PDB Short entry for 2AQY HEADER 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)P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)- COMPND 3 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 SAPIENS SOURCE 4 (HUMAN).; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS (3+1) G-QUADRUPLEX ASSEMBLY, ASYMMETRIC DIMERIC G-QUADRUPLEX, KEYWDS 2 TELOMERIC DNA., DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.ZHANG,A.T.PHAN,D.J.PATEL REVDAT 3 09-MAR-22 2AQY 1 REMARK 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 INTO AN JRNL TITL 2 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 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: REMARK 3 ADDITIONAL COMMENTS ABOUT THE NMR REFINEMENT CAN BE PLACED HERE, REMARK 3 E.G. REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 517 RESTRAINTS, 466 ARE NOE- REMARK 3 DERIVED REMARK 3 DISTANCE CONSTRAINTS, 22 DIHEDRAL ANGLE RESTRAINTS,51 DISTANCE REMARK 3 RESTRAINTS REMARK 3 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 DEPOSITION ID IS D_1000034210. 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 NA+ REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 100MM NACL, 2MM PHOSPHATE REMARK 210 BUFFER, 90% H2O, 10% D2O; 100MM REMARK 210 NACL, 2MM PHOSPHATE BUFFER, 100% REMARK 210 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 THE REMARK 210 LEAST RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 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 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 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 DI A 2 C3' - O3' - P ANGL. DEV. = 16.1 DEGREES REMARK 500 1 DG A 3 C4' - C3' - C2' ANGL. DEV. = -6.0 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 DG A 9 C3' - O3' - P ANGL. DEV. = 9.9 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 DT A 10 C3' - O3' - P ANGL. DEV. = 7.4 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 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 13 C3' - O3' - P ANGL. DEV. = 11.6 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 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 DA B 18 C3' - O3' - P ANGL. DEV. = 15.8 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 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. = -4.5 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