10 20 30 40 50 60 70 80 2AQY - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 18-AUG-05 2AQY
TITLE (3+1) ASSEMBLY OF THREE HUMAN TELOMERIC DNA REPEATS INTO AN TITLE 2 ASYMMETRICAL DIMERIC G-QUADRUPLEX
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*(OIP) COMPND 3 P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3'; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: THREE REPEATS OF HUMAN TELOMERIC DNA; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: G2(OIP) MUTATION; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*TP*AP*GP*GP*GP*(DU))-3'; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: SINGLE REPEATS OF HUMAN TELOMERIC DNA; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES; COMPND 15 OTHER_DETAILS: T22(DU) MUTATION
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HOMO SOURCE 4 SAPIENS (HUMAN).; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES
KEYWDS (3+1) G-QUADRUPLEX ASSEMBLY, ASYMMETRIC DIMERIC G- KEYWDS 2 QUADRUPLEX, TELOMERIC DNA.
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR N.ZHANG,A.T.PHAN,D.J.PATEL
REVDAT 2 24-FEB-09 2AQY 1 VERSN REVDAT 1 07-MAR-06 2AQY 0
JRNL AUTH N.ZHANG,A.T.PHAN,D.J.PATEL JRNL TITL (3 + 1) ASSEMBLY OF THREE HUMAN TELOMERIC REPEATS JRNL TITL 2 INTO AN ASYMMETRIC DIMERIC G-QUADRUPLEX JRNL REF J.AM.CHEM.SOC. V. 127 17277 2005 JRNL REFN ISSN 0002-7863 JRNL PMID 16332077 JRNL DOI 10.1021/JA0543090
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ADDITIONAL COMMENTS ABOUT THE NMR REMARK 3 REFINEMENT CAN BE PLACED HERE, E.G. THE STRUCTURES ARE BASED REMARK 3 ON A TOTAL OF 517 RESTRAINTS, 466 ARE NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 22 DIHEDRAL ANGLE RESTRAINTS,51 DISTANCE REMARK 3 RESTRAINTS FROM HYDROGEN BONDS.
REMARK 4 REMARK 4 2AQY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-05. REMARK 100 THE RCSB ID CODE IS RCSB034210.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 273; 283 REMARK 210 PH : 6.8; 6.8; 6.8 REMARK 210 IONIC STRENGTH : 100MM NA+; 100MM NA+; 100MM REMARK 210 NA+ REMARK 210 PRESSURE : 1ATM; 1ATM; 1ATM REMARK 210 SAMPLE CONTENTS : 100MM NACL, 2MM PHOSPHATE REMARK 210 BUFFER, 90% H2O, 10% D2O; REMARK 210 100MM NACL, 2MM PHOSPHATE REMARK 210 BUFFER, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY 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 : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING MOLECULAR DYNAMICS REMARK 210 MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED,BACK CALCULATED DATA REMARK 210 AGREE WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM,STRUCTURES WITH REMARK 210 ACCEPTABLE COVALENT GEOMETRY, REMARK 210 STRUCTURES WITH FAVORABLE NON- REMARK 210 BOND ENERGY,STRUCTURES WITH REMARK 210 THE LEAST RESTRAINT REMARK 210 VIOLATIONS,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY,TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 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 DT A 4 C2' DT A 4 C1' 0.071 REMARK 500 1 DT A 4 C5 DT A 4 C7 0.052 REMARK 500 1 DT A 5 C5 DT A 5 C7 0.045 REMARK 500 1 DG A 9 C5' DG A 9 C4' 0.059 REMARK 500 1 DT A 10 C5 DT A 10 C7 0.068 REMARK 500 1 DT A 11 C5' DT A 11 C4' 0.044 REMARK 500 1 DT A 11 C5 DT A 11 C7 0.041 REMARK 500 1 DA A 12 C2' DA A 12 C1' 0.060 REMARK 500 1 DT A 16 C2' DT A 16 C1' 0.084 REMARK 500 1 DT A 16 C5 DT A 16 C7 0.054 REMARK 500 1 DT B 17 C5 DT B 17 C7 0.052 REMARK 500 1 DG B 20 C5' DG B 20 C4' 0.043 REMARK 500 1 DG B 20 C4' DG B 20 C3' -0.069 REMARK 500 1 DG B 20 C3' DG B 20 C2' -0.078 REMARK 500 1 DG B 21 C5' DG B 21 C4' 0.061 REMARK 500 2 DT A 4 C5 DT A 4 C7 0.056 REMARK 500 2 DT A 5 C5 DT A 5 C7 0.044 REMARK 500 2 DT A 10 C5 DT A 10 C7 0.067 REMARK 500 2 DT A 11 C5 DT A 11 C7 0.045 REMARK 500 2 DA A 12 C5' DA A 12 C4' 0.044 REMARK 500 2 DA A 12 C4' DA A 12 C3' 0.071 REMARK 500 2 DA A 12 C2' DA A 12 C1' 0.079 REMARK 500 2 DT A 16 C2' DT A 16 C1' 0.093 REMARK 500 2 DT A 16 C5 DT A 16 C7 0.056 REMARK 500 2 DT B 17 C5 DT B 17 C7 0.063 REMARK 500 2 DG B 20 C4' DG B 20 C3' -0.077 REMARK 500 2 DG B 20 C3' DG B 20 C2' -0.062 REMARK 500 3 DG A 3 C5' DG A 3 C4' 0.052 REMARK 500 3 DT A 4 C5 DT A 4 C7 0.053 REMARK 500 3 DT A 5 C5 DT A 5 C7 0.048 REMARK 500 3 DA A 6 C3' DA A 6 C2' -0.049 REMARK 500 3 DG A 9 C5' DG A 9 C4' 0.044 REMARK 500 3 DT A 10 C5 DT A 10 C7 0.069 REMARK 500 3 DT A 11 C5 DT A 11 C7 0.046 REMARK 500 3 DA A 12 C5' DA A 12 C4' 0.051 REMARK 500 3 DG A 13 C5' DG A 13 C4' 0.048 REMARK 500 3 DG A 14 C3' DG A 14 C2' -0.060 REMARK 500 3 DT A 16 C2' DT A 16 C1' 0.099 REMARK 500 3 DT A 16 C5 DT A 16 C7 0.054 REMARK 500 3 DT B 17 C5 DT B 17 C7 0.063 REMARK 500 3 DG B 20 C4' DG B 20 C3' -0.095 REMARK 500 3 DG B 20 C3' DG B 20 C2' -0.072 REMARK 500 4 DT A 4 C5 DT A 4 C7 0.042 REMARK 500 4 DT A 5 C5' DT A 5 C4' 0.045 REMARK 500 4 DT A 5 C5 DT A 5 C7 0.043 REMARK 500 4 DT A 10 C5 DT A 10 C7 0.069 REMARK 500 4 DT A 11 C5 DT A 11 C7 0.050 REMARK 500 4 DA A 12 C4' DA A 12 C3' 0.062 REMARK 500 4 DG A 14 C3' DG A 14 C2' -0.073 REMARK 500 4 DT A 16 C2' DT A 16 C1' 0.081 REMARK 500 REMARK 500 THIS ENTRY HAS 123 BOND DEVIATIONS. 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' - C4' - C3' ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DG A 3 C4' - C3' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DI A 2 C3' - O3' - P ANGL. DEV. = 16.0 DEGREES REMARK 500 1 DT A 4 N1 - C1' - C2' ANGL. DEV. = 12.2 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 5 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DG A 7 C4' - C3' - C2' ANGL. DEV. = -8.9 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 9 C4' - C3' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 9 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT A 10 C4' - C3' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DT A 10 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DG A 9 C3' - O3' - P ANGL. DEV. = 9.9 DEGREES REMARK 500 1 DT A 11 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 10 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DA A 12 C4' - C3' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DA A 12 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DA A 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 13 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG A 13 O4' - C1' - C2' ANGL. DEV. = -8.0 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 14 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DG A 14 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 13 C3' - O3' - P ANGL. DEV. = 11.6 DEGREES REMARK 500 1 DG A 15 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DG A 15 C3' - O3' - P ANGL. DEV. = 11.0 DEGREES REMARK 500 1 DT B 17 C3' - C2' - C1' ANGL. DEV. = -9.8 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT B 17 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 1 DG B 19 C4' - C3' - C2' ANGL. DEV. = -9.0 DEGREES REMARK 500 1 DG B 19 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DA B 18 C3' - O3' - P ANGL. DEV. = 15.8 DEGREES REMARK 500 1 DG B 20 C5' - C4' - C3' ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DG B 20 C4' - C3' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DG B 20 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG B 21 O4' - C4' - C3' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG B 21 C4' - C3' - C2' ANGL. DEV. = -10.7 DEGREES REMARK 500 1 DG B 21 O4' - C1' - C2' ANGL. DEV. = -10.8 DEGREES REMARK 500 1 DG B 21 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DU B 22 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DU B 22 O4' - C1' - N1 ANGL. DEV. = 8.6 DEGREES REMARK 500 2 DG A 1 O4' - C4' - C3' ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG A 1 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 2 DG A 3 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DG A 3 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 403 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
DBREF 2AQY A 1 16 PDB 2AQY 2AQY 1 16 DBREF 2AQY B 17 22 PDB 2AQY 2AQY 17 22
SEQRES 1 A 16 DG DI DG DT DT DA DG DG DG DT DT DA DG SEQRES 2 A 16 DG DG DT SEQRES 1 B 6 DT DA DG DG DG DU
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