HEADER RNA 04-JUL-08 2K63 OBSLTE 16-APR-14 2K63 2M24 TITLE NMR SOLUTION STRUCTURE OF THE D3'-HAIRPIN INCLUDING THE EXON BINDING TITLE 2 SITE 1 (EBS1) OF THE GROUP II INTRON SC.AI5(GAMMA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 29-MER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS GROUP II INTRON, RIBOZYME, SPLICING, EXON BINDING SITE 1, EBS1, METAL KEYWDS 2 ION, MAGNESIUM, RNA 29-MER, HAIRPIN, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.KRUSCHEL,R.K.O.SIGEL REVDAT 2 16-APR-14 2K63 1 OBSLTE VERSN REVDAT 1 14-JUL-09 2K63 0 JRNL AUTH D.KRUSCHEL,R.K.O.SIGEL JRNL TITL SOLUTION STRUCTURE OF THE 5'-SPLICE SITE OF A GROUP II JRNL TITL 2 INTRON RIBOZYME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH 2.16 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K63 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-08. REMARK 100 THE RCSB ID CODE IS RCSB100722. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 298; 303; 278; 283; 293; REMARK 210 293; 298; 303; 298; 278 REMARK 210 PH : 6.3-6.5; 6.3-6.5; 6.3-6.5; 6.5- REMARK 210 6.8; 6.5-6.8; 6.5-6.8; 6.3; 6.3; REMARK 210 6.3; 6.8; 6.8 REMARK 210 IONIC STRENGTH : 10; 10-17; 10; 10-18; 10; 10; REMARK 210 10; 10; 10; 10; 10 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4-1.2 MM RNA (29-MER), 10 MM REMARK 210 POTASSIUM CHLORIDE, 10 UM EDTA, REMARK 210 0-7 MM MGCL2, 100% D2O; 0.4-1.2 REMARK 210 MM RNA (29-MER), 10 MM POTASSIUM REMARK 210 CHLORIDE, 10 UM EDTA, 0-8 MM REMARK 210 MGCL2, 90% H2O/10% D2O; 0.6 MM REMARK 210 SELECTIVELY DEUTERATED AT 3',4', REMARK 210 5',5'',5 RNA (29-MER), 10 MM REMARK 210 POTASSIUM CHLORIDE, 10 UM EDTA, REMARK 210 100% D2O; 0.7 MM [U-100% 13C; U- REMARK 210 100% 15N] RNA (29-MER), 10 MM REMARK 210 POTASSIUM CHLORIDE, 10 UM EDTA, REMARK 210 90% H2O/10% D2O; 0.7 MM [U-100% REMARK 210 13C; U-100% 15N] RNA (29-MER), 10 REMARK 210 MM POTASSIUM CHLORIDE, 10 UM REMARK 210 EDTA, 25.6 MG/ML PF1 PHAGE, 90% REMARK 210 H2O/10% D2O; 1.0 MM [U-100% 13C; REMARK 210 U-100% 15N] RNA (29-MER), 10 MM REMARK 210 POTASSIUM CHLORIDE, 10 UM EDTA, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 2D JNN HNN-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, 2.0, 2.1, SPARKY REMARK 210 3.1, DYANA 1.5, CNSSOLVE 1.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED WITH A COMBINATION OF NOE AND REMARK 210 RESIDUAL DIPOLAR COUPLING DATA. IN ADDITION, MAGNESIUM TITRATION REMARK 210 FROM 0 - 7 MM MGCL2 WERE PERFORMED ELUCIDATING 4 SPECIFIC METAL REMARK 210 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' G A 14 H5' C A 15 1.45 REMARK 500 O2' A A 10 H6 U A 11 1.46 REMARK 500 HO2' A A 10 O5' U A 11 1.54 REMARK 500 O2' U A 24 H5' A A 25 1.58 REMARK 500 HO2' U A 9 O4' A A 10 1.58 REMARK 500 H2' U A 18 O4' G A 19 1.59 REMARK 500 O6 G A 13 H5'' A A 16 1.60 REMARK 500 O2' U A 9 O4' A A 10 2.13 REMARK 500 O2' A A 10 O5' U A 11 2.18 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. = -2.7 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 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. = 3.8 DEGREES REMARK 500 1 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 13 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 19 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 19 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 G A 21 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 21 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 23 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 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. = 4.7 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 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. = -2.5 DEGREES REMARK 500 2 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 13 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 G A 19 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 19 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 21 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 21 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 23 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 461 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15856 RELATED DB: BMRB REMARK 900 NMR DATA RELATED TO NMR SOLUTION STRUCTURE OF THE D3'- REMARK 900 HAIRPIN INCLUDING EBS1 OF THE GROUP II INTRON SC.AI5(GAMMA) REMARK 900 RELATED ID: 2K64 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF THE D3'-HAIRPIN INCLUDING EBS1 REMARK 900 TOGETHER WITH IBS1 OF THE GROUP II INTRON SC.AI5(GAMMA) REMARK 900 RELATED ID: 15857 RELATED DB: BMRB REMARK 900 NMR DATA RELATED TO NMR SOLUTION STRUCTURE OF THE D3'- REMARK 900 HAIRPIN INCLUDING EBS1 AND IBS1 OF THE GROUP II INTRON REMARK 900 SC.AI5(GAMMA) REMARK 900 RELATED ID: 2K65 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF THE EXON/INTRON BINDING SITE 1 REMARK 900 (EBS1/IBS1) OF THE GROUP II INTRON SC.AI5(GAMMA) REMARK 900 RELATED ID: 15858 RELATED DB: BMRB REMARK 900 NMR DATA RELATED TO NMR SOLUTION STRUCTURE OF THE EXON/ REMARK 900 INTRON BINDING SITE 1 (EBS1/IBS1) OF THE GROUP II INTRON REMARK 900 SC.AI5(GAMMA) REMARK 900 RELATED ID: 2K66 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF THE D3'-STEM CLOSED BY A GAAA REMARK 900 TETRALOOP OF THE GROUP II INTRON SC.AI5(GAMMA) REMARK 900 RELATED ID: 15859 RELATED DB: BMRB REMARK 900 NMR DATA RELATED TO NMR SOLUTION STRUCTURE OF THE D3'-STEM REMARK 900 CLOSED BY A GAAA TETRALOOP OF THE GROUP II INTRON REMARK 900 SC.AI5(GAMMA) REMARK 900 RELATED ID: 1R2P RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF DOMAIN 5 FROM THE AI5(GAMMA) GROUP II REMARK 900 INTRON REMARK 900 RELATED ID: 5962 RELATED DB: BMRB REMARK 900 NMR DATA RELATED TO SOLUTION STRUCTURE OF DOMAIN 5 FROM THE REMARK 900 AI5(GAMMA) GROUP II INTRON REMARK 900 RELATED ID: 2AHT RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF DOMAIN 6 FROM THE AI5(GAMMA)GROUP II REMARK 900 INTRON REMARK 900 RELATED ID: 6756 RELATED DB: BMRB REMARK 900 NMR DATA RELATED TO SOLUTION STRUCTURE OF DOMAIN 6 FROM THE REMARK 900 AI5(GAMMA)GROUP II INTRON REMARK 900 RELATED ID: 1KXK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A RNA MOLECULE CONTAINING DOMAIN 5 AND REMARK 900 6 OF THE YEAST AI5G GROUP II SELF-SPLICING INTRON REMARK 900 RELATED ID: 3BWP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A SELF-SPLICED GROUP II INTRON DBREF 2K63 A 1 29 PDB 2K63 2K63 1 29 SEQRES 1 A 29 G G A G U A U G U A U U G SEQRES 2 A 29 G C A C U G A G C A U A C SEQRES 3 A 29 U C 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