10 20 30 40 50 60 70 80 1MSY - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 19-SEP-02 1MSY
TITLE GUAA TETRALOOP MUTANT OF 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 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: GUAA TETRALOOP MUTANT
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: A2660U AND G2661U DOUBLE MUTANT OF THE SRL SOURCE 4 DOMAIN FROM E.COLI RRNA
KEYWDS A-MINOR MOTIF, SARCIN/RICIN LOOP, RNA STRUCTURE, RNA KEYWDS 2 TERTIARY CONTACTS, RNA MOTIFS, CONFORMATIONAL CHANGE, RNA- KEYWDS 3 PROTEIN RECOGNITION, HYDRATION
EXPDTA X-RAY DIFFRACTION
AUTHOR C.C.CORRELL,K.SWINGER
REVDAT 2 24-FEB-09 1MSY 1 VERSN REVDAT 1 25-FEB-03 1MSY 0
JRNL AUTH C.C.CORRELL,K.SWINGER JRNL TITL COMMON AND DISTINCTIVE FEATURES OF GNRA TETRALOOPS JRNL TITL 2 BASED ON A GUAA TETRALOOP STRUCTURE AT 1.4 A JRNL TITL 3 RESOLUTION JRNL REF RNA V. 9 355 2003 JRNL REFN ISSN 1355-8382 JRNL PMID 12592009 JRNL DOI 10.1261/RNA.2147803
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.41 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.00 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) : 0.164 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.164 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 11.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1419 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 14372 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.138 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.137 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.800 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1082 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 10030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 582 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 109 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 662.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6236 REMARK 3 NUMBER OF RESTRAINTS : 8182 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.019 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.006 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.079 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL 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 3 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
REMARK 4 REMARK 4 1MSY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-02. REMARK 100 THE RCSB ID CODE IS RCSB017157.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97764 REMARK 200 MONOCHROMATOR : SI-111 DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32300 REMARK 200 R SYM FOR SHELL (I) : 0.32300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 483D REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, POTASSIUM MOPS, REMARK 280 MAGNESIUM CHLORIDE, MANGANESE CHLORIDE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 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 28.98700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.26700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.98700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.26700 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: 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 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 C6 U A2647 LIES ON A SPECIAL POSITION. REMARK 375 N1 G A2673 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3002 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3004 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3068 LIES ON A SPECIAL POSITION.
REMARK 400 REMARK 400 COMPOUND REMARK 400 A CRYSTALLOGRAPHIC TWO-FOLD AXIS PASSES REMARK 400 THROUGH THE TERMINAL GU WOBBLEBASE PAIR. REMARK 400 EACH MOLECULE ABOUT THE 2-FOLD CONTRIBUTES REMARK 400 ONE NUCLEOTIDE TO THE WOBBLE PAIR AND THE REMARK 400 NUCLEOTIDE THAT COULD FORM THE REMARK 400 INTRAMOLECULAR CLOSING PAIR IS DISORDERED. REMARK 400 NOTE THAT THE OCCUPANCIES FOR THESE REMARK 400 NUCLEOTIDES IS 0.5.
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 A A2657 N1 - C2 - N3 ANGL. DEV. = 3.4 DEGREES REMARK 500 G A2659 N9 - C1' - C2' ANGL. DEV. = -8.7 DEGREES REMARK 500 G A2659 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 G A2659 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 G A2663 O5' - P - OP1 ANGL. DEV. = 7.4 DEGREES REMARK 500 A A2662 C3' - O3' - P ANGL. DEV. = -8.4 DEGREES REMARK 500 G A2664 C5 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 G A2673 N1 - C6 - O6 ANGL. DEV. = -4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 480D RELATED DB: PDB REMARK 900 WT SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA REMARK 900 RELATED ID: 1JBR RELATED DB: PDB REMARK 900 RIBOTOXIN RESTRICTOCIN AND A 31- MER SRD RNA INHIBITOR REMARK 900 RELATED ID: 1JBS RELATED DB: PDB REMARK 900 RIBOTOXIN RESTRICTOCIN AND A 29-MER SRD RNA ANALOG REMARK 900 RELATED ID: 1JBT RELATED DB: PDB REMARK 900 RIBOTOXIN RESTRICTOCIN AND A 29-MER SRD RNA ANALOG REMARK 900 RELATED ID: 483D RELATED DB: PDB REMARK 900 WT SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA
DBREF 1MSY A 2647 2673 PDB 1MSY 1MSY 2647 2673
SEQRES 1 A 27 U G C U C C U A G U A C G SEQRES 2 A 27 U A A G G A C C G G A G U SEQRES 3 A 27 G
FORMUL 2 HOH *109(H2 O)
CRYST1 57.974 22.534 58.465 90.00 101.72 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 0.017249 0.000000 0.003578 0.00000
SCALE2 0.000000 0.044377 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017468 0.00000