10 20 30 40 50 60 70 80 483D - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER RNA 23-JUL-99 483D
TITLE CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI TITLE 2 23 S RRNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SARICIN/RICIN RRNA DOMAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 27 NA LONG SARCIN/RICIN DOMAIN; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE OCCURS NATURALLY IN E.COLI 28 S SOURCE 4 RIBOSOMAL RNA
KEYWDS SACIN/RICIN DOMAIN RNA RECOGNITION RIBOSOMES ELONGATION KEYWDS 2 FACTORS CRYSTAL STRUCTURE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.C.CORRELL,I.G.WOOL,A.MUNISHKIN
REVDAT 2 24-FEB-09 483D 1 VERSN REVDAT 1 08-OCT-99 483D 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. 1.11 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.156 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.152 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1267 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 23932 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.136 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.132 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1045 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 19828 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 682 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 732.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 8 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7554 REMARK 3 NUMBER OF RESTRAINTS : 10247 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.006 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.011 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.027 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : G. PARKINSON, J. VOJTECHOVSKY, REMARK 3 L. CLOWNEY, A.T. BRUNGER, H.M. REMARK 3 BERMAN: ACTA CRYST.D, 52, 57 REMARK 3 (1996) REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28 (1995) 53-56
REMARK 4 REMARK 4 483D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-99. REMARK 100 THE RCSB ID CODE IS RCSB009392.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9188 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : BENT CYLINDRICAL SI-MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25407 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.110 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : 0.04200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 2.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.48700 REMARK 200 R SYM FOR SHELL (I) : 0.48700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.0 - 3.2 M (NH4)2SO4, (50 MM REMARK 280 KMOPS, 10 MM MGCL2, 10MM MNCL2), 2.5 MG/ML RNA, PH 7.00, VAPOR REMARK 280 DIFFUSION, HANGING DROP
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 38.17650 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 57.26475 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 19.08825 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: 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 A2655 C6 - C5 - N7 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A2655 C3' - O3' - P ANGL. DEV. = 11.5 DEGREES REMARK 500 G A2659 N9 - C1' - C2' ANGL. DEV. = -11.0 DEGREES REMARK 500 G A2669 C3' - C2' - C1' ANGL. DEV. = -4.4 DEGREES REMARK 500 G A2669 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A2671 C5 - C6 - O6 ANGL. DEV. = -3.8 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 A1141 DISTANCE = 5.87 ANGSTROMS
DBREF 483D A 2647 2673 PDB 483D 483D 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 *155(H2 O)
CRYST1 29.481 29.481 76.353 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 0.033920 0.000000 0.000000 0.00000
SCALE2 0.000000 0.033920 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013097 0.00000