Header list of 1n4b.pdb file
Complete list - 22 201 Bytes
HEADER DNA 30-OCT-02 1N4B
TITLE SOLUTION STRUCTURE OF THE UNDECAMER CGAAAC*TTTCG
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*AP*AP*CP*TP*TP*TP*CP*G)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: INTERSTRAND CROSS-LINKED DNA;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: 5'-D(*CP*GP*AP*AP*AP*D00*TP*TP*TP*CP*G)-3';
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES;
COMPND 10 OTHER_DETAILS: INTERSTRAND CROSS-LINKED DNA
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS INTERSTRAND CROSS-LINK, ALKYLATED DNA, MODIFIED CYTOSINE, ALKYLATED
KEYWDS 2 CYTOSINE, DNA
EXPDTA SOLUTION NMR
AUTHOR M.WEBBA DA SILVA,A.M.NORONHA,D.M.NOLL,P.S.MILLER,O.M.COLVIN,
AUTHOR 2 M.P.GAMCSIK
REVDAT 3 25-JUN-14 1N4B 1 HETNAM
REVDAT 2 24-FEB-09 1N4B 1 VERSN
REVDAT 1 04-NOV-03 1N4B 0
JRNL AUTH M.WEBBA DA SILVA,A.M.NORONHA,D.M.NOLL,P.S.MILLER,O.M.COLVIN,
JRNL AUTH 2 M.P.GAMCSIK
JRNL TITL SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING
JRNL TITL 2 MISPAIR-ALIGNED N4C-ETHYL-N4C INTERSTRAND CROSS-LINKED
JRNL TITL 3 CYTOSINES
JRNL REF BIOCHEMISTRY V. 41 15181 2002
JRNL REFN ISSN 0006-2960
JRNL PMID 12484755
JRNL DOI 10.1021/BI026368L
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.8
REMARK 3 AUTHORS : BRUNGER, A.T.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 A TOTAL OF 449 RESTRAINTS WERE USED
REMARK 3 243 NON-EXCHANGEABLE
REMARK 3 53 EXCHANGEABLE
REMARK 3 44 HYDROGEN BOND
REMARK 3 109 DIHEDRAL ANGLE
REMARK 4
REMARK 4 1N4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-NOV-02.
REMARK 100 THE RCSB ID CODE IS RCSB017501.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293; 273
REMARK 210 PH : 7.4; 7.4
REMARK 210 IONIC STRENGTH : 100 MM NACL; 100 MM NACL
REMARK 210 PRESSURE : NORMAL; NORMAL
REMARK 210 SAMPLE CONTENTS : THE SYNTHESIS BY SOLID PHASE
REMARK 210 METHODS OF DNA DUPLEXES THAT
REMARK 210 CONTAIN AN N4-C-ETHYL-N4C
REMARK 210 INTERSTRAND CROSS-LINK HAS BEEN
REMARK 210 DESCRIBED [BIOCHEMISTRY,41(2002)
REMARK 210 760-771]. 2 MM SINGLE STRAND
REMARK 210 CONCENTRATION IN 0.3 ML
REMARK 210 CONTAINING 10 MM SODIUM PHOSPHATE
REMARK 210 (PH 7.4) AND 100 MM NACL.
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED
REMARK 210 ANNEALING MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : THE STRUCTURE SUBMITTED IS THE
REMARK 210 LOWEST ENERGY STRUCTURE OF A AN
REMARK 210 ENSEMBLE OF SELECTED TEN
REMARK 210 STRUCTURES
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 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME;
REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 470 RES CSSEQI ATOMS
REMARK 470 D00 B 6 C2
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 N4 DC A 6 C10 D00 B 6 1.47
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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG A 2 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES
REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DA A 4 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES
REMARK 500 DA A 4 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES
REMARK 500 DA A 4 O4' - C1' - C2' ANGL. DEV. = -10.9 DEGREES
REMARK 500 DC A 6 O4' - C1' - C2' ANGL. DEV. = -11.1 DEGREES
REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = -7.1 DEGREES
REMARK 500 DC A 6 C2 - N3 - C4 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DC A 6 N3 - C4 - C5 ANGL. DEV. = -5.3 DEGREES
REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -9.4 DEGREES
REMARK 500 DT A 7 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES
REMARK 500 DT A 8 O4' - C1' - C2' ANGL. DEV. = -9.8 DEGREES
REMARK 500 DT A 9 C5' - C4' - O4' ANGL. DEV. = 7.9 DEGREES
REMARK 500 DT A 9 O4' - C1' - C2' ANGL. DEV. = -10.6 DEGREES
REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DC A 10 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES
REMARK 500 DC A 10 O4' - C1' - C2' ANGL. DEV. = -13.0 DEGREES
REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DG A 11 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES
REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG B 2 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 DG B 2 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES
REMARK 500 DA B 3 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES
REMARK 500 DA B 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DA B 4 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES
REMARK 500 DA B 4 O4' - C1' - C2' ANGL. DEV. = -11.4 DEGREES
REMARK 500 DT B 7 O4' - C1' - C2' ANGL. DEV. = -9.8 DEGREES
REMARK 500 DT B 7 C4 - C5 - C6 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES
REMARK 500 DT B 8 O4' - C1' - C2' ANGL. DEV. = -10.4 DEGREES
REMARK 500 DT B 8 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DT B 9 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES
REMARK 500 DT B 9 O4' - C1' - C2' ANGL. DEV. = -11.1 DEGREES
REMARK 500 DT B 9 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DC B 10 C4' - C3' - O3' ANGL. DEV. = 12.1 DEGREES
REMARK 500 DC B 10 O4' - C1' - C2' ANGL. DEV. = -13.3 DEGREES
REMARK 500 DC B 10 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DG B 11 O4' - C4' - C3' ANGL. DEV. = -3.1 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 DC A 6 0.11 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 DA A 4 -46.3 D D OUTSIDE RANGE
REMARK 500 DC A 10 -45.9 D D OUTSIDE RANGE
REMARK 500 DA B 4 -47.3 D D OUTSIDE RANGE
REMARK 500 DT B 8 -46.1 D D OUTSIDE RANGE
REMARK 500 DC B 10 -46.5 D D OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1N4B A 1 11 PDB 1N4B 1N4B 1 11
DBREF 1N4B B 1 11 PDB 1N4B 1N4B 1 11
SEQRES 1 A 11 DC DG DA DA DA DC DT DT DT DC DG
SEQRES 1 B 11 DC DG DA DA DA D00 DT DT DT DC DG
MODRES 1N4B D00 B 6 DC
HET D00 B 6 33
HETNAM D00 2'-DEOXY-N-ETHYLCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
FORMUL 2 D00 C11 H18 N3 O7 P
LINK O3' DA B 5 P D00 B 6 1555 1555 1.61
LINK O3' D00 B 6 P DT B 7 1555 1555 1.60
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 - 22 201 Bytes