Header list of 2akg.pdb file
Complete list - 9 20 Bytes
HEADER DNA 03-AUG-05 2AKG
TITLE THALLIUM FORM OF THE G-QUADRUPLEX FROM OXYTRICHA NOVA, D(G4T4G4)2
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SEQUENCE OBTAINED FROM STERKIELLA NOVA (OXYTRICHA
SOURCE 4 NOVA) TELOMERE
KEYWDS DEOXYRIBONUCLEIC ACID, G-QUADRUPLEX, THALLIUM, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR M.L.GILL,S.A.STROBEL,J.P.LORIA
REVDAT 4 09-MAR-22 2AKG 1 REMARK
REVDAT 3 24-FEB-09 2AKG 1 VERSN
REVDAT 2 06-DEC-05 2AKG 1 JRNL
REVDAT 1 08-NOV-05 2AKG 0
JRNL AUTH M.L.GILL,S.A.STROBEL,J.P.LORIA
JRNL TITL (205)TL NMR METHODS FOR THE CHARACTERIZATION OF MONOVALENT
JRNL TITL 2 CATION BINDING TO NUCLEIC ACIDS
JRNL REF J.AM.CHEM.SOC. V. 127 16723 2005
JRNL REFN ISSN 0002-7863
JRNL PMID 16305263
JRNL DOI 10.1021/JA055358F
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 6.1B, CNS 1.1
REMARK 3 AUTHORS : VARIAN, INC (VNMR), BRUNGER, ADAMS, CLORE, DELANO,
REMARK 3 GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES,
REMARK 3 PANNU, READ, RICE, SIMONSON, WARREN (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2AKG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-05.
REMARK 100 THE DEPOSITION ID IS D_1000033999.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298; 278
REMARK 210 PH : 6.5; 6.5
REMARK 210 IONIC STRENGTH : NULL; NULL
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 0.005 M DNA, 0.0001 M EDTA-D12,
REMARK 210 0.050 M THALLIUM-NITRATE, PH 6.0,
REMARK 210 100% D2O; 0.005 M DNA, 0.0001 M
REMARK 210 EDTA-D12, 0.050 M THALLIUM-
REMARK 210 NITRATE, PH 6.0, 90% H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 31P-1H COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS; INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY 3.110, CNS 1.1
REMARK 210 METHOD USED : (1) DISTANCE GEOMETRY WITH
REMARK 210 SIMULATED ANNEALING; (2) TORSION
REMARK 210 ANGLE DYNAMICS (2000 K FOR 60 PS
REMARK 210 WITH 15 FS TIMESTEPS); (3)
REMARK 210 CARTESIAN DYNAMICS (1000 K FOR 5
REMARK 210 PS WITH 5 FS TIMESTEPS); (4)
REMARK 210 RESTRAINED MOLECULAR DYNAMICS
REMARK 210 (100 CYCLES OF 200 STEPS EACH)
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
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: THIS STRUCTURE WAS DETERMINED WITHOUT THE USE OF
REMARK 210 ISOTOPICALLY ENRICHED NUCLEOTIDES.
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 DG A 3 P DG A 3 OP1 -0.133
REMARK 500 1 DG A 3 P DG A 3 OP2 -0.129
REMARK 500 1 DT A 5 P DT A 5 OP1 -0.130
REMARK 500 1 DT A 5 P DT A 5 OP2 -0.133
REMARK 500 1 DG A 10 P DG A 10 OP1 -0.129
REMARK 500 1 DG A 10 P DG A 10 OP2 -0.133
REMARK 500 1 DG A 12 P DG A 12 OP1 -0.130
REMARK 500 1 DG A 12 P DG A 12 OP2 -0.133
REMARK 500 1 DG B 15 P DG B 15 OP1 -0.130
REMARK 500 1 DG B 15 P DG B 15 OP2 -0.133
REMARK 500 1 DT B 17 P DT B 17 OP1 -0.134
REMARK 500 1 DT B 17 P DT B 17 OP2 -0.130
REMARK 500 1 DG B 22 P DG B 22 OP1 -0.134
REMARK 500 1 DG B 22 P DG B 22 OP2 -0.130
REMARK 500 1 DG B 24 P DG B 24 OP1 -0.133
REMARK 500 1 DG B 24 P DG B 24 OP2 -0.129
REMARK 500 2 DG A 3 P DG A 3 OP1 -0.134
REMARK 500 2 DG A 3 P DG A 3 OP2 -0.129
REMARK 500 2 DT A 5 P DT A 5 OP1 -0.129
REMARK 500 2 DT A 5 P DT A 5 OP2 -0.134
REMARK 500 2 DG A 10 P DG A 10 OP1 -0.129
REMARK 500 2 DG A 10 P DG A 10 OP2 -0.132
REMARK 500 2 DG A 12 P DG A 12 OP1 -0.129
REMARK 500 2 DG A 12 P DG A 12 OP2 -0.133
REMARK 500 2 DG B 15 P DG B 15 OP1 -0.129
REMARK 500 2 DG B 15 P DG B 15 OP2 -0.134
REMARK 500 2 DT B 17 P DT B 17 OP1 -0.134
REMARK 500 2 DT B 17 P DT B 17 OP2 -0.129
REMARK 500 2 DG B 22 P DG B 22 OP1 -0.133
REMARK 500 2 DG B 22 P DG B 22 OP2 -0.128
REMARK 500 2 DG B 24 P DG B 24 OP1 -0.133
REMARK 500 2 DG B 24 P DG B 24 OP2 -0.129
REMARK 500 3 DG A 3 P DG A 3 OP1 -0.133
REMARK 500 3 DG A 3 P DG A 3 OP2 -0.130
REMARK 500 3 DT A 5 P DT A 5 OP1 -0.130
REMARK 500 3 DT A 5 P DT A 5 OP2 -0.133
REMARK 500 3 DG A 10 P DG A 10 OP1 -0.129
REMARK 500 3 DG A 10 P DG A 10 OP2 -0.132
REMARK 500 3 DG A 12 P DG A 12 OP1 -0.128
REMARK 500 3 DG A 12 P DG A 12 OP2 -0.133
REMARK 500 3 DG B 15 P DG B 15 OP1 -0.129
REMARK 500 3 DG B 15 P DG B 15 OP2 -0.133
REMARK 500 3 DT B 17 P DT B 17 OP1 -0.133
REMARK 500 3 DT B 17 P DT B 17 OP2 -0.131
REMARK 500 3 DG B 22 P DG B 22 OP1 -0.133
REMARK 500 3 DG B 22 P DG B 22 OP2 -0.128
REMARK 500 3 DG B 24 P DG B 24 OP1 -0.134
REMARK 500 3 DG B 24 P DG B 24 OP2 -0.128
REMARK 500 4 DG A 3 P DG A 3 OP1 -0.133
REMARK 500 4 DG A 3 P DG A 3 OP2 -0.129
REMARK 500
REMARK 500 THIS ENTRY HAS 160 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 2 DT A 5 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES
REMARK 500 3 DT B 17 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES
REMARK 500 4 DG A 9 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES
REMARK 500 4 DT B 17 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES
REMARK 500 4 DG B 21 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES
REMARK 500 6 DG A 9 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES
REMARK 500 6 DG B 21 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES
REMARK 500 8 DT A 5 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES
REMARK 500 8 DT B 17 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
DBREF 2AKG A 1 12 PDB 2AKG 2AKG 1 12
DBREF 2AKG B 13 24 PDB 2AKG 2AKG 13 24
SEQRES 1 A 12 DG DG DG DG DT DT DT DT DG DG DG DG
SEQRES 1 B 12 DG 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 - 9 20 Bytes