 0.3185 REMARK 3 9 2.8635 - 2.7534 0.89 1282 134 0.3333 0.3878 REMARK 3 10 2.7534 - 2.6584 0.89 1350 157 0.3483 0.3609 REMARK 3 11 2.6584 - 2.5753 0.89 1335 140 0.3487 0.4161 REMARK 3 12 2.5753 - 2.5018 0.86 1266 129 0.3530 0.4193 REMARK 3 13 2.5018 - 2.4359 0.87 1305 150 0.3935 0.4054 REMARK 3 14 2.4359 - 2.3765 0.84 1255 140 0.4252 0.4854 REMARK 3 15 2.3765 - 2.3225 0.80 1173 132 0.4290 0.4510 REMARK 3 16 2.3225 - 2.2700 0.74 1111 124 0.5074 0.5943 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.61 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 20.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 27.02090 REMARK 3 B22 (A**2) : -0.18050 REMARK 3 B33 (A**2) : 10.74610 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : -0.00000 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 : 0.002 2238 REMARK 3 ANGLE : 0.513 3521 REMARK 3 CHIRALITY : 0.053 447 REMARK 3 PLANARITY : 0.003 97 REMARK 3 DIHEDRAL : 20.971 1109 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 3SD1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-11. REMARK 100 THE RCSB ID CODE IS RCSB066054. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-10 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) : NULL 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 : XSCALE REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13840 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 REMARK 200 RESOLUTION RANGE LOW (A) : 52.517 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.79000 REMARK 200 R SYM FOR SHELL (I) : 0.79000 REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 52.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 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 13.81000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.77500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.09500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.77500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.81000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.09500 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 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 FOZ A 97 REMARK 610 FOZ A 98 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 IRI A 90 REMARK 615 IRI A 91 REMARK 615 IRI A 92 REMARK 615 IRI A 93 REMARK 615 IRI A 94 REMARK 615 IRI A 95 REMARK 615 IRI A 96 REMARK 615 FOZ A 97 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 90 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 91 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 92 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 93 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 94 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 95 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 96 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOZ A 97 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOZ A 98 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SD3 RELATED DB: PDB DBREF 3SD1 A 1 89 PDB 3SD1 3SD1 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 IRI A 90 7 HET IRI A 91 7 HET IRI A 92 7 HET IRI A 93 7 HET IRI A 94 7 HET IRI A 95 7 HET IRI A 96 7 HET FOZ A 97 25 HET FOZ A 98 25 HETNAM IRI IRIDIUM HEXAMMINE ION HETNAM FOZ N-[4-({[(6S)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8- HETNAM 2 FOZ HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L- HETNAM 3 FOZ GLUTAMIC ACID FORMUL 2 IRI 7(H18 IR N6 3+) FORMUL 9 FOZ 2(C20 H23 N7 O7) FORMUL 11 HOH *40(H2 O) SITE 1 AC1 5 U A 25 G A 26 A A 47 C A 48 SITE 2 AC1 5 HOH A 125 SITE 1 AC2 3 U A 29 G A 30 U A 31 SITE 1 AC3 4 U A 14 U A 15 U A 69 A A 71 SITE 1 AC4 2 G A 61 C A 88 SITE 1 AC5 5 U A 76 U A 77 G A 78 IRI A 95 SITE 2 AC5 5 HOH A 121 SITE 1 AC6 3 G A 9 IRI A 94 HOH A 136 SITE 1 AC7 2 U A 21 C A 88 SITE 1 AC8 5 U A 25 G A 26 C A 53 G A 54 SITE 2 AC8 5 G A 68 SITE 1 AC9 7 U A 7 A A 8 U A 35 U A 42 SITE 2 AC9 7 G A 44 C A 79 A A 80 CRYST1 27.620 68.190 157.550 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 0.036206 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014665 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006347 0.00000