Header list of 1q8n.pdb file
Complete list - r 2 2 Bytes
HEADER RNA 21-AUG-03 1Q8N TITLE SOLUTION STRUCTURE OF THE MALACHITE GREEN RNA BINDING APTAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA APTAMER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED IN VITRO AND DOES NOT SOURCE 4 OCCUR NATURALLY. KEYWDS RNA APTAMER, MALACHITE GREEN, BASE TRIPLE, BASE QUADRUPLE, RNA LIGAND KEYWDS 2 INTERACTIONS, RNA EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR J.FLINDERS,S.C.DEFINA,D.M.BRACKETT,C.BAUGH,C.WILSON,T.DIECKMANN REVDAT 3 02-MAR-22 1Q8N 1 REMARK REVDAT 2 24-FEB-09 1Q8N 1 VERSN REVDAT 1 23-MAR-04 1Q8N 0 JRNL AUTH J.FLINDERS,S.C.DEFINA,D.M.BRACKETT,C.BAUGH,C.WILSON, JRNL AUTH 2 T.DIECKMANN JRNL TITL RECOGNITION OF PLANAR AND NONPLANAR LIGANDS IN THE MALACHITE JRNL TITL 2 GREEN-RNA APTAMER COMPLEX. JRNL REF CHEMBIOCHEM V. 5 62 2004 JRNL REFN ISSN 1439-4227 JRNL PMID 14695514 JRNL DOI 10.1002/CBIC.200300701 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CNS 1.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), A.T. BRUNGER, P.D. ADAMS, G.M. REMARK 3 CLORE, W.L. DELANO, P. GROS, R.W. GROSSE-KUNSTLEVE, REMARK 3 J.S. JIANG, J. KUSZEWSKI, M. NILGES, N.S. PANNU, REMARK 3 R.J. READ, L.M.R ICE, T. SIMONSON, G.L. WARREN REMARK 3 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS BASED ON 423 NOE REMARK 3 CONSTRAINTS (148 INTRANUCLEOTIDE, 119 SEQUENTIAL, 66 MEDIUM TO REMARK 3 LONG RANGE, AND 90 RNA TO LIGAND NOES) AND 219 DIHEDRAL ANGLE REMARK 3 RESTRAINTS. REMARK 4 REMARK 4 1Q8N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000020054. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 274; 298; 274; 298; 274 REMARK 210 PH : 5.8; 5.8; 5.8; 5.8; 5.8 REMARK 210 IONIC STRENGTH : 10MM KCL; 10MM KCL; 10MM KCL; REMARK 210 10MM KCL; 10MM KCL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2MM RNA APTAMER, 10MM REMARK 210 PHOSPHATE BUFFER, 90% H2O, 10% REMARK 210 D2O; 1.5MM RNA APTAMER, 10MM REMARK 210 PHOSPHATE BUFFER, 100% D2O; REMARK 210 1.5MM RNA APTAMER, 10MM REMARK 210 PHOSPHATE BUFFER, 90% H2O, 10% REMARK 210 D2O; 1MM RNA APTAMER U-15N,13C, REMARK 210 10MM PHOSPHATE BUFFER, 100% D2O; REMARK 210 1MM RNA APTAMER U-15N,13C, 10MM REMARK 210 PHOSPHATE BUFFER, 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; REMARK 210 3D_13C-SEPARATED_NOESY; 2D HMQC; REMARK 210 HCNCH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.1, XEASY 1.3.13 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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: THIS STRUCTURE WAS DETERMINED WITH THE AID OF THE CRYSTAL REMARK 210 STRUCTURE OF A SIMILAR RNA APTAMER. 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 H22 G A 23 H61 A A 27 0.98 REMARK 500 HO2' U A 11 N1 A A 26 1.32 REMARK 500 H2' A A 26 O4' A A 27 1.45 REMARK 500 H22 G A 29 N1 A A 31 1.49 REMARK 500 H1 G A 2 O2 C A 37 1.54 REMARK 500 H22 G A 23 N6 A A 27 1.58 REMARK 500 O2' A A 31 H5 U A 32 1.58 REMARK 500 O6 G A 2 N3 C A 37 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 U A 4 0.06 SIDE CHAIN REMARK 500 1 G A 29 0.06 SIDE CHAIN REMARK 500 2 G A 29 0.06 SIDE CHAIN REMARK 500 3 G A 24 0.05 SIDE CHAIN REMARK 500 4 G A 29 0.06 SIDE CHAIN REMARK 500 5 G A 29 0.06 SIDE CHAIN REMARK 500 6 G A 29 0.06 SIDE CHAIN REMARK 500 7 G A 29 0.06 SIDE CHAIN REMARK 500 8 U A 4 0.06 SIDE CHAIN REMARK 500 8 G A 29 0.06 SIDE CHAIN REMARK 500 9 U A 4 0.06 SIDE CHAIN REMARK 500 9 G A 29 0.06 SIDE CHAIN REMARK 500 10 G A 24 0.05 SIDE CHAIN REMARK 500 10 G A 29 0.06 SIDE CHAIN REMARK 500 11 U A 4 0.06 SIDE CHAIN REMARK 500 11 G A 29 0.06 SIDE CHAIN REMARK 500 12 G A 29 0.06 SIDE CHAIN REMARK 500 13 G A 24 0.05 SIDE CHAIN REMARK 500 13 G A 29 0.06 SIDE CHAIN REMARK 500 14 G A 29 0.06 SIDE CHAIN REMARK 500 15 G A 24 0.05 SIDE CHAIN REMARK 500 16 U A 4 0.06 SIDE CHAIN REMARK 500 16 G A 24 0.05 SIDE CHAIN REMARK 500 16 G A 29 0.06 SIDE CHAIN REMARK 500 17 G A 24 0.05 SIDE CHAIN REMARK 500 17 G A 29 0.06 SIDE CHAIN REMARK 500 18 G A 24 0.05 SIDE CHAIN REMARK 500 18 G A 29 0.06 SIDE CHAIN REMARK 500 19 U A 4 0.06 SIDE CHAIN REMARK 500 19 G A 24 0.05 SIDE CHAIN REMARK 500 19 G A 29 0.05 SIDE CHAIN REMARK 500 20 G A 24 0.06 SIDE CHAIN REMARK 500 21 G A 29 0.06 SIDE CHAIN REMARK 500 22 G A 24 0.05 SIDE CHAIN REMARK 500 22 G A 29 0.06 SIDE CHAIN REMARK 500 23 U A 4 0.06 SIDE CHAIN REMARK 500 23 G A 29 0.06 SIDE CHAIN REMARK 500 24 G A 24 0.05 SIDE CHAIN REMARK 500 25 G A 29 0.06 SIDE CHAIN 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 MGR A 39 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F1T RELATED DB: PDB REMARK 900 A VARIANT RNA COMPLEXED WITH TETRAMETHYL-ROSAMINE DBREF 1Q8N A 1 38 PDB 1Q8N 1Q8N 1 38 SEQRES 1 A 38 G G A U C C C G A C U G G SEQRES 2 A 38 C G A G A G C C A G G U A SEQRES 3 A 38 A C G A A U G G A U C C HET MGR A 39 50 HETNAM MGR MALACHITE GREEN FORMUL 2 MGR C23 H25 N2 1+ SITE 1 AC1 6 C A 7 G A 8 G A 24 C A 28 SITE 2 AC1 6 G A 29 A A 30 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
Complete list - r 2 2 Bytes