Header list of 1u64.pdb file
Complete list - 2 20 Bytes
HEADER DNA 29-JUL-04 1U64
TITLE THE SOLUTION STRUCTURE OF D(G3T4G4)2
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: G-RICH DNA OLIGOMER
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: OLIGOMER HAS BEEN PREPARED ON SOLID STATE SUPPORT
SOURCE 4 USING PHOSPHORAMIDITE CHEMISTRY
KEYWDS G-QUADRUPLEX, MONOVALENT CATIONS, DNA
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR P.SKET,M.CRNUGELJ,J.PLAVEC
REVDAT 3 02-MAR-22 1U64 1 REMARK
REVDAT 2 24-FEB-09 1U64 1 VERSN
REVDAT 1 26-OCT-04 1U64 0
JRNL AUTH P.SKET,M.CRNUGELJ,J.PLAVEC
JRNL TITL D(G3T4G4) FORMS UNUSUAL DIMERIC G-QUADRUPLEX STRUCTURE WITH
JRNL TITL 2 THE SAME GENERAL FOLD IN THE PRESENCE OF K+, NA+ OR NH4+
JRNL TITL 3 IONS.
JRNL REF BIOORG.MED.CHEM. V. 12 5735 2004
JRNL REFN ISSN 0968-0896
JRNL PMID 15498650
JRNL DOI 10.1016/J.BMC.2004.08.009
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 6.1B, AMBER 7
REMARK 3 AUTHORS : VARIAN (VNMR), KOLLMAN, AT ALL (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: 414 NOE-DERIVED DISTANCE RESTRAINTS
REMARK 3 ASSOCIATED WITH THE NONEXCHANGEABLE AND EXCHANGEABLE PROTONS; 24
REMARK 3 HYDROGEN-BOND RESTRAINTS; 66 TORSION ANGLE RESTRAINTS FOR SUGAR
REMARK 3 MOIETIES. FOR EACH OF FIVE DIFFERENT INITIAL STRUCTURES TEN
REMARK 3 SIMULATED ANNEALING CALCULATIONS AT 700 K WITH NMR RESTRAINTS
REMARK 3 USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL WERE
REMARK 3 PERFORMED FOR 60 PS. THE RESULTING STRUCTURES WERE SUBJECTED TO
REMARK 3 ENERGY MINIMIZATION
REMARK 4
REMARK 4 1U64 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-04.
REMARK 100 THE DEPOSITION ID IS D_1000023292.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278; 298
REMARK 210 PH : 5.5; 5.5
REMARK 210 IONIC STRENGTH : 15MM KCL; 15MM KCL
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 4MM DG3T4G4 PER STRAND; 90% H2O,
REMARK 210 10% D2O, 15MM KCL; PH 5.5
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; PE-COSY; 2D TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 2000
REMARK 210 METHOD USED : SIMULATED ANNEALING, ENERGY
REMARK 210 MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8
REMARK 210 CONFORMERS, SELECTION CRITERIA : 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 : 5
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR 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 1 DG B 20 C6 DG B 20 N1 -0.043
REMARK 500 2 DG B 20 C6 DG B 20 N1 -0.044
REMARK 500 3 DG B 20 C6 DG B 20 N1 -0.043
REMARK 500 4 DG B 20 C6 DG B 20 N1 -0.043
REMARK 500 5 DG B 20 C6 DG B 20 N1 -0.042
REMARK 500 6 DG B 20 C6 DG B 20 N1 -0.044
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 DG A 1 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 1 DG A 1 N3 - C4 - C5 ANGL. DEV. = -3.5 DEGREES
REMARK 500 1 DG A 1 N3 - C4 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DG A 2 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 DT A 6 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 1 DT A 7 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES
REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES
REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES
REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DG B 12 N3 - C2 - N2 ANGL. DEV. = -5.8 DEGREES
REMARK 500 1 DG B 13 N3 - C2 - N2 ANGL. DEV. = -6.3 DEGREES
REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES
REMARK 500 1 DT B 16 C4 - C5 - C7 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 DT B 16 C6 - C5 - C7 ANGL. DEV. = -6.7 DEGREES
REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 10.1 DEGREES
REMARK 500 1 DT B 17 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES
REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 DT B 18 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DG B 19 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DG B 19 O4' - C1' - N9 ANGL. DEV. = 12.9 DEGREES
REMARK 500 1 DG B 19 C6 - N1 - C2 ANGL. DEV. = -3.9 DEGREES
REMARK 500 1 DG B 19 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 DG B 19 N1 - C2 - N2 ANGL. DEV. = 6.1 DEGREES
REMARK 500 1 DG B 19 N3 - C2 - N2 ANGL. DEV. = -8.7 DEGREES
REMARK 500 1 DG B 19 C5 - C6 - O6 ANGL. DEV. = -4.9 DEGREES
REMARK 500 1 DG B 20 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES
REMARK 500 1 DG B 20 O4' - C1' - N9 ANGL. DEV. = 10.7 DEGREES
REMARK 500 1 DG B 20 N3 - C4 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DG B 20 N1 - C2 - N2 ANGL. DEV. = -9.4 DEGREES
REMARK 500 1 DG B 20 N3 - C2 - N2 ANGL. DEV. = 7.7 DEGREES
REMARK 500 1 DG B 20 N1 - C6 - O6 ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DG B 21 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 DG B 22 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 12.5 DEGREES
REMARK 500 1 DG B 22 C5 - C6 - O6 ANGL. DEV. = -4.1 DEGREES
REMARK 500 2 DG A 1 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 2 DG A 1 N3 - C4 - C5 ANGL. DEV. = -3.5 DEGREES
REMARK 500 2 DG A 1 N3 - C4 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 2 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 346 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1U64 A 1 11 PDB 1U64 1U64 1 11
DBREF 1U64 B 12 22 PDB 1U64 1U64 12 22
SEQRES 1 A 11 DG DG DG DT DT DT DT DG DG DG DG
SEQRES 1 B 11 DG DG DG DT DT DT DT DG DG 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 - 2 20 Bytes