10 20 30 40 50 60 70 80 3D0X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 02-MAY-08 3D0X
TITLE CRYSTAL STRUCTURE OF THE UNBOUND LYSINE RIBOSWITCH
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (161-MER); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS RNA, RIBOSWITCH
EXPDTA X-RAY DIFFRACTION
AUTHOR R.T.BATEY,A.D.GARST,A.HEROUX,R.P.RAMBO
REVDAT 3 24-FEB-09 3D0X 1 VERSN REVDAT 2 14-OCT-08 3D0X 1 JRNL REVDAT 1 01-JUL-08 3D0X 0
JRNL AUTH A.D.GARST,A.HEROUX,R.P.RAMBO,R.T.BATEY JRNL TITL CRYSTAL STRUCTURE OF THE LYSINE RIBOSWITCH JRNL TITL 2 REGULATORY MRNA ELEMENT. JRNL REF J.BIOL.CHEM. V. 283 22347 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18593706 JRNL DOI 10.1074/JBC.C800120200
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 19610 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.190 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 17.1130 - 6.9590 0.96 1204 149 0.1290 0.1440 REMARK 3 2 6.9590 - 5.5870 0.99 1243 146 0.1330 0.1650 REMARK 3 3 5.5870 - 4.8990 1.00 1265 137 0.1300 0.1550 REMARK 3 4 4.8990 - 4.4600 1.00 1263 140 0.1580 0.1810 REMARK 3 5 4.4600 - 4.1450 0.99 1247 137 0.1630 0.2200 REMARK 3 6 4.1450 - 3.9040 1.00 1262 148 0.1760 0.2500 REMARK 3 7 3.9040 - 3.7110 1.00 1277 136 0.1880 0.2470 REMARK 3 8 3.7110 - 3.5510 1.00 1272 140 0.1960 0.2190 REMARK 3 9 3.5510 - 3.4150 1.00 1260 140 0.2180 0.2550 REMARK 3 10 3.4150 - 3.2980 1.00 1279 145 0.2290 0.3000 REMARK 3 11 3.2980 - 3.1960 1.00 1251 148 0.2450 0.2470 REMARK 3 12 3.1960 - 3.1050 1.00 1257 142 0.2730 0.3250 REMARK 3 13 3.1050 - 3.0230 1.00 1258 148 0.3150 0.3600 REMARK 3 14 3.0230 - 2.9500 1.00 1273 143 0.3510 0.3830 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 : 0.21 REMARK 3 B_SOL : 8.99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.97000 REMARK 3 B22 (A**2) : -7.97000 REMARK 3 B33 (A**2) : 15.94100 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 : 0.004 3898 REMARK 3 ANGLE : 1.050 6088 REMARK 3 CHIRALITY : 0.069 804 REMARK 3 PLANARITY : 0.002 161 REMARK 3 DIHEDRAL : 19.332 1607 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 3D0X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-08. REMARK 100 THE RCSB ID CODE IS RCSB047452.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI 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 : 19610 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 19.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.620 REMARK 200 R MERGE (I) : 9.00000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.63 REMARK 200 R MERGE FOR SHELL (I) : 35.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 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: PDB ENTRY 3D0U WITHOUT LYSINE REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE, MAGNESIUM REMARK 280 CHLORIDE, IRIDIUM HEXAMMINE, SODIUM HEPES
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.83200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.41600 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: 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 1 P G A 1 OP3 -0.127 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 G A 1 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 A A 3 O3' - P - O5' ANGL. DEV. = -19.7 DEGREES REMARK 500 A A 3 O3' - P - OP2 ANGL. DEV. = -17.4 DEGREES REMARK 500 A A 3 O3' - P - OP1 ANGL. DEV. = -19.9 DEGREES REMARK 500 G A 77 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES REMARK 500 G A 77 O3' - P - OP2 ANGL. DEV. = 10.4 DEGREES REMARK 500 G A 152 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 181 DISTANCE = 5.36 ANGSTROMS REMARK 525 HOH A 184 DISTANCE = 5.47 ANGSTROMS REMARK 525 HOH A 190 DISTANCE = 5.79 ANGSTROMS REMARK 525 HOH A 193 DISTANCE = 5.39 ANGSTROMS REMARK 525 HOH A 195 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH A 199 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 203 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 208 DISTANCE = 5.45 ANGSTROMS REMARK 525 HOH A 209 DISTANCE = 5.51 ANGSTROMS REMARK 525 HOH A 211 DISTANCE = 5.44 ANGSTROMS REMARK 525 HOH A 217 DISTANCE = 5.67 ANGSTROMS REMARK 525 HOH A 218 DISTANCE = 5.39 ANGSTROMS REMARK 525 HOH A 219 DISTANCE = 5.58 ANGSTROMS REMARK 525 HOH A 220 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 221 DISTANCE = 5.50 ANGSTROMS
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D0U RELATED DB: PDB REMARK 900 LYSINE RIBOSWITCH BOUND TO LYSINE
DBREF 3D0X A 1 161 PDB 3D0X 3D0X 1 161
SEQRES 1 A 161 G G A C G G A G G C G C G SEQRES 2 A 161 C C C G A G A U G A G U A SEQRES 3 A 161 G G C U G U C C C A U C A SEQRES 4 A 161 G G G G A G G A A U C G G SEQRES 5 A 161 G G A C G G C U G A A A G SEQRES 6 A 161 G C G A G G G C G C C G A SEQRES 7 A 161 A G C G A G C A G A G U U SEQRES 8 A 161 C C U C C C G C U C U G C SEQRES 9 A 161 U U G G C U G G G G G U G SEQRES 10 A 161 A G G G G A A U A C C C U SEQRES 11 A 161 U A C C A C U G U C G C G SEQRES 12 A 161 A A A G C G G A G A G C C SEQRES 13 A 161 G U C C A
FORMUL 2 HOH *60(H2 O)
CRYST1 120.193 120.193 58.248 90.00 90.00 120.00 P 32 3
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 0.008320 0.004804 0.000000 0.00000
SCALE2 0.000000 0.009607 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017168 0.00000