Header list of 1d6d.pdb file
Complete list - 16 20 Bytes
HEADER DNA 13-OCT-99 1D6D
TITLE SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS INTERDIGITATED
TITLE 2 BETWEEN A-T BASE PAIRS AND GGGG TETRADS; NMR, 8 STRUCT.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*AP*AP*GP*GP*TP*TP*TP*TP*AP*AP*GP*G)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMAN TELOMERIC
SOURCE 4 DNA, HUMAN IG SUPERFAMILY CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED PROTEIN
SOURCE 5 GENE AND 16S RRNA OF HENRICA NIPONICA.
KEYWDS MULTI-STRANDED DNA ARCHITECTURE, G-TETRAD, T-(A-A) TRIAD, A(SYN)-
KEYWDS 2 A(ANTI) PLATFORM, ZIPPER MOTIF, BASE-SUGAR STACKING, DNA
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR V.V.KURYAVYI,A.KETTANI,W.WANG,R.JONES,D.J.PATEL
REVDAT 5 16-FEB-22 1D6D 1 REMARK
REVDAT 4 24-FEB-09 1D6D 1 VERSN
REVDAT 3 01-APR-03 1D6D 1 JRNL
REVDAT 2 03-FEB-00 1D6D 1 JRNL
REVDAT 1 17-JAN-00 1D6D 0
JRNL AUTH V.KURYAVYI,A.KETTANI,W.WANG,R.JONES,D.J.PATEL
JRNL TITL A DIAMOND-SHAPED ZIPPER-LIKE DNA ARCHITECTURE CONTAINING
JRNL TITL 2 TRIADS SANDWICHED BETWEEN MISMATCHES AND TETRADS.
JRNL REF J.MOL.BIOL. V. 295 455 2000
JRNL REFN ISSN 0022-2836
JRNL PMID 10623538
JRNL DOI 10.1006/JMBI.1999.3345
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : A.BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 100 INITIAL DNA STRUCTURES
REMARK 3 WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY
REMARK 3 PROTOCOL OF X-PLOR WITH THE DISTANCE RESTRAINTS OBTAINED
REMARK 3 EXPERIMENTALLY SPECIFIED AS NOE WITH THE "SUM" AVERAGING
REMARK 3 OPTION.TEN BEST STRUCTURES SELECTED ON THE BASIS OF GOOD
REMARK 3 COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND
REMARK 3 FAVOURABLE NON-BONDED ENERGY WERE FURTHER OPTIMIZED WITH
REMARK 3 RESTRAINED MOLECULAR DYNAMICS, MOLECULAR MECHANICS AND
REMARK 3 RELAXATION MATRIX INTENSITY REFINEMENT.THE PROTOCOLS ARE AS
REMARK 3 FOLLOWS. THE DYNAMICS WAS INITIATED AT 300K AND THE TEMPERATURE
REMARK 3 WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS THE FORCE
REMARK 3 CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN THE
REMARK 3 PROPORTION 1: 4:8 FOR THREE CLASSES OF NOE: EXCHANGEABLE,
REMARK 3 NONEXCHANGEABLE AND HYDROGEN BONDS, RESP. THE STRUCTURES WERE
REMARK 3 THEN SLOWLY COOLED TO 300K IN 2.8 PS AND EQUILIBRATED AT 300K
REMARK 3 FOR 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST
REMARK 3 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO
REMARK 3 3000 STEPS OF MINIMIZATION. THE HYDROGEN BONDS OF THE GGGG
REMARK 3 TETRADS, AND NON- CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE
REMARK 3 MAINTAINED THROUGHOUT. THE OBTAINED STRUCTURES WERE SUBJECTED TO
REMARK 3 RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSIY VOLUMES
REMARK 3 WERE USED AS RESTRAINTS. THE RELAXATION PATHWAYS WERE CALCULATED
REMARK 3 USING CUTOFF 4.5 ANGSTROM AND 7.25 NS ISOTROPIC CORRELATION
REMARK 3 TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. VALUE OF 1.16 A.
REMARK 3 IN TWO STRUCTURES THE RESIDUES T6 AND T8 DEVIATE FROM TWO
REMARK 3 CLUSTERS FORMED BY REST OF 8 STRUCTURES, AND THESE TWO
REMARK 3 STRUCTURES WERE OMITTED FROM DEPOSITION.
REMARK 4
REMARK 4 1D6D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-99.
REMARK 100 THE DEPOSITION ID IS D_1000009829.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278
REMARK 210 PH : 6.9
REMARK 210 IONIC STRENGTH : 150MM NACL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 5-10 MM DNA (SINGLE STRANDS);
REMARK 210 5MM SODIUM PHOSPHATE BUFFER; 5-
REMARK 210 10 MM DNA (SINGLE STRANDS); 5MM
REMARK 210 SODIUM PHOSPHATE BUFFER; 5-10 MM
REMARK 210 DNA (SINGLE STRANDS); 5MM SODIUM
REMARK 210 PHOSPHATE BUFFER;SINGLE BASE
REMARK 210 SUBSTITUTED FOR 8-BRDG, 8-BRDA,
REMARK 210 DU, 5BRDU OR 2,6DA.; 5-10 MM DNA
REMARK 210 (SINGLE STRANDS); 5MM SODIUM
REMARK 210 PHOSPHATE BUFFER;SINGLE BASE
REMARK 210 SUBSTITUTED FOR 8-BRDG, 8-BRDA,
REMARK 210 DU, 5BRDU OR 2,6DA.
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF-COSY; COSY-45;
REMARK 210 1H-31P COSY ON ORIGINAL AND SITE-
REMARK 210 SPECIFIC SUBSTITUTED SAMPLES
REMARK 210 CONTAINING 8BR-A, 8BR-G,DU,5BR-
REMARK 210 DU,2,6-DA ANALOGS.
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : VARIAN UNITY INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 5.0, FELIX 97.0, X-PLOR 3.1
REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED
REMARK 210 ANNEALING, DISTANCE RESTRAINED
REMARK 210 MOLECULAR DYNAMICS REFINEMENT
REMARK 210 AND RELAXATION MATRIX INTENSITY
REMARK 210 REFINEMENT
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8
REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH
REMARK 210 EXPERIMENTAL NOESY SPECTRUM,
REMARK 210 STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY,STRUCTURES
REMARK 210 WITH FAVORABLE NON-BOND ENERGY,
REMARK 210 STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3
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: 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
REMARK 500 REMARK: NULL
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 1 DA A 10 C5' DA A 10 C4' 0.045
REMARK 500 1 DA B 10 C5' DA B 10 C4' 0.045
REMARK 500 2 DA A 10 C5' DA A 10 C4' 0.048
REMARK 500 2 DA B 10 C5' DA B 10 C4' 0.048
REMARK 500 3 DA A 10 C5' DA A 10 C4' 0.042
REMARK 500 4 DA A 10 C5' DA A 10 C4' 0.045
REMARK 500 4 DA B 10 C5' DA B 10 C4' 0.046
REMARK 500 5 DA A 10 C5' DA A 10 C4' 0.050
REMARK 500 5 DA B 10 C5' DA B 10 C4' 0.050
REMARK 500 6 DA A 10 C5' DA A 10 C4' 0.042
REMARK 500 6 DA B 10 C5' DA B 10 C4' 0.042
REMARK 500 8 DA A 10 C5' DA A 10 C4' 0.054
REMARK 500 8 DA B 10 C5' DA B 10 C4' 0.054
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 1 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DA A 1 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 DA A 9 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES
REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DG A 12 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 1 DA B 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DA B 1 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DA B 2 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DA B 2 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 DG B 3 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DG B 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DG B 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 1 DG B 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DG B 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DG B 4 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 1 DT B 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT B 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DA B 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 DA B 9 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DA B 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DA B 10 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DG B 11 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DG B 11 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES
REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG B 12 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES
REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DA A 1 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 386 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1D6D A 1 12 PDB 1D6D 1D6D 1 12
DBREF 1D6D B 1 12 PDB 1D6D 1D6D 1 12
SEQRES 1 A 12 DA DA DG DG DT DT DT DT DA DA DG DG
SEQRES 1 B 12 DA DA DG DG DT DT DT DT DA DA DG DG
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 - 16 20 Bytes