HEADER RNA 26-AUG-05 2AU4 TITLE CLASS I GTP APTAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLASS I RNA APTAMER TO GTP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO SELECTION KEYWDS RNA, APTAMER EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR J.M.CAROTHERS,J.H.DAVIS,J.J.CHOU,J.W.SZOSTAK REVDAT 5 22-MAY-24 2AU4 1 REMARK REVDAT 4 09-MAR-22 2AU4 1 REMARK REVDAT 3 24-FEB-09 2AU4 1 VERSN REVDAT 2 18-APR-06 2AU4 1 JRNL REVDAT 1 28-MAR-06 2AU4 0 JRNL AUTH J.M.CAROTHERS,J.H.DAVIS,J.J.CHOU,J.W.SZOSTAK JRNL TITL SOLUTION STRUCTURE OF AN INFORMATIONALLY COMPLEX JRNL TITL 2 HIGH-AFFINITY RNA APTAMER TO GTP. JRNL REF RNA V. 12 567 2006 JRNL REFN ISSN 1355-8382 JRNL PMID 16510427 JRNL DOI 10.1261/RNA.2251306 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.3, XPLOR-NIH 2.9.2 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), CLORE, TJANDRA, SCHWIETERS, REMARK 3 KUSZEWSKI (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL OF 434 REMARK 3 RESTRAINTS REMARK 4 REMARK 4 2AU4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000034313. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 303; 298; 303 REMARK 210 PH : 6.1; 6.1; 6.1; 6.8 REMARK 210 IONIC STRENGTH : 5 MM MGCL2, 75 MM KCL; 5 MM REMARK 210 MGCL2, 75 MM KCL; 5 MM MGCL2, 75 REMARK 210 MM KCL; 5 MM MGCL2, 75 MM KCL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 3.3 MM CLASS I APTAMER U-15N, REMARK 210 13C, 3.63 MM GTP LIGAND NA, 10 % REMARK 210 PHOSPHATE BUFFER NA, 99% D2O; REMARK 210 0.9 MM CLASS I APTAMER NA, 0.99 REMARK 210 NM GTP LIGAND U-15N, 13C, 10 % REMARK 210 PHOSPATE BUFFER NA, 99% D2O; 3.3 REMARK 210 MM CLASS I APTAMER U-15N, 13C; REMARK 210 3.63 MM GTP LIGAND NA; 10 % REMARK 210 PHOSPHATE BUFFER NA, 95% H2O, 5% REMARK 210 D2O; 0.9 MM CLASS I APTAMER NA; REMARK 210 0.99 NM GTP LIGAND U-15N, 13C; REMARK 210 10 % PHOSPATE BUFFER NA, 95% H2O, REMARK 210 5% D2O; 0.8 MM CLASS I RNA REMARK 210 APTAMER U-15N,13C, 0.9 MM GTP NA, REMARK 210 10% PHOSPHATE BUFFER NA, 95% REMARK 210 H2O, 5% D2O; 0.5 MM CLASS I RNA REMARK 210 APTAMER U-15N,13C, 0.55 MM GTP REMARK 210 NA, 18 ML/MG PF1 PHAGE NA, 10% REMARK 210 PHOSPHATE BUFFER NA, 95% H2O, 5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY; DQF- REMARK 210 COSY; 2D 1H DECOUPLED 13C-1H CT REMARK 210 HSQC; 2D 13C-1H CT-TROSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITY; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR-NIH 2.9.2, SPARKY 3 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 H21 G A 31 O6 GTP A 42 1.43 REMARK 500 HO2' G A 24 O5' G A 25 1.47 REMARK 500 O2' A A 8 HO2' GTP A 42 1.47 REMARK 500 H1 G A 17 O2 U A 28 1.52 REMARK 500 N3 A A 8 H21 G A 11 1.54 REMARK 500 H3 U A 14 N1 A A 33 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 G A 1 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 A A 7 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 U A 10 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 G A 12 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 U A 14 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G A 17 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G A 19 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 G A 19 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 U A 22 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 G A 24 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 G A 24 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 24 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 G A 25 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 25 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 G A 27 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 27 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 U A 28 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 G A 29 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 G A 29 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 G A 29 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 U A 30 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 G A 31 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 G A 31 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 31 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 A A 32 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 A A 32 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 33 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 58 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 42 DBREF 2AU4 A 1 41 PDB 2AU4 2AU4 1 41 SEQRES 1 A 41 G G G A C G A A G U G G U SEQRES 2 A 41 U G G G C G C U U C G G C SEQRES 3 A 41 G U G U G A A A A C G U C SEQRES 4 A 41 C C HET GTP A 42 45 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 2 GTP C10 H16 N5 O14 P3 SITE 1 AC1 7 A A 8 G A 9 G A 11 G A 15 SITE 2 AC1 7 G A 16 G A 31 A A 32 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