Header list of 1i34.pdb file
Complete list - 23 20 Bytes
HEADER DNA 12-FEB-01 1I34
TITLE SOLUTION DNA QUADRUPLEX WITH DOUBLE CHAIN REVERSAL LOOP AND TWO
TITLE 2 DIAGONAL LOOPS CONNECTING GGGG TETRADS FLANKED BY G-(T-T) TRIAD AND
TITLE 3 T-T-T TRIPLE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*CP*AP*GP*GP*GP*TP*TP*TP*TP*GP
COMPND 3 *GP*T)-3';
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS DIAGONAL LOOP, DOUBLE CHAIN REVERSAL LOOP, G(SYN)-G(SYN)-G(ANTI)-
KEYWDS 2 G(ANTI) TETRADS, G-(T-T) TRIAD, UNIMOLECULAR G-QUADRUPLEX, T-T-T
KEYWDS 3 TRIPLE, DEOXYRIBONUCLEIC ACID, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR V.KURYAVYI,A.MAJUMDAR,A.SHALLOP,N.CHERNICHENKO,E.SKRIPKIN,R.JONES,
AUTHOR 2 D.J.PATEL
REVDAT 3 23-FEB-22 1I34 1 REMARK
REVDAT 2 24-FEB-09 1I34 1 VERSN
REVDAT 1 27-JUN-01 1I34 0
JRNL AUTH V.KURYAVYI,A.MAJUMDAR,A.SHALLOP,N.CHERNICHENKO,E.SKRIPKIN,
JRNL AUTH 2 R.JONES,D.J.PATEL
JRNL TITL A DOUBLE CHAIN REVERSAL LOOP AND TWO DIAGONAL LOOPS DEFINE
JRNL TITL 2 THE ARCHITECTURE OF A UNIMOLECULAR DNA QUADRUPLEX CONTAINING
JRNL TITL 3 A PAIR OF STACKED G(SYN)-G(SYN)-G(ANTI)-G(ANTI) TETRADS
JRNL TITL 4 FLANKED BY A G-(T-T) TRIAD AND A T-T-T TRIPLE.
JRNL REF J.MOL.BIOL. V. 310 181 2001
JRNL REFN ISSN 0022-2836
JRNL PMID 11419945
JRNL DOI 10.1006/JMBI.2001.4759
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER, A.T. ET AL.
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. FOURTEEN STRUCTURES WERE
REMARK 3 IDENTIFIED BASED ON THE CRITERION ACCEPTABLE COVALENT GEOMETRY,
REMARK 3 LOW DISTANCE RESTRAINT VIOLATIONS AND FAVORABLE NON-BONDED
REMARK 3 ENERGY. THE VARIATION IN ENERGIES WITHIN THIS SUBSET OF
REMARK 3 STRUCTURES WAS 46 KCAL/MOL AND WAS SEPARATED FROM THE REMAINING
REMARK 3 STRUCTURES BY A GAP OF 200 KCAL/MOL. THE TEN BEST STRUCTURES
REMARK 3 FROM THIS SUBSET OF FOURTEEN 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. SOFT PLANARITY RESTRAINTS WERE SWITCHED OFF BEFORE
REMARK 3 THE EQUILIBRATION STAGE.THE COORDINATES SAVED EVERY 0.5 PS
REMARK 3 DURING THE LAST 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE
REMARK 3 WAS SUBJECTED TO 3000 STEPS OF MINIMIZATION. THE DIHEDRAL ANGLE
REMARK 3 RESTRAINTS AND HYDROGEN BONDS OF THE GGGG TETRADS WERE
REMARK 3 MAINTAINED THROUGHOUT. THE OBTAINED STRUCTURES WERE SUBJECTED TO
REMARK 3 RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY VOLUMES
REMARK 3 WERE USED AS RESTRAINTS AND NON-EXCHANGEABLE PROTON DISTANCE
REMARK 3 RESTRAINTS WITH THE SCALE FACTOR OF 0.1 RELATIVE TO THE
REMARK 3 INTENSITY RESTRAINTS. SOFT PLANARITY RESTRAINTS MAINTAINED
REMARK 3 DURING RELAXATION REFINEMENTS WERE SWITCHED OFF BEFORE THE FINAL
REMARK 3 STEPS OF MINIMIZATION. THE RELAXATION PATHWAYS WERE CALCULATED
REMARK 3 USING CUTOFF 4.5 ANGSTROM AND 7.91 NS ISOTROPIC CORRELATION
REMARK 3 TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. VALUE OF 1.07 A.
REMARK 4
REMARK 4 1I34 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-01.
REMARK 100 THE DEPOSITION ID IS D_1000012843.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278.00
REMARK 210 PH : 6.80
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 10MM DNA (SINGLE STRANDS); 5MM
REMARK 210 SODIUM PHOSPHATE BUFFER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF-COSY; COSY-45
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 6.0, FELIX 2000, INSIGHT II
REMARK 210 2000
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 : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : 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,BACK-
REMARK 210 CALCULATED DATA AGREE WITH
REMARK 210 EXPERIMENTAL NOESY SPECTRUM
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3
REMARK 210
REMARK 210 REMARK: SITE-SPECIFIC SUBSTITUTED SAMPLES CONTAINING 8BR-A,8BR
REMARK 210 -G,DU,5BR-DU, 2,6A, I, 5ME-C ANALOGS AND SITE-SPECIFIC OR
REMARK 210 UNIFORMLY 13C AND 15N LABELED SAMPLES HAVE BEEN USED
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: 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.0 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. = 3.5 DEGREES
REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DG A 13 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DG A 13 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES
REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DG A 18 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 DG A 18 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DG A 19 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DG A 19 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 2 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 2 DG A 7 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 378 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1I34 A 1 20 PDB 1I34 1I34 1 20
SEQRES 1 A 20 DG DG DT DT DT DT DG DG DC DA DG DG DG
SEQRES 2 A 20 DT DT DT DT DG DG DT
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 - 23 20 Bytes