HEADER DNA 18-MAR-97 1AFZ TITLE SOLUTION NMR STRUCTURE OF AN 11 BASE-PAIR OLIGONUCLEOTIDE FROM THE TITLE 2 HUMAN N-RAS PROTOONCOGENE ENCODING FOR AMINO ACIDS 11-13 OF P21, TITLE 3 MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*AP*CP*CP*AP*CP*CP*TP*GP*CP*C)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA DUPLEX, HUMAN N-RAS GENE, CODON 12 SEQUENCE, DEOXYRIBONUCLEIC KEYWDS 2 ACID, DNA EXPDTA SOLUTION NMR AUTHOR I.S.ZEGAR,M.P.STONE REVDAT 3 16-FEB-22 1AFZ 1 REMARK REVDAT 2 24-FEB-09 1AFZ 1 VERSN REVDAT 1 20-AUG-97 1AFZ 0 JRNL AUTH I.S.ZEGAR,M.P.STONE JRNL TITL SOLUTION STRUCTURE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE JRNL TITL 2 HUMAN N-RAS CODON 12 SEQUENCE REFINED FROM 1H NMR USING JRNL TITL 3 MOLECULAR DYNAMICS RESTRAINED BY NUCLEAR OVERHAUSER EFFECTS. JRNL REF CHEM.RES.TOXICOL. V. 9 114 1996 JRNL REFN ISSN 0893-228X JRNL PMID 8924579 JRNL DOI 10.1021/TX9500787 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1AFZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170768. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; 2QF-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, X-PLOR, MARDIGRAS, CORMA REMARK 210 METHOD USED : NOE-RESTRAINED MOLECULAR REMARK 210 DYNAMICS/SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : THIS STRUCTURE PROVIDED THE BEST REMARK 210 -FIT FOR THE NOE DATA BASED ON REMARK 210 THE RELAXATION MATRIX ANALYSIS REMARK 210 USING CORMA. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: SEE JRNL CITATION ABOVE FOR ADDITIONAL NMR EXPERIMENTAL REMARK 210 DETAILS. SOLVENT SYSTEM : D2O, H2O 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA A 4 O3' - P - O5' ANGL. DEV. = -35.4 DEGREES REMARK 500 DA A 4 O3' - P - OP2 ANGL. DEV. = -26.6 DEGREES REMARK 500 DA A 4 O3' - P - OP1 ANGL. DEV. = 21.8 DEGREES REMARK 500 DA A 4 OP1 - P - OP2 ANGL. DEV. = -22.3 DEGREES REMARK 500 DA A 4 O5' - P - OP1 ANGL. DEV. = -25.6 DEGREES REMARK 500 DA A 4 O5' - P - OP2 ANGL. DEV. = 19.8 DEGREES REMARK 500 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 4 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 6 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 8 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 13 O3' - P - O5' ANGL. DEV. = -36.0 DEGREES REMARK 500 DA B 13 O3' - P - OP2 ANGL. DEV. = -19.9 DEGREES REMARK 500 DA B 13 O3' - P - OP1 ANGL. DEV. = 24.6 DEGREES REMARK 500 DA B 13 OP1 - P - OP2 ANGL. DEV. = -20.5 DEGREES REMARK 500 DA B 13 O5' - P - OP1 ANGL. DEV. = -31.2 DEGREES REMARK 500 DA B 13 O5' - P - OP2 ANGL. DEV. = 16.8 DEGREES REMARK 500 DA B 13 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 14 O3' - P - O5' ANGL. DEV. = -35.8 DEGREES REMARK 500 DC B 14 O3' - P - OP2 ANGL. DEV. = -31.2 DEGREES REMARK 500 DC B 14 O3' - P - OP1 ANGL. DEV. = 16.3 DEGREES REMARK 500 DC B 14 OP1 - P - OP2 ANGL. DEV. = -20.2 DEGREES REMARK 500 DC B 14 O5' - P - OP1 ANGL. DEV. = -20.8 DEGREES REMARK 500 DC B 14 O5' - P - OP2 ANGL. DEV. = 24.4 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA B 16 O3' - P - O5' ANGL. DEV. = -36.5 DEGREES REMARK 500 DA B 16 O3' - P - OP2 ANGL. DEV. = 16.7 DEGREES REMARK 500 DA B 16 O3' - P - OP1 ANGL. DEV. = -30.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 87 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AF1 RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE DBREF 1AFZ A 1 11 PDB 1AFZ 1AFZ 1 11 DBREF 1AFZ B 12 22 PDB 1AFZ 1AFZ 12 22 SEQRES 1 A 11 DG DG DC DA DG DG DT DG DG DT DG SEQRES 1 B 11 DC DA DC DC DA DC DC DT DG DC DC 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