Header list of 1r2l.pdb file
Complete list - 2 202 Bytes
HEADER DNA 29-SEP-03 1R2L TITLE A PARALLEL STRANDED DNA DUPLEX WITH AN A-G MISMATCH BASE-PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*(DNR)P*(DNR) COMPND 3 P*DAP*DTP*DAP*DAP*DTP*DTP*DTP*DAP*(DNR)P*(DNR))-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: PS-DNA; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(P*CP*CP*TP*AP*TP*GP*AP*AP*AP*TP*CP*C)-3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: PS-DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE DNA DUPLEX WAS SYNTHESIZED WITH AN APPLIED SOURCE 4 BIOSYSTEMS MODEL 380B DNA SYNTHESIZER USING SOLID STATE SOURCE 5 PHOSPHORAMIDATE CHEMISTRY.; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES KEYWDS PS-DNA, A:G MISMATCH, PARALLEL DNA DUPLEX, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR R.P.VENKITAKRISHNAN,S.R.BHAUMIK,K.V.R.CHARY,G.GOVIL,K.LIU,F.B.HOWARD, AUTHOR 2 T.H.MILES REVDAT 3 02-MAR-22 1R2L 1 REMARK LINK REVDAT 2 24-FEB-09 1R2L 1 VERSN REVDAT 1 12-OCT-04 1R2L 0 JRNL AUTH R.P.VENKITAKRISHNAN,S.R.BHAUMIK,K.V.R.CHARY,G.GOVIL,K.LIU, JRNL AUTH 2 F.B.HOWARD,T.H.MILES JRNL TITL A PARALLEL STRANDED DNA DUPLEX WITH AN A-G MISMATCH JRNL TITL 2 BASE-PAIR: (CCATAATTTACC:CCTATGAAATCC) JRNL REF RECENT TRENDS IN 1 2004 JRNL REF 2 BIOPHYS.RES. JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 3.1 REMARK 3 AUTHORS : MSI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE RESULTING STRUCTURE WAS ENERGY REMARK 3 MINIMIZED USING THE NMR CONSTRAINTS REMARK 4 REMARK 4 1R2L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000020358. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 6.8; 5.5 REMARK 210 IONIC STRENGTH : 0.1 M NACL, 100% D2O; 0.1 M REMARK 210 NACL, 10% D2O, 90% H2O REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 5 MM CONCENTRATION OF EACH REMARK 210 STRAND TO FORM THE DUPLEX REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; JUMP RETURN REMARK 210 NOESY; E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : INSIGHT II REMARK 210 METHOD USED : FROM THE STRUCTURE 1JUU, THE REMARK 210 REQUIRED T BASE WAS REPLACED BY REMARK 210 G USING INSIGHTII. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY MINIMIZED USING THE NMR REMARK 210 CONSTRAINTS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR REMARK 210 TECHNIQUES 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT A 8 C5 DT A 8 C7 0.041 REMARK 500 DT A 9 C5 DT A 9 C7 0.040 REMARK 500 DT B 3 C5 DT B 3 C7 0.036 REMARK 500 DT B 10 C5 DT B 10 C7 0.039 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 DA A 3 C4 - C5 - C6 ANGL. DEV. = -4.2 DEGREES REMARK 500 DA A 3 C5 - C6 - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT A 4 N1 - C2 - O2 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT A 4 N3 - C2 - O2 ANGL. DEV. = -7.2 DEGREES REMARK 500 DT A 4 C6 - C5 - C7 ANGL. DEV. = -15.5 DEGREES REMARK 500 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA A 5 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = -6.7 DEGREES REMARK 500 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 6 C5 - C6 - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DA A 6 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 7 N3 - C2 - O2 ANGL. DEV. = -6.7 DEGREES REMARK 500 DT A 7 C4 - C5 - C7 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -6.1 DEGREES REMARK 500 DT A 8 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT A 9 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 10 C4 - C5 - C6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA A 10 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 10 N1 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 DC B 1 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC B 2 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT B 3 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT B 3 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 4 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 4 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 4 N1 - C6 - N6 ANGL. DEV. = -7.7 DEGREES REMARK 500 DT B 5 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 DT B 5 C4 - C5 - C7 ANGL. DEV. = 6.2 DEGREES REMARK 500 DT B 5 C6 - C5 - C7 ANGL. DEV. = -9.2 DEGREES REMARK 500 DG B 6 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 6 N3 - C2 - N2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG B 6 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 7 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA B 7 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA B 7 N1 - C6 - N6 ANGL. DEV. = -7.3 DEGREES REMARK 500 DA B 8 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 8 C5 - C6 - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA B 8 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 DA B 9 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 9 C5 - C6 - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA B 9 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT B 10 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 DC B 11 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC B 12 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC B 12 N3 - C4 - N4 ANGL. DEV. = -5.3 DEGREES 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 DA A 3 0.22 SIDE CHAIN REMARK 500 DT A 4 0.11 SIDE CHAIN REMARK 500 DA A 5 0.09 SIDE CHAIN REMARK 500 DA A 6 0.11 SIDE CHAIN REMARK 500 DT A 7 0.09 SIDE CHAIN REMARK 500 DC B 1 0.10 SIDE CHAIN REMARK 500 DC B 2 0.09 SIDE CHAIN REMARK 500 DT B 3 0.10 SIDE CHAIN REMARK 500 DA B 4 0.15 SIDE CHAIN REMARK 500 DT B 5 0.08 SIDE CHAIN REMARK 500 DA B 7 0.06 SIDE CHAIN REMARK 500 DA B 8 0.13 SIDE CHAIN REMARK 500 DC B 11 0.08 SIDE CHAIN REMARK 500 DC B 12 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JUU RELATED DB: PDB REMARK 900 NMR STRUCTURE OF A PARALLEL STRANDED DNA DUPLEX AT ATOMIC RESOLUTION DBREF 1R2L A 1 12 PDB 1R2L 1R2L 1 12 DBREF 1R2L B 1 12 PDB 1R2L 1R2L 1 12 SEQRES 1 A 12 DNR DNR DA DT DA DA DT DT DT DA DNR DNR SEQRES 1 B 12 DC DC DT DA DT DG DA DA DA DT DC DC MODRES 1R2L DNR A 1 DC MODRES 1R2L DNR A 2 DC MODRES 1R2L DNR A 11 DC MODRES 1R2L DNR A 12 DC HET DNR A 1 31 HET DNR A 2 31 HET DNR A 11 31 HET DNR A 12 31 HETNAM DNR 2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 DNR 4(C9 H15 N3 O7 P 1+) LINK O3' DNR A 1 P DNR A 2 1555 1555 1.62 LINK O3' DNR A 2 P DA A 3 1555 1555 1.62 LINK O3' DA A 10 P DNR A 11 1555 1555 1.62 LINK O3' DNR A 11 P DNR A 12 1555 1555 1.62 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
Complete list - 2 202 Bytes