Header list of 2aqy.pdb file
Complete list - 9 20 Bytes
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
MODEL 1
Complete list - 9 20 Bytes