10 20 30 40 50 60 70 80 480D - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER RNA 20-JUL-99 480D
TITLE CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI TITLE 2 23 S RRNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SARCIN/RICIN DOMAIN FROM 23 S RRNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SARCIN/RICIN DOMAIN; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS SARCIN/RICIN LOOP OR DOMAIN, RNA RECOGNITION, RIBOSOMES, KEYWDS 2 ELONGATION FACTORS, CRYSTAL STRUCTURE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.C.CORRELL,I.G.WOOL,A.MUNISHKIN
REVDAT 2 24-FEB-09 480D 1 VERSN REVDAT 1 08-OCT-99 480D 0
JRNL AUTH C.C.CORRELL,I.G.WOOL,A.MUNISHKIN JRNL TITL THE TWO FACES OF THE ESCHERICHIA COLI 23 S RRNA JRNL TITL 2 SARCIN/RICIN DOMAIN: THE STRUCTURE AT 1.11 A JRNL TITL 3 RESOLUTION. JRNL REF J.MOL.BIOL. V. 292 275 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10493875 JRNL DOI 10.1006/JMBI.1999.3072
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.C.CORRELL,A.MUNISHKIN,Y.-L.CHAN,Z.REN,I.G.WOOL REMARK 1 TITL CRYSTAL STRUCTURE OF THE RIBOSOMAL RNA DOMAIN REMARK 1 TITL 2 ESSENTIAL FOR BINDING ELONGATION FACTORS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 95 13436 1998 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.95.23.13436 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.P.RIFE,S.G.STALLINGS,C.C.CORRELL,A.DALLAS, REMARK 1 AUTH 2 T.A.STEITZ,P.B.MOORE REMARK 1 TITL COMPARISON OF THE CRYSTAL AND SOLUTION STRUCTURES REMARK 1 TITL 2 OF TWO RNA OLIGONUCLEOTIDES REMARK 1 REF BIOPHYS.J. V. 76 65 1999 REMARK 1 REFN ISSN 0006-3495 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.A.SZEWCZAK,P.B.MOORE REMARK 1 TITL THE SARCIN/RICIN LOOP, A MODULAR RNA REMARK 1 REF J.MOL.BIOL. V. 247 81 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1994.0124 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.A.SZEWCZAK,P.B.MOORE REMARK 1 TITL THE CONFORMATION OF THE SARCIN/RICIN LOOP FROM 28 REMARK 1 TITL 2 S RIBOSOMAL RNA REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 90 9581 1993 REMARK 1 REFN ISSN 0027-8424
REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 10535 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : R FREE REMARK 3 FREE R VALUE TEST SET SELECTION : 10% OF DATA THAT WAS REMARK 3 RANDOMLY SELECTED. OVERALL REMARK 3 R FOR ALL DATA WAS NEVER REMARK 3 CALCULATED REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1075 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 420 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 39 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 579 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.83 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 30.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.10 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AFTER BULK SOLVENT CORRECTION AND REMARK 3 ANISOTROPIC SCALING OF FOBS, CYCLES OF POWELL MINIMIZATION REMARK 3 FOLLOWED BY B-FACTOR REFINEMENT WERE DONE.
REMARK 4 REMARK 4 480D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-99. REMARK 100 THE RCSB ID CODE IS RCSB009367.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 7.0 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 : MSC MIRROR BOX REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.45900 REMARK 200 R SYM FOR SHELL (I) : 0.45900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: THE RELATED RAT SARCIN/RICIN STRUCTURE (430D) REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.0 - 3.2 M (NH4)2SO4, BUFFER X (50 REMARK 280 MM POTASIUM MOPS, PH 7.0; 10 MM MGCL2; AND 10 MM MNCL2), AND ~ REMARK 280 2.5 MG/ML RNA, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 38.21000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.31500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.10500 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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OP2 C A 2658 O HOH A 1032 2.14 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 430D RELATED DB: PDB REMARK 900 THE STRUCTURE OF THE RELATED RAT SEQUENCE DETERMINED BY X- REMARK 900 RAY CRYSTALLOGRAPHY
DBREF 480D A 2647 2673 PDB 480D 480D 2647 2673
SEQRES 1 A 27 U G C U C C U A G U A C G SEQRES 2 A 27 A G A G G A C C G G A G U SEQRES 3 A 27 G
FORMUL 2 HOH *84(H2 O)
CRYST1 29.950 29.950 76.420 90.00 90.00 90.00 P 43 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 0.033389 0.000000 0.000000 0.00000
SCALE2 0.000000 0.033389 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013086 0.00000