Header list of 1c34.pdb file
Complete list - 16 20 Bytes
HEADER DNA 24-JUL-99 1C34
TITLE SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE
CAVEAT 1C34 SEVEN RIBOSE CARBONS HAVE INCORRECT CHIRALITY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-
COMPND 3 3');
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: THROMBIN BINDING APTAMER INTERMIDIATE
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS APTAMER, THROMBIN BINDING, POTASSIUM, METAL BINDING SITES,
KEYWDS 2 QUADRUPLEX, INTERMEDIATE, DNA
EXPDTA SOLUTION NMR
NUMMDL 11
AUTHOR P.H.BOLTON,V.M.MARATHIAS,K.WANG
REVDAT 5 16-FEB-22 1C34 1 REMARK
REVDAT 4 24-FEB-09 1C34 1 VERSN
REVDAT 3 16-MAY-00 1C34 1 CAVEAT JRNL EXPDTA
REVDAT 2 29-DEC-99 1C34 1 JRNL
REVDAT 1 18-AUG-99 1C34 0
JRNL AUTH V.M.MARATHIAS,P.H.BOLTON
JRNL TITL STRUCTURES OF THE POTASSIUM-SATURATED, 2:1, AND
JRNL TITL 2 INTERMEDIATE, 1:1, FORMS OF A QUADRUPLEX DNA.
JRNL REF NUCLEIC ACIDS RES. V. 28 1969 2000
JRNL REFN ISSN 0305-1048
JRNL PMID 10756199
JRNL DOI 10.1093/NAR/28.9.1969
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH P.H.BOLTON,V.M.MARATHIAS,K.WANG
REMARK 1 TITL DETERMINATION OF THE NUMBER AND LOCATION OF THE MANGANESE
REMARK 1 TITL 2 BINDING SITES OF DNA QUADRUPLEXES IN SOLUTION BY EPR AND NMR
REMARK 1 TITL 3 IN THE PRESENCE AND ABSENCE OF THROMBIN
REMARK 1 REF J.MOL.BIOL. V. 260 378 1996
REMARK 1 REFN ISSN 0022-2836
REMARK 1 DOI 10.1006/JMBI.1996.0408
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 6.1B, FELIX 970, X-PLOR 3.1
REMARK 3 AUTHORS : VARIAN (VNMR), MSI (FELIX), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1C34 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-99.
REMARK 100 THE DEPOSITION ID IS D_1000009397.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 288; 278
REMARK 210 PH : 7.0; 7.0
REMARK 210 IONIC STRENGTH : 140 MM NACL,; 140 MM NACL,
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 140 MM NACL, 1.4 MM KCL, 20 MM
REMARK 210 TRISD11 PH=7.0; 140 MM NACL, 1.4
REMARK 210 MM KCL, 20 MM TRISD11 PH=7.0
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; PE-COSY; ROESY; BASD
REMARK 210 -TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 400 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA; UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 6.1B, FELIX 970, X-PLOR 3.1
REMARK 210 METHOD USED : STRUCTURE REFINEMENT OF THE DNA
REMARK 210 WAS PREFORMED USING COMPLETE
REMARK 210 RELAXATION MATRIX, RESTRAINED
REMARK 210 MOLECULAR DYNAMICS.
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 11
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11
REMARK 210 CONFORMERS, SELECTION CRITERIA : 80 TO 100PS STRUCTURES FROM
REMARK 210 DYNAMICS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE IS THE INTERMEDIATE FORM OF THE 15MER
REMARK 210 QUADRUPLEX WITH ONLY 1 POTASSSIUM PER DNA MOLECULE.
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 OP1 DG A 11 H3 DT A 12 1.37
REMARK 500 H1 DG A 10 O6 DG A 15 1.43
REMARK 500 O6 DG A 1 H1 DG A 15 1.48
REMARK 500 H22 DG A 8 O4 DT A 9 1.52
REMARK 500 H1 DG A 1 O6 DG A 6 1.54
REMARK 500 H3 DT A 7 N3 DG A 11 1.57
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 3 C6 DT A 3 N1 -0.043
REMARK 500 1 DG A 5 C5' DG A 5 C4' 0.042
REMARK 500 1 DT A 9 C5 DT A 9 C7 0.040
REMARK 500 2 DT A 4 C5 DT A 4 C7 0.055
REMARK 500 3 DG A 1 C5' DG A 1 C4' 0.044
REMARK 500 3 DT A 12 C5 DT A 12 C7 0.040
REMARK 500 4 DT A 3 N3 DT A 3 C4 -0.067
REMARK 500 4 DT A 3 C4 DT A 3 C5 -0.057
REMARK 500 4 DT A 3 C6 DT A 3 N1 -0.069
REMARK 500 4 DT A 3 C2 DT A 3 O2 -0.057
REMARK 500 4 DT A 4 C5 DT A 4 C7 0.044
REMARK 500 4 DT A 9 N1 DT A 9 C2 0.052
REMARK 500 4 DT A 13 C5 DT A 13 C7 0.044
REMARK 500 5 DT A 3 C4 DT A 3 C5 -0.077
REMARK 500 5 DG A 15 C2' DG A 15 C1' 0.072
REMARK 500 6 DT A 4 C5 DT A 4 C7 0.050
REMARK 500 6 DT A 9 C5 DT A 9 C7 0.042
REMARK 500 6 DT A 12 C5 DT A 12 C7 0.040
REMARK 500 6 DT A 13 C5 DT A 13 C7 0.046
REMARK 500 6 DG A 15 C2' DG A 15 C1' 0.065
REMARK 500 7 DG A 2 O3' DT A 3 P -0.101
REMARK 500 7 DT A 3 C5 DT A 3 C7 0.047
REMARK 500 7 DT A 4 C5 DT A 4 C7 0.043
REMARK 500 7 DT A 9 C5 DT A 9 C7 0.047
REMARK 500 7 DT A 12 C3' DT A 12 C2' 0.073
REMARK 500 7 DT A 13 C5 DT A 13 C7 0.040
REMARK 500 8 DT A 3 C5 DT A 3 C7 0.037
REMARK 500 8 DT A 13 C5 DT A 13 C7 0.043
REMARK 500 8 DG A 15 C2' DG A 15 C1' 0.061
REMARK 500 9 DT A 4 C5 DT A 4 C7 0.036
REMARK 500 9 DT A 12 C3' DT A 12 C2' 0.079
REMARK 500 10 DT A 3 N3 DT A 3 C4 -0.051
REMARK 500 10 DT A 3 C4 DT A 3 C5 -0.064
REMARK 500 10 DT A 3 C6 DT A 3 N1 -0.048
REMARK 500 10 DT A 13 C5 DT A 13 C7 0.039
REMARK 500 11 DG A 1 C5' DG A 1 C4' 0.046
REMARK 500 11 DG A 2 C5' DG A 2 C4' 0.046
REMARK 500 11 DT A 7 C5 DT A 7 C7 0.044
REMARK 500 11 DT A 13 C5 DT A 13 C7 0.039
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 C4' - C3' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES
REMARK 500 1 DG A 2 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES
REMARK 500 1 DG A 2 O4' - C1' - C2' ANGL. DEV. = -8.8 DEGREES
REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 7.9 DEGREES
REMARK 500 1 DT A 3 C3' - C2' - C1' ANGL. DEV. = -6.4 DEGREES
REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DT A 3 N1 - C2 - N3 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DT A 4 P - O5' - C5' ANGL. DEV. = 11.3 DEGREES
REMARK 500 1 DT A 4 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - C2' ANGL. DEV. = -11.5 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 1 DT A 4 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -6.2 DEGREES
REMARK 500 1 DG A 5 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES
REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES
REMARK 500 1 DG A 6 O4' - C1' - C2' ANGL. DEV. = -9.1 DEGREES
REMARK 500 1 DT A 7 C5' - C4' - O4' ANGL. DEV. = 9.0 DEGREES
REMARK 500 1 DT A 7 O4' - C1' - C2' ANGL. DEV. = -8.8 DEGREES
REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 8.3 DEGREES
REMARK 500 1 DG A 8 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DG A 8 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 DT A 9 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DT A 9 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 10.4 DEGREES
REMARK 500 1 DT A 9 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES
REMARK 500 1 DT A 9 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES
REMARK 500 1 DG A 10 O4' - C1' - C2' ANGL. DEV. = -7.3 DEGREES
REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DG A 11 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DG A 11 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DT A 12 C3' - C2' - C1' ANGL. DEV. = -7.2 DEGREES
REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DT A 12 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES
REMARK 500 1 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DT A 13 O4' - C1' - C2' ANGL. DEV. = -8.7 DEGREES
REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DT A 13 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES
REMARK 500 1 DT A 13 C3' - O3' - P ANGL. DEV. = 9.1 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. = -5.6 DEGREES
REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 7.7 DEGREES
REMARK 500 1 DG A 15 O4' - C1' - C2' ANGL. DEV. = -7.7 DEGREES
REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES
REMARK 500 2 DG A 1 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES
REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES
REMARK 500 2 DG A 2 C4' - C3' - C2' ANGL. DEV. = -5.4 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 471 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1C34 A 1 15 PDB 1C34 1C34 1 15
SEQRES 1 A 15 DG DG DT DT DG DG DT DG DT DG DG DT DT
SEQRES 2 A 15 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 - 16 20 Bytes