HEADER RNA 20-AUG-02 1MHK TITLE CRYSTAL STRUCTURE ANALYSIS OF A 26MER RNA MOLECULE, REPRESENTING A NEW TITLE 2 RNA MOTIF, THE HOOK-TURN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA 12-MER BCH12; COMPND 3 CHAIN: S; COMPND 4 FRAGMENT: FRAGMENT OF 5S RRNA LOOP E; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SHORT STRAND; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA 14-MER BCH12; COMPND 9 CHAIN: L; COMPND 10 FRAGMENT: FRAGMENT OF 5S RRNA LOOP E; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: LONG STRAND SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: 5S RRNA LOOP E REGION, SEQUENCE FROM CHROMATIUM SOURCE 4 MINUTISSIMUM; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: 5S RRNA LOOP E REGION, SEQUENCE FROM CHROMATIUM SOURCE 8 MINUTISSIMUM KEYWDS HELIX, 180 DEGREE TURN, RNA EXPDTA X-RAY DIFFRACTION AUTHOR S.SZEP,J.WANG,P.B.MOORE REVDAT 4 14-FEB-24 1MHK 1 REMARK LINK REVDAT 3 24-FEB-09 1MHK 1 VERSN REVDAT 2 25-MAR-03 1MHK 1 JRNL SEQRES LINK ATOM REVDAT 1 06-SEP-02 1MHK 0 JRNL AUTH S.SZEP,J.WANG,P.B.MOORE JRNL TITL THE CRYSTAL STRUCTURE OF A 26-NUCLEOTIDE RNA CONTAINING A JRNL TITL 2 HOOK-TURN JRNL REF RNA V. 9 44 2003 JRNL REFN ISSN 1355-8382 JRNL PMID 12554875 JRNL DOI 10.1261/RNA.2107303 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 STANDARD PARAMETER FILES:DNA_RNAREP.PARAM REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 3011 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) : 0.239 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.400 REMARK 3 FREE R VALUE TEST SET COUNT : 252 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.017 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 359 REMARK 3 BIN R VALUE (WORKING SET) : 0.4040 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 31 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 548 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.17000 REMARK 3 B22 (A**2) : 5.29000 REMARK 3 B33 (A**2) : -11.46000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 20.29000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.42 REMARK 3 ESD FROM SIGMAA (A) : 0.59 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.57 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.080 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 14.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.460 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 54.18 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 : DNA-RNA_REP-BR2.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNA-BR2.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MHK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016915. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-01; 13-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 193; 193 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; NSLS REMARK 200 BEAMLINE : NULL; X25 REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 0.91939 REMARK 200 MONOCHROMATOR : FOCUSING MIRRORS; DOUBLE CRYSTAL REMARK 200 OPTICS : FOCUSING MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC; CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3220 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 17.69 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12800 REMARK 200 FOR THE DATA SET : 10.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.59 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34200 REMARK 200 FOR SHELL : 2.550 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 6MER A-FORM RNA HELIX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MAGNESIUM CHLORIDE, REMARK 280 SPERMIDINE, TRIS-HYDROGEN CHLORIDE, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP AT 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 15.08450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.25500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 15.08450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.25500 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: S, L 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH S 16 LIES ON A SPECIAL POSITION. REMARK 375 HOH L 19 LIES ON A SPECIAL POSITION. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR S 13 DBREF 1MHK S 1 12 PDB 1MHK 1MHK 1 12 DBREF 1MHK L 1 14 PDB 1MHK 1MHK 1 14 SEQRES 1 S 12 C C A U G C G A A C C G SEQRES 1 L 14 C G A U C C U A G U G U G SEQRES 2 L 14 G HET BR S 13 1 HETNAM BR BROMIDE ION FORMUL 3 BR BR 1- FORMUL 4 HOH *21(H2 O) LINK C5 U S 4 BR BR S 13 1555 1555 1.88 SITE 1 AC1 2 A S 3 U S 4 CRYST1 30.169 62.510 50.933 90.00 98.76 90.00 C 1 2 1 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 0.033147 0.000000 0.005108 0.00000 SCALE2 0.000000 0.015997 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019865 0.00000