Header list of 1emq.pdb file
Complete list - 16 202 Bytes
HEADER DNA 17-MAR-00 1EMQ
TITLE NMR OBSERVATION OF T-TETRADS IN A PARALLEL STRANDED DNA QUADRUPLEX
TITLE 2 FORMED BY SACCHAROMYCES CEREVISIAE TELOMERE REPEATS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3');
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 FRAGMENT: YEAST TELOMERE REPEATS;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: ONLY TWO REPEATS AND ONE C AT 3' END
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS TWO REPEATS OF SACCHAROMYCES
SOURCE 4 CEREVISIAE TELOMERE SEQUENCE
KEYWDS T-TETRAD, G-QUADRUPLEX, TELOMERE, YEAST, SACCHAROMYCES CEREVISIAE,
KEYWDS 2 DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR R.V.HOSUR,P.K.PATEL
REVDAT 4 16-FEB-22 1EMQ 1 REMARK
REVDAT 3 24-FEB-09 1EMQ 1 VERSN
REVDAT 2 01-APR-03 1EMQ 1 JRNL
REVDAT 1 04-APR-00 1EMQ 0
JRNL AUTH P.K.PATEL,R.V.HOSUR
JRNL TITL NMR OBSERVATION OF T-TETRADS IN A PARALLEL STRANDED DNA
JRNL TITL 2 QUADRUPLEX FORMED BY SACCHAROMYCES CEREVISIAE TELOMERE
JRNL TITL 3 REPEATS.
JRNL REF NUCLEIC ACIDS RES. V. 27 2457 1999
JRNL REFN ISSN 0305-1048
JRNL PMID 10352174
JRNL DOI 10.1093/NAR/27.12.2457
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 230, IRMA 2.3
REMARK 3 AUTHORS : MSI (FELIX), MSI (IRMA)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 234 NOES CONSTARINT. 20
REMARK 3 HYDROGEN BONDS CONSTRAINTS. 8 CONVERGANT STRUCTURE AFTER IRMA
REMARK 3 REFINEMENT. R1 FACTOR = 0.31-0.33. R.M.S.D.S FROM AVERAGE
REMARK 3 STRUCTURE 0.2-0.4. NIL VIOLATION EXCEEDING 0.2 A.
REMARK 4
REMARK 4 1EMQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-00.
REMARK 100 THE DEPOSITION ID IS D_1000010727.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 1-2 MM DNA IN 0.6
REMARK 210 ML(90%H20/10%D2O) HAVING 10 MM
REMARK 210 POTASSIUM PHOSPHATE, 0.2 MM EDTA,
REMARK 210 PH 7.0 AND 100 MM KCL; 1-2 MM
REMARK 210 DNA IN 0.6 ML(D2O) HAVING 10 MM
REMARK 210 POTASSIUM PHOSPHATE, 0.2 MM EDTA,
REMARK 210 PH 7.0 AND 100 MM KCL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; E-COSY; 2D-TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS; AMX
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 6.1, DISCOVER 3.1
REMARK 210 METHOD USED : AN INITIAL MODEL OF QUADRUPLEX
REMARK 210 WAS GENERATED ON A IRIS
REMARK 210 WORKASTATION.ENERGY MINIMIZATION
REMARK 210 BY STEEPEST DESCENT FOLLOWED BY
REMARK 210 CONJUGATE GRADIENTS METHODS WAS
REMARK 210 DONE USING AMBER FORCE FIELD.
REMARK 210 CONFORMATIONAL SEARCH FOR THE
REMARK 210 CQUADRUPLEX WAS PERFORMED BY
REMARK 210 SIMULATED ANNEALING-REASTARINED
REMARK 210 MOLECULAR DYNAMICS USING AMBER
REMARK 210 FORCEFIELD. RELAXATION MATRIX
REMARK 210 REFINEMENT WAS PERFORMED.
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 8
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: 0-70 C TEMPERATURE DEPENDENT ONE DIMENSIONAL SPECTRA. PH
REMARK 210 DEPENDENT SPECTRA.
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: TETRAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D
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 DT A 101 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DT A 101 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES
REMARK 500 DT A 104 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES
REMARK 500 DT A 104 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES
REMARK 500 DG A 106 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DG A 106 N3 - C2 - N2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 DC A 107 N3 - C4 - N4 ANGL. DEV. = -5.4 DEGREES
REMARK 500 DT B 201 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT B 201 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DT B 204 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DT B 204 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DG B 206 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DC B 207 N3 - C4 - N4 ANGL. DEV. = -5.0 DEGREES
REMARK 500 DT C 401 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DT C 401 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 DT C 401 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DT C 404 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES
REMARK 500 DT C 404 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DT C 404 N1 - C2 - N3 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DT C 404 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES
REMARK 500 DG C 406 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DC C 407 N3 - C4 - N4 ANGL. DEV. = -4.5 DEGREES
REMARK 500 DT D 301 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DT D 301 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES
REMARK 500 DT D 304 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 DT D 304 C6 - C5 - C7 ANGL. DEV. = -5.0 DEGREES
REMARK 500 DG D 306 O4' - C1' - N9 ANGL. DEV. = 2.6 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 DG A 102 0.09 SIDE CHAIN
REMARK 500 DT A 104 0.06 SIDE CHAIN
REMARK 500 DC A 107 0.08 SIDE CHAIN
REMARK 500 DG B 202 0.09 SIDE CHAIN
REMARK 500 DT B 204 0.08 SIDE CHAIN
REMARK 500 DC B 207 0.09 SIDE CHAIN
REMARK 500 DG C 402 0.13 SIDE CHAIN
REMARK 500 DG C 406 0.05 SIDE CHAIN
REMARK 500 DC C 407 0.14 SIDE CHAIN
REMARK 500 DG D 302 0.09 SIDE CHAIN
REMARK 500 DT D 304 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1EMQ A 101 107 PDB 1EMQ 1EMQ 101 107
DBREF 1EMQ B 201 207 PDB 1EMQ 1EMQ 201 207
DBREF 1EMQ C 401 407 PDB 1EMQ 1EMQ 401 407
DBREF 1EMQ D 301 307 PDB 1EMQ 1EMQ 301 307
SEQRES 1 A 7 DT DG DG DT DG DG DC
SEQRES 1 B 7 DT DG DG DT DG DG DC
SEQRES 1 C 7 DT DG DG DT DG DG DC
SEQRES 1 D 7 DT DG DG DT DG DG DC
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 - 16 202 Bytes