Header list of 1l0r.pdb file
Complete list - 23 20 Bytes
HEADER DNA 12-FEB-02 1L0R
TITLE NMR SOLUTION STRUCTURE OF NOGALAMYCIN INTERCALATION BETWEEN CO-AXIALLY
TITLE 2 STACKED HAIRPINS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*GP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: CO-AXIALLY STACKED DNA HAIRPIN
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY SOLID PHASE USING
SOURCE 4 PHOSPHORAMIDITE CHEMISTRY.
KEYWDS GAA LOOP, SINGLE STRAND BREAK, DRUG-DNA RECOGNITION, NOGALAMYCIN
KEYWDS 2 INTERCALATION, DNA
EXPDTA SOLUTION NMR
AUTHOR H.E.L.WILLIAMS,M.L.COLGRAVE,M.S.SEARLE
REVDAT 5 23-FEB-22 1L0R 1 REMARK LINK
REVDAT 4 24-FEB-09 1L0R 1 VERSN
REVDAT 3 21-SEP-04 1L0R 1 ATOM
REVDAT 2 01-APR-03 1L0R 1 JRNL
REVDAT 1 19-JUN-02 1L0R 0
JRNL AUTH H.E.L.WILLIAMS,M.L.COLGRAVE,M.S.SEARLE
JRNL TITL DRUG RECOGNITION OF A DNA SINGLE STRAND BREAK: NOGALAMYCIN
JRNL TITL 2 INTERCALATION BETWEEN COAXIALLY STACKED HAIRPINS.
JRNL REF EUR.J.BIOCHEM. V. 269 1726 2002
JRNL REFN ISSN 0014-2956
JRNL PMID 11895443
JRNL DOI 10.1046/J.1432-1327.2002.02819.X
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.6-3.1, AMBER 6
REMARK 3 AUTHORS :
REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH,
REMARK 3 WEINER,KOLLMAN (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1L0R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-02.
REMARK 100 THE DEPOSITION ID IS D_1000015539.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278
REMARK 210 PH : 6.4
REMARK 210 IONIC STRENGTH : 100MM NA+ 10MM PO4-
REMARK 210 PRESSURE : ATMOSPHERIC ATM
REMARK 210 SAMPLE CONTENTS : 3MM HAIRPIN; 10MM PHOSPHATE,
REMARK 210 100MM NACL; 0.6MM NAN3; 0.6MM
REMARK 210 NA4 EDTA; 2MM
REMARK 210 TRIMETHYLISILYLPROPANOATE D2O;
REMARK 210 3MM HAIRPIN; 10MM PHOSPHATE,
REMARK 210 100MM NACL; 0.6MM NAN3; 0.6MM
REMARK 210 NA4 EDTA; 2MM
REMARK 210 TRIMETHYLISILYLPROPANOATE 10%
REMARK 210 D2O, 90% H2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D NOESY WITH
REMARK 210 WATERGATE SUPPRESION; DQF-COSY;
REMARK 210 TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : ANSIG 3.3, AMBER 6
REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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: 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: 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES
REMARK 500 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DA A 1 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES
REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES
REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES
REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES
REMARK 500 DG A 8 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES
REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES
REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES
REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DA A 11 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES
REMARK 500 DA A 11 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DA A 11 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DA A 12 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DA A 12 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES
REMARK 500 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DC A 14 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 DC A 14 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 DG A 3 0.06 SIDE CHAIN
REMARK 500 DT A 7 0.08 SIDE CHAIN
REMARK 500 DG A 8 0.05 SIDE CHAIN
REMARK 500 DC A 9 0.19 SIDE CHAIN
REMARK 500 DG A 10 0.05 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 16 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DA A 5 O4'
REMARK 620 2 DA A 5 N3 70.9
REMARK 620 N 1
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 16
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 18
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 19
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 22
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NGP A 15
DBREF 1L0R A 1 14 PDB 1L0R 1L0R 1 14
SEQRES 1 A 14 DA DC DG DA DA DG DT DG DC DG DA DA DG
SEQRES 2 A 14 DC
HET NA A 16 1
HET NA A 17 1
HET NA A 18 1
HET NA A 19 1
HET NA A 20 1
HET NA A 21 1
HET NA A 22 1
HET NA A 23 1
HET NA A 24 1
HET NA A 25 1
HET NA A 26 1
HET NA A 27 1
HET NGP A 15 106
HETNAM NA SODIUM ION
HETNAM NGP NOGALAMYCIN (PROTONATED FORM)
FORMUL 2 NA 12(NA 1+)
FORMUL 14 NGP C39 H52 N O16 1+
FORMUL 15 HOH *2194(H2 O)
LINK O4' DA A 5 NA NA A 16 1555 1555 2.44
LINK N3 DA A 5 NA NA A 16 1555 1555 2.53
LINK NA NA A 18 O HOH A 825 1555 1555 2.48
LINK NA NA A 19 O HOH A1100 1555 1555 2.46
LINK NA NA A 22 O HOH A1917 1555 1555 2.49
SITE 1 AC1 2 DA A 5 DG A 6
SITE 1 AC2 1 HOH A 825
SITE 1 AC3 1 HOH A1100
SITE 1 AC4 1 HOH A1917
SITE 1 AC5 8 DA A 1 DC A 2 DT A 7 DG A 8
SITE 2 AC5 8 DC A 9 DG A 13 DC A 14 HOH A1360
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
Complete list - 23 20 Bytes