Header list of 214d.pdb file
Complete list - r 9 2 Bytes
HEADER DNA 07-JUL-95 214D TITLE THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O- TITLE 2 METHYL-BETA-D-ARAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*GP*CP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 2'-OCH3-ARAT DNA, TAXA; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*GP*CP*TP*AP*(T41)P*AP*TP*GP*CP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 SYNONYM: 2'-OCH3-ARAT DNA, TAXA; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, DOUBLE HELIX EXPDTA SOLUTION NMR NUMMDL 40 AUTHOR C.H.GOTFREDSEN,H.P.SPIELMANN,J.WENGEL,J.P.JACOBSEN REVDAT 3 09-MAR-22 214D 1 REMARK LINK REVDAT 2 24-FEB-09 214D 1 VERSN REVDAT 1 15-OCT-95 214D 0 JRNL AUTH C.H.GOTFREDSEN,H.P.SPIELMANN,J.WENGEL,J.P.JACOBSEN JRNL TITL STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE JRNL TITL 2 2'-O-METHYL-BETA-D-ARAT: COMBINED USE OF NMR, RESTRAINED JRNL TITL 3 MOLECULAR DYNAMICS, AND FULL RELAXATION MATRIX REFINEMENT. JRNL REF BIOCONJUG.CHEM. V. 7 680 1996 JRNL REFN ISSN 1043-1802 JRNL PMID 8950487 JRNL DOI 10.1021/BC960061F REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT WAS BASED ON TOTAL REMARK 3 RELAXATION MATRIX ANALYSIS OF THE NOESY CROSS PEAK INTENSITIES REMARK 3 USING THE PROGRAM MARDIGRAS. IMPROVED PROCEDURES TO CONSIDER THE REMARK 3 EXPERIMENTAL "NOISE" IN NOESY SPECTRA DURING THESE CALCULATIONS REMARK 3 HAVE BEEN EMPLOYED (H.LIU, H.P.SPIELMANN, D.E.WEMMER, AND REMARK 3 T.L.JAMES (1995) IN PREPARATION). THE NOE-DERIVED DISTANCE REMARK 3 RESTRAINTS WERE APPLIED IN RESTRAINED MOLECULAR DYNAMICS REMARK 3 CALCULATIONS WITH AMBER FORCEFIELD POTENTIALS AS IMPLEMENTED IN REMARK 3 DISCOVER. THE ROOT-MEAN-SQUARE (RMS) DEVIATION OF THE REMARK 3 COORDINATES FOR THE FORTY STRUCTURES OF THE DUPLEX WAS 0.82 REMARK 3 ANGSTROMS. REMARK 4 REMARK 4 214D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177575. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: 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 1 DA A 4 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA A 4 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DA A 4 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DA A 4 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DA A 4 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DA A 4 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DA A 4 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DA A 4 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 3 DA A 4 O4' - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 3 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 3 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DA A 4 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 4 DA A 4 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 4 DA A 4 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 4 DA A 6 C3' - C2' - C1' ANGL. DEV. = 7.3 DEGREES REMARK 500 4 DA A 6 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 4 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 5 DA A 4 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 5 DA A 4 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 5 DA A 4 O4' - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 5 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 5 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 6 DA A 4 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 6 DA A 4 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 6 DA A 4 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 6 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 6 DA B 16 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 6 DA B 16 C4' - C3' - C2' ANGL. DEV. = 5.5 DEGREES REMARK 500 6 DA B 16 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 6 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 7 DA A 4 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 7 DA A 4 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 7 DA A 4 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 7 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 7 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 8 DA A 4 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 8 DA A 4 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 8 DA A 4 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 8 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 8 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 9 DA A 4 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 9 DA A 4 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 9 DA A 4 O4' - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 209 ANGLE DEVIATIONS. 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 DG A 2 0.07 SIDE CHAIN REMARK 500 1 DA A 6 0.08 SIDE CHAIN REMARK 500 1 DC A 10 0.07 SIDE CHAIN REMARK 500 1 DA B 18 0.05 SIDE CHAIN REMARK 500 2 DG A 2 0.07 SIDE CHAIN REMARK 500 2 DA A 6 0.08 SIDE CHAIN REMARK 500 2 DC A 10 0.07 SIDE CHAIN REMARK 500 3 DG A 2 0.07 SIDE CHAIN REMARK 500 3 DA A 6 0.08 SIDE CHAIN REMARK 500 3 DC A 10 0.07 SIDE CHAIN REMARK 500 3 DA B 18 0.06 SIDE CHAIN REMARK 500 4 DG A 2 0.07 SIDE CHAIN REMARK 500 4 DA A 6 0.08 SIDE CHAIN REMARK 500 4 DT A 7 0.08 SIDE CHAIN REMARK 500 4 DC A 10 0.08 SIDE CHAIN REMARK 500 4 DA B 18 0.05 SIDE CHAIN REMARK 500 5 DG A 2 0.07 SIDE CHAIN REMARK 500 5 DA A 6 0.08 SIDE CHAIN REMARK 500 5 DC A 10 0.07 SIDE CHAIN REMARK 500 5 DA B 18 0.06 SIDE CHAIN REMARK 500 6 DG A 2 0.07 SIDE CHAIN REMARK 500 6 DA A 6 0.09 SIDE CHAIN REMARK 500 6 DC A 10 0.06 SIDE CHAIN REMARK 500 6 DA B 16 0.08 SIDE CHAIN REMARK 500 6 DA B 18 0.06 SIDE CHAIN REMARK 500 7 DG A 2 0.07 SIDE CHAIN REMARK 500 7 DA A 6 0.08 SIDE CHAIN REMARK 500 7 DC A 10 0.07 SIDE CHAIN REMARK 500 8 DG A 2 0.07 SIDE CHAIN REMARK 500 8 DA A 6 0.08 SIDE CHAIN REMARK 500 8 DC A 10 0.07 SIDE CHAIN REMARK 500 8 DA B 18 0.05 SIDE CHAIN REMARK 500 9 DG A 2 0.07 SIDE CHAIN REMARK 500 9 DA A 6 0.08 SIDE CHAIN REMARK 500 9 DC A 10 0.07 SIDE CHAIN REMARK 500 9 DA B 18 0.06 SIDE CHAIN REMARK 500 10 DG A 2 0.07 SIDE CHAIN REMARK 500 10 DA A 6 0.08 SIDE CHAIN REMARK 500 10 DC A 10 0.07 SIDE CHAIN REMARK 500 10 DA B 18 0.06 SIDE CHAIN REMARK 500 11 DG A 2 0.07 SIDE CHAIN REMARK 500 11 DA A 6 0.08 SIDE CHAIN REMARK 500 11 DC A 10 0.07 SIDE CHAIN REMARK 500 11 DA B 18 0.05 SIDE CHAIN REMARK 500 12 DG A 2 0.07 SIDE CHAIN REMARK 500 12 DA A 6 0.08 SIDE CHAIN REMARK 500 12 DC A 10 0.07 SIDE CHAIN REMARK 500 12 DA B 18 0.06 SIDE CHAIN REMARK 500 13 DG A 2 0.07 SIDE CHAIN REMARK 500 13 DA A 6 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 157 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 214D A 1 11 PDB 214D 214D 1 11 DBREF 214D B 12 22 PDB 214D 214D 12 22 SEQRES 1 A 11 DC DG DC DA DT DA DT DA DG DC DC SEQRES 1 B 11 DG DG DC DT DA T41 DA DT DG DC DG MODRES 214D T41 B 17 T HET T41 B 17 36 HETNAM T41 1-(2-O-METHYL-BETA-D-ARABINOFURANOSYL)THYMIDINE 5'- HETNAM 2 T41 MONOPHOSPHATE FORMUL 2 T41 C11 H17 N2 O9 P LINK O3' DA B 16 P T41 B 17 1555 1555 1.62 LINK O3' T41 B 17 P DA B 18 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 MODEL 1
Complete list - r 9 2 Bytes