PDB Short entry for 4ENC HEADER RNA 12-APR-12 4ENC TITLE CRYSTAL STRUCTURE OF FLUORIDE RIBOSWITCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLUORIDE RIBOSWITCH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: THERMOTOGA PETROPHILA; SOURCE 4 ORGANISM_TAXID: 93929; SOURCE 5 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 SOURCE 6 RNA POLYMERASE. KEYWDS PSEUDOKNOT, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.M.REN,K.R.RAJASHANKAR,D.J.PATEL REVDAT 4 13-SEP-23 4ENC 1 REMARK LINK REVDAT 3 13-FEB-13 4ENC 1 AUTHOR REVDAT 2 20-JUN-12 4ENC 1 JRNL REVDAT 1 09-MAY-12 4ENC 0 JRNL AUTH A.REN,K.R.RAJASHANKAR,D.J.PATEL JRNL TITL FLUORIDE ION ENCAPSULATION BY MG2+ IONS AND PHOSPHATES IN A JRNL TITL 2 FLUORIDE RIBOSWITCH. JRNL REF NATURE V. 486 85 2012 JRNL REFN ISSN 0028-0836 JRNL PMID 22678284 JRNL DOI 10.1038/NATURE11152 REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 8701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 416 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 28.5072 - 3.2761 0.99 2907 139 0.1948 0.2051 REMARK 3 2 3.2761 - 2.6009 1.00 2806 142 0.2427 0.3318 REMARK 3 3 2.6009 - 2.2720 0.93 2572 135 0.4303 0.5150 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 54.61 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.520 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.090 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) : 1.32250 REMARK 3 B22 (A**2) : -4.25110 REMARK 3 B33 (A**2) : 3.49140 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 : 0.026 1275 REMARK 3 ANGLE : 0.780 2016 REMARK 3 CHIRALITY : 0.059 260 REMARK 3 PLANARITY : 0.008 52 REMARK 3 DIHEDRAL : 13.225 621 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -12.2254 18.5787 -11.2387 REMARK 3 T TENSOR REMARK 3 T11: 0.4400 T22: 0.4560 REMARK 3 T33: 0.3635 T12: 0.1055 REMARK 3 T13: 0.0008 T23: -0.0684 REMARK 3 L TENSOR REMARK 3 L11: 1.4311 L22: 6.3485 REMARK 3 L33: 3.3136 L12: 1.6307 REMARK 3 L13: -0.3307 L23: -2.5385 REMARK 3 S TENSOR REMARK 3 S11: -0.0578 S12: -0.1024 S13: -0.0845 REMARK 3 S21: 0.3416 S22: 0.0913 S23: -0.4467 REMARK 3 S31: -0.4484 S32: -0.4713 S33: -0.0220 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 4ENC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071834. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(220) SIDE REMARK 200 BOUNCE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8726 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.272 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : 0.07700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 4ENB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES SODIUM, PH 6.5, 35-40% W/V REMARK 280 MPD, VAPOR DIFFUSION, TEMPERATURE 293K, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 28.50500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.61150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.50500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.61150 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 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 107 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 5 OP1 REMARK 620 2 A A 6 OP1 80.4 REMARK 620 3 A A 6 O3' 121.4 81.3 REMARK 620 4 U A 7 OP1 168.0 89.5 49.8 REMARK 620 5 HOH A 204 O 114.6 70.4 110.4 67.3 REMARK 620 6 HOH A 206 O 83.5 124.4 148.8 107.8 69.1 REMARK 620 N 1 2 3 4 5 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 A A 6 OP2 REMARK 620 2 U A 7 OP2 87.3 REMARK 620 3 U A 41 OP1 161.3 81.7 REMARK 620 4 G A 42 OP2 97.0 167.8 91.1 REMARK 620 5 HOH A 202 O 77.9 83.0 85.8 86.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 6 OP1 REMARK 620 2 G A 42 OP1 86.1 REMARK 620 3 HOH A 204 O 101.4 171.7 REMARK 620 4 HOH A 207 O 83.1 89.8 87.7 REMARK 620 5 HOH A 208 O 158.9 88.2 83.6 76.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 7 OP1 REMARK 620 2 G A 8 OP2 86.0 REMARK 620 3 HOH A 203 O 87.2 93.7 REMARK 620 4 HOH A 204 O 85.2 92.3 170.0 REMARK 620 5 HOH A 205 O 173.2 92.8 99.5 88.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 40 OP2 REMARK 620 2 HOH A 201 O 99.9 REMARK 620 3 HOH A 209 O 98.2 95.0 REMARK 620 4 HOH A 210 O 87.9 76.5 170.4 REMARK 620 5 HOH A 211 O 162.7 80.9 98.9 75.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 52 O3' REMARK 620 2 G A 52 O2' 66.1 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 107 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EN5 RELATED DB: PDB REMARK 900 RELATED ID: 4ENA RELATED DB: PDB REMARK 900 RELATED ID: 4ENB RELATED DB: PDB REMARK 900 RELATED ID: 3VRS RELATED DB: PDB DBREF 4ENC A 1 52 PDB 4ENC 4ENC 1 52 SEQRES 1 A 52 G G G C G A U G A G G C C SEQRES 2 A 52 C G C C C A A A C U G C C SEQRES 3 A 52 C U G A A A A G G G C U G SEQRES 4 A 52 A U G G C C U C U A C U G HET MG A 101 1 HET MG A 102 1 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET F A 106 1 HET K A 107 1 HETNAM MG MAGNESIUM ION HETNAM F FLUORIDE ION HETNAM K POTASSIUM ION FORMUL 2 MG 5(MG 2+) FORMUL 7 F F 1- FORMUL 8 K K 1+ FORMUL 9 HOH *21(H2 O) LINK OP1 G A 5 K K A 107 1555 1555 2.54 LINK OP2 A A 6 MG MG A 103 1555 1555 1.97 LINK OP1 A A 6 MG MG A 104 1555 1555 2.03 LINK OP1 A A 6 K K A 107 1555 1555 2.82 LINK O3' A A 6 K K A 107 1555 1555 3.21 LINK OP1 U A 7 MG MG A 101 1555 1555 2.13 LINK OP2 U A 7 MG MG A 103 1555 1555 2.17 LINK OP1 U A 7 K K A 107 1555 1555 2.35 LINK OP2 G A 8 MG MG A 101 1555 1555 2.00 LINK OP2 A A 40 MG MG A 102 1555 1555 2.08 LINK OP1 U A 41 MG MG A 103 1555 1555 1.99 LINK OP2 G A 42 MG MG A 103 1555 1555 2.06 LINK OP1 G A 42 MG MG A 104 1555 1555 2.06 LINK O3' G A 52 MG MG A 105 1555 1555 2.23 LINK O2' G A 52 MG MG A 105 1555 1555 2.63 LINK MG MG A 101 O HOH A 203 1555 1555 2.10 LINK MG MG A 101 O HOH A 204 1555 1555 2.01 LINK MG MG A 101 O HOH A 205 1555 1555 2.07 LINK MG MG A 102 O HOH A 201 1555 1555 2.07 LINK MG MG A 102 O HOH A 209 1555 1555 2.09 LINK MG MG A 102 O HOH A 210 1555 1555 2.01 LINK MG MG A 102 O HOH A 211 1555 1555 2.10 LINK MG MG A 103 O HOH A 202 1555 1555 2.16 LINK MG MG A 104 O HOH A 204 1555 1555 2.08 LINK MG MG A 104 O HOH A 207 1555 1555 2.07 LINK MG MG A 104 O HOH A 208 1555 1555 2.15 LINK K K A 107 O HOH A 204 1555 1555 2.70 LINK K K A 107 O HOH A 206 1555 1555 2.60 SITE 1 AC1 9 U A 7 G A 8 MG A 103 MG A 104 SITE 2 AC1 9 F A 106 K A 107 HOH A 203 HOH A 204 SITE 3 AC1 9 HOH A 205 SITE 1 AC2 5 A A 40 HOH A 201 HOH A 209 HOH A 210 SITE 2 AC2 5 HOH A 211 SITE 1 AC3 8 A A 6 U A 7 U A 41 G A 42 SITE 2 AC3 8 MG A 101 MG A 104 F A 106 HOH A 202 SITE 1 AC4 10 A A 6 U A 7 G A 42 MG A 101 SITE 2 AC4 10 MG A 103 F A 106 K A 107 HOH A 204 SITE 3 AC4 10 HOH A 207 HOH A 208 SITE 1 AC5 1 G A 52 SITE 1 AC6 11 A A 6 U A 7 U A 41 G A 42 SITE 2 AC6 11 MG A 101 MG A 103 MG A 104 HOH A 203 SITE 3 AC6 11 HOH A 204 HOH A 205 HOH A 208 SITE 1 AC7 7 G A 5 A A 6 U A 7 MG A 101 SITE 2 AC7 7 MG A 104 HOH A 204 HOH A 206 CRYST1 57.010 75.223 42.905 90.00 90.00 90.00 P 21 21 2 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 0.017541 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013294 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023307 0.00000