HEADER RIBONUCLEIC ACID 20-APR-05 1ZFR OBSLTE 06-MAR-07 1ZFR 2OUE TITLE CRYSTAL STRUCTURE OF A JUNCTIONLESS ALL-RNA HAIRPIN TITLE 2 RIBOZYME AT 2.05 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)- COMPND 3 3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'- COMPND 12 R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: 5'- COMPND 17 R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C) COMPND 18 -3'; COMPND 19 CHAIN: D; COMPND 20 ENGINEERED: YES; COMPND 21 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DERIVED FROM SATELLITE TOBACCO RINGSPOT SOURCE 4 VIRUS; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: DERIVED FROM SATELLITE TOBACCO RINGSPOT SOURCE 8 VIRUS; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: DERIVED FROM SATELLITE TOBACCO RINGSPOT SOURCE 12 VIRUS; SOURCE 13 MOL_ID: 4; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: DERIVED FROM SATELLITE TOBACCO RINGSPOT SOURCE 16 VIRUS KEYWDS HAIRPIN RIBOZYME, ALL-RNA, MUTATION, LOW SALT, S-TURN, E- KEYWDS 2 LOOP, RIBOSE ZIPPER, CATALYTIC RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.E.WEDEKIND REVDAT 2 06-MAR-07 1ZFR 1 OBSLTE REVDAT 1 14-FEB-06 1ZFR 0 JRNL AUTH J.SALTER,J.KRUCINSKA,S.ALAM,V.GRUM-TOKARS, JRNL AUTH 2 J.E.WEDEKIND JRNL TITL WATER IN THE ACTIVE SITE OF AN ALL-RNA HAIRPIN JRNL TITL 2 RIBOZYME AND EFFECTS OF GUA8 BASE VARIANTS ON THE JRNL TITL 3 GEOMETRY OF PHOSPHORYL TRANSFER. JRNL REF BIOCHEMISTRY V. 45 686 2006 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : CNS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1422181.380 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 21645 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) : 0.254 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1709 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 4 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4892 REMARK 3 BIN R VALUE (WORKING SET) : 0.5740 REMARK 3 BIN FREE R VALUE : 0.6100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 404 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 : 1312 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.32000 REMARK 3 B22 (A**2) : -13.55000 REMARK 3 B33 (A**2) : 23.86000 REMARK 3 B12 (A**2) : -9.38000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.45 REMARK 3 ESD FROM SIGMAA (A) : 0.74 REMARK 3 LOW RESOLUTION CUTOFF (A) : 30.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.79 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.92 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) : 2.170 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.670 ; 3.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.640 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.640 ; 4.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 61.93 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 : ION.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : COBALT.PAR REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 2 : COBALT.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZFR COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS FILE IS A TEST VERSION. REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-05-01) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY THE NUCLEIC ACID DATABASE REMARK 100 ON 02-MAY-2005. REMARK 100 THE NDB ID CODE IS UR0059. REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4' INSTEAD OF O1'. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-2004 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9764 REMARK 200 MONOCHROMATOR : BENT TRIANGULAR ASYMMETRIC REMARK 200 CUT SI(111) MONOCHROMATOR REMARK 200 OPTICS : BENT TRIANGULAR ASYMMETRIC REMARK 200 CUT SI(111) MONOCHROMATOR REMARK 200 (PROVIDES HORIZONTAL REMARK 200 FOCUSSING), RH-COATED SI REMARK 200 MIRROR FOR VERTICAL FOCUSSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC Q-210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : CRYSTAL CLEAR (D*TREK) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21699 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03000 REMARK 200 FOR THE DATA SET : 24.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43200 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1X9C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000 MME, LITHIUM SULFATE, REMARK 280 CACODYLATE, SPERMIDINE, COBALT HEXAAMINE, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,1/3+Z REMARK 290 3555 -X+Y,-X,2/3+Z REMARK 290 4555 -X,-Y,1/2+Z REMARK 290 5555 Y,-X+Y,5/6+Z REMARK 290 6555 X-Y,X,1/6+Z REMARK 290 7555 Y,X,1/3-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,2/3-Z REMARK 290 10555 -Y,-X,5/6-Z REMARK 290 11555 -X+Y,Y,1/2-Z REMARK 290 12555 X,X-Y,1/6-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 -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 43.75000 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 87.50000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.62500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 109.37500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.87500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.75000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 87.50000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 109.37500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 65.62500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 21.87500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1X9C RELATED DB: PDB REMARK 900 MINIMAL HAIRPIN RIBOZYME, A2M AT A-1, U39C MUTANT (LOW SALT) REMARK 900 RELATED ID: 1X9K RELATED DB: PDB REMARK 900 MINIMAL HAIRPIN RIBOZYME, A2M AT A-1, U39C MUTANT (HIGH REMARK 900 SALT) REMARK 900 RELATED ID: 1XXX RELATED DB: PDB REMARK 900 MINIMAL HAIRPIN RIBOZYME, A2M AT A-1, G8I AND U39C REMARK 900 MUTATIONS (LOW SALT) REMARK 900 RELATED ID: 1XXY RELATED DB: PDB REMARK 900 MINIMAL HAIRPIN RIBOZYME, 2'-OH AT A-1, G8A AND U39C REMARK 900 MUTATIONS (LOW SALT) REMARK 900 RELATED ID: 1XYZ RELATED DB: PDB REMARK 900 MINIMAL HAIRPIN RIBOZYME, 2'-OH AT A-1, G8U AND U39C REMARK 900 MUTATIONS (LOW SALT) REMARK 900 RELATED ID: 1ZFT RELATED DB: PDB REMARK 900 AN ALL-RNA HAIRPIN RIBOZYME WITH MUTATIONS G8I, U39C AND REMARK 900 2MA AT A-1 (LOW SALT) REMARK 900 RELATED ID: 1ZFV RELATED DB: PDB REMARK 900 AN ALL-RNA HAIRPIN RIBOZYME WITH MUTATIONS G8A, U39C AND 2' REMARK 900 -OH AT A-1 (LOW SALT) REMARK 900 RELATED ID: 1ZFX RELATED DB: PDB REMARK 900 ALL-RNA HAIRPIN RIBOZYME WITH MUTATIONS G8U AND U39C (LOW REMARK 900 SALT) SEQRES 1 A 13 U C C C A2M G U C C A C C G SEQRES 1 B 12 C G G U G A G A A G G G SEQRES 1 C 17 G G C A G A G A A A C A C SEQRES 2 C 17 A C G A SEQRES 1 D 19 U C G U G G U A C A U U A SEQRES 2 D 19 C C U G C C MODRES 1ZFR A2M A 5 A 2'-METHYL-ADENOSINE-5'-MONOPHOSPHATE HET A2M A 5 23 HET SO4 103 5 HET NCO 101 7 HET NCO 102 7 HETNAM A2M 2'-O-METHYL-ADENOSINE-5'-MONOPHOSPHATE HETNAM SO4 SULFATE ION HETNAM NCO COBALT HEXAMMINE ION FORMUL 1 A2M C11 H16 N5 O7 P FORMUL 5 SO4 O4 S 2- FORMUL 6 NCO 2(CO H18 N6 3+) FORMUL 8 HOH *84(H2 O) CRYST1 93.272 93.272 131.250 90.00 90.00 120.00 P 61 2 2 12 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 0.010721 0.006190 0.000000 0.00000 SCALE2 0.000000 0.012380 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007619 0.00000