HEADER RNA 28-JUL-05 2AHT TITLE SOLUTION STRUCTURE OF DOMAIN 6 FROM THE AI5(GAMMA)GROUP II INTRON COMPND MOL_ID: 1; COMPND 2 MOLECULE: 27-MER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 OTHER_DETAILS: THE SEQUENCE OCCURS NATURALLY IN THE MITOCHONDRIAL SOURCE 6 COX GENE 1 OF SACCHAROMYCES CEREVISIAE AND WAS SYNTHESIZED IN VITRO SOURCE 7 USING T7 POLYMERASE AND SYNTHETIC DNA OLIGONUCLEOTIDES. NUCLEOTIDES SOURCE 8 A859-U864 AND G871-A876 (WILD TYPE NOMENCLATURE) WERE REMOVED. KEYWDS GROUP II INTRON, RIBOZYME, SPLICING, BRANCHING, DOMAIN 6, RNA, KEYWDS 2 TETRALOOP, BRANCH-POINT A, GU WOBBLE PAIRS, METAL ION, MAGNESIUM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.C.ERAT,O.ZERBE,T.FOX,R.K.O.SIGEL REVDAT 4 23-OCT-19 2AHT 1 SOURCE REMARK REVDAT 3 20-OCT-10 2AHT 1 JRNL REVDAT 2 24-FEB-09 2AHT 1 VERSN REVDAT 1 17-OCT-06 2AHT 0 JRNL AUTH M.C.ERAT,O.ZERBE,T.FOX,R.K.O.SIGEL JRNL TITL SOLUTION STRUCTURE OF DOMAIN 6 FROM A SELF-SPLICING GROUP II JRNL TITL 2 INTRON RIBOZYME: A MG(2+) BINDING SITE IS LOCATED CLOSE TO JRNL TITL 3 THE STACKED BRANCH ADENOSINE. JRNL REF CHEMBIOCHEM V. 8 306 2007 JRNL REFN ISSN 1439-4227 JRNL PMID 17200997 JRNL DOI 10.1002/CBIC.200600459 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, X-PLOR NIH REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AHT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000033911. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 293; 275; 283; 293; 303; REMARK 210 283 REMARK 210 PH : 6.8; 6.8; 6.8; 6.8; 6.8; 6.8; REMARK 210 6.8 REMARK 210 IONIC STRENGTH : 100MM KCL, 0.01MM EDTA, 0-12MM REMARK 210 MGCL2; 100MM KCL, 0.01MM EDTA, 0- REMARK 210 12MM MGCL2; 100MM KCL, 0.01MM REMARK 210 EDTA, 0-12MM MGCL2; 100MM KCL, REMARK 210 0.01MM EDTA, 0-12MM MGCL2; 100MM REMARK 210 KCL, 0.01MM EDTA, 0-12MM MGCL2; REMARK 210 100MM KCL, 0.01MM EDTA; 100MM REMARK 210 KCL, 0.01MM EDTA REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM; 1 REMARK 210 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4-0.8MM D6SHORT RNA, 99.999% REMARK 210 D2O; 0.4-0.8MM D6SHORT RNA, 90% REMARK 210 H2O, 10% D2O; 0.2-1.1MM D6SHORT REMARK 210 RNA, FULLY 13C15N-LABELED, REMARK 210 99.999% D2O; 0.5MM D6SHORT RNA, REMARK 210 FULLY 13C15N-LABELED, 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 13C1H HSQC; REMARK 210 15N1H HSQC; HCCH-TOCSY; HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.1, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE MOLECULAR DYNAMICS REMARK 210 CARTESIAN SPACE SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: MAGNESIUM TITRATION FROM 0-12MM MGCL2, ELUCIDATING 4-5 REMARK 210 SPECIFIC METAL ION BINDING SITES REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 O2' A A 3 H5' G A 4 1.54 REMARK 500 O2' G A 1 H8 G A 2 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 1 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 23 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 23 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 23 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 23 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 500 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R2P RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF DOMAIN 5 REMARK 900 RELATED ID: 5962 RELATED DB: BMRB REMARK 900 NMR DATA RELATED TO SOLUTION STRUCTURE OF DOMAIN 5 REMARK 900 RELATED ID: 1KXK RELATED DB: PDB REMARK 900 XRAY STRUCTURE OF D56 DBREF 2AHT A 1 27 PDB 2AHT 2AHT 1 27 SEQRES 1 A 27 G G A G C G G G G G U G U SEQRES 2 A 27 A A A C C U A U C G C U C SEQRES 3 A 27 C CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1