Header list of 1luh.pdb file
Complete list - 23 202 Bytes
HEADER DNA 22-MAY-02 1LUH
TITLE SOLUTION NMR STRUCTURE OF SELF-COMPLIMENTARY DUPLEX 5'-D(TCCG*CGGA)2
TITLE 2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE N2 POSITION OF G*
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*TP*CP*CP*(TME)GP*CP*GP*GP*A)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: DETAILS OF THE SYNTHESIS ARE DESCRIBED IN THE JOURNAL
SOURCE 4 ARTICLE.
KEYWDS DNA DUPLEX, GUANINE N2-GUANINE N2 INTERSTRAND CROSSLINK, DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR P.D.DOOLEY,M.ZHANG,G.A.KORBEL,L.V.NECHEV,C.M.HARRIS,M.P.STONE,
AUTHOR 2 T.M.HARRIS
REVDAT 3 23-FEB-22 1LUH 1 REMARK LINK
REVDAT 2 24-FEB-09 1LUH 1 VERSN
REVDAT 1 11-FEB-03 1LUH 0
JRNL AUTH P.D.DOOLEY,M.ZHANG,G.A.KORBEL,L.V.NECHEV,C.M.HARRIS,
JRNL AUTH 2 M.P.STONE,T.M.HARRIS
JRNL TITL NMR DETERMINATION OF THE CONFORMATION OF A TRIMETHYLENE
JRNL TITL 2 INTERSTRAND CROSS-LINK IN AN OLIGODEOXYNUCLEOTIDE DUPLEX
JRNL TITL 3 CONTAINING A 5'-D(GPC) MOTIF
JRNL REF J.AM.CHEM.SOC. V. 125 62 2003
JRNL REFN ISSN 0002-7863
JRNL PMID 12515507
JRNL DOI 10.1021/JA0207798
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 95, X-PLOR 3.1
REMARK 3 AUTHORS : BIOSYM TECHNOLOGIES (FELIX), A.T.BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: FURTHER DETAILS ABOUT THE STRUCTURAL
REMARK 3 REFINEMENT INCLUDING THE TRIMETHYLENE CHAIN CAN BE FOUND IN THE
REMARK 3 JOURNAL ARTICLE.
REMARK 4
REMARK 4 1LUH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-02.
REMARK 100 THE DEPOSITION ID IS D_1000016282.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 7.10
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 2 MM CROSSLINKED DUPLEX, 10 MM
REMARK 210 SODIUM PHOSPHATE BUFFER, 0.1 M
REMARK 210 NACL, 50 MM EDTA, PH 7.1; 2 MM
REMARK 210 CROSSLINKED DUPLEX, 10 MM SODIUM
REMARK 210 PHOSPHATE BUFFER, 0.1 M NACL, 50
REMARK 210 MM EDTA, PH 7.1
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; PE-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : AMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MARDIGRAS, X-PLOR 3.1, CORMA
REMARK 210 3.85
REMARK 210 METHOD USED : NOE-RESTRAINED MOLECULAR
REMARK 210 DYNAMICS; SIMULATED ANNEALING
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: 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: 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 DT A 1 C3' DT A 1 C2' 0.081
REMARK 500 DT A 1 C5 DT A 1 C7 0.037
REMARK 500 DC A 2 C2' DC A 2 C1' 0.069
REMARK 500 DC A 5 N1 DC A 5 C6 -0.105
REMARK 500 DG A 6 C8 DG A 6 N9 -0.084
REMARK 500 DG A 7 C3' DG A 7 C2' -0.071
REMARK 500 DA A 8 C3' DA A 8 C2' 0.112
REMARK 500 DA A 8 C2' DA A 8 C1' 0.111
REMARK 500 DT B 9 C3' DT B 9 C2' 0.081
REMARK 500 DT B 9 C5 DT B 9 C7 0.037
REMARK 500 DC B 10 C2' DC B 10 C1' 0.068
REMARK 500 DC B 13 N1 DC B 13 C6 -0.104
REMARK 500 DG B 14 C8 DG B 14 N9 -0.084
REMARK 500 DG B 15 C3' DG B 15 C2' -0.071
REMARK 500 DA B 16 C3' DA B 16 C2' 0.112
REMARK 500 DA B 16 C2' DA B 16 C1' 0.111
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 2 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES
REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DC A 5 C6 - N1 - C2 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DC A 5 C6 - N1 - C1' ANGL. DEV. = -7.8 DEGREES
REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DG A 6 C5 - N7 - C8 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DG A 6 N7 - C8 - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 DA A 8 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DA A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 DC B 10 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES
REMARK 500 DC B 10 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DG B 12 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DC B 13 C6 - N1 - C2 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DC B 13 C6 - N1 - C1' ANGL. DEV. = -7.8 DEGREES
REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DG B 14 C5 - N7 - C8 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DG B 14 N7 - C8 - N9 ANGL. DEV. = 6.1 DEGREES
REMARK 500 DG B 15 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 DG B 15 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DG B 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 DA B 16 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DA B 16 C8 - N9 - C4 ANGL. DEV. = -2.5 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 DC A 3 0.06 SIDE CHAIN
REMARK 500 DC B 11 0.06 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TME B 1
DBREF 1LUH A 1 8 PDB 1LUH 1LUH 1 8
DBREF 1LUH B 9 16 PDB 1LUH 1LUH 9 16
SEQRES 1 A 8 DT DC DC DG DC DG DG DA
SEQRES 1 B 8 DT DC DC DG DC DG DG DA
HET TME B 1 9
HETNAM TME PROPANE
FORMUL 3 TME C3 H8
LINK N2 DG A 4 C3 TME B 1 1555 1555 1.49
LINK C1 TME B 1 N2 DG B 12 1555 1555 1.49
SITE 1 AC1 4 DG A 4 DC A 5 DG B 12 DC B 13
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 - 23 202 Bytes