Header list of 1hz2.pdb file
Complete list - 23 202 Bytes
HEADER DNA 23-JAN-01 1HZ2
TITLE SOLUTION NMR STRUCTURE OF SELF-COMPLEMENTARY DUPLEX 5'-D(AGGCG*CCT)2
TITLE 2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE N2 POSITION OF G*. MODEL
TITLE 3 OF A MALONDIALDEHYDE CROSSLINK
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*AP*GP*GP*CP*GP*CP*CP*T)-3');
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS DNA DUPLEX, INTERSTRAND CROSSLINK, DNA
EXPDTA SOLUTION NMR
AUTHOR P.A.DOOLEY,D.TSAROUHTSIS,G.A.KORBEL,L.V.NECHEV,J.SHEARER,I.S.ZEGAR,
AUTHOR 2 C.M.HARRIS,M.P.STONE,T.M.HARRIS
REVDAT 4 23-FEB-22 1HZ2 1 REMARK LINK
REVDAT 3 24-FEB-09 1HZ2 1 VERSN
REVDAT 2 01-AUG-01 1HZ2 1 JRNL
REVDAT 1 07-FEB-01 1HZ2 0
JRNL AUTH P.A.DOOLEY,D.TSAROUHTSIS,G.A.KORBEL,L.V.NECHEV,J.SHEARER,
JRNL AUTH 2 I.S.ZEGAR,C.M.HARRIS,M.P.STONE,T.M.HARRIS
JRNL TITL STRUCTURAL STUDIES OF AN OLIGODEOXYNUCLEOTIDE CONTAINING A
JRNL TITL 2 TRIMETHYLENE INTERSTRAND CROSS-LINK IN A 5'-(CPG) MOTIF:
JRNL TITL 3 MODEL OF A MALONDIALDEHYDE CROSS-LINK.
JRNL REF J.AM.CHEM.SOC. V. 123 1730 2001
JRNL REFN ISSN 0002-7863
JRNL PMID 11456774
JRNL DOI 10.1021/JA003163W
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 95, X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER, A. T. (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 1HZ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-01.
REMARK 100 THE DEPOSITION ID IS D_1000012701.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303; 298
REMARK 210 PH : 7.1; 7.1
REMARK 210 IONIC STRENGTH : NULL; NULL
REMARK 210 PRESSURE : AMBIENT; 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, CPANEL,
REMARK 210 SPHINX/LINSHA
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: 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 N2 DG A 5 H31 TME A 9 1.30
REMARK 500 H2'' DC B 14 O5' DC B 15 1.51
REMARK 500 H2'' DC A 6 O5' DC A 7 1.55
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 DA A 1 C8 DA A 1 N9 -0.107
REMARK 500 DG A 2 C8 DG A 2 N9 -0.064
REMARK 500 DC A 4 C4' DC A 4 C3' -0.080
REMARK 500 DC A 4 C3' DC A 4 C2' 0.100
REMARK 500 DC A 4 C2' DC A 4 C1' 0.068
REMARK 500 DG A 5 C8 DG A 5 N9 -0.048
REMARK 500 DG A 5 N9 DG A 5 C4 -0.050
REMARK 500 DC A 6 O4' DC A 6 C1' -0.086
REMARK 500 DC A 6 O4' DC A 6 C4' -0.129
REMARK 500 DC A 6 C1' DC A 6 N1 -0.114
REMARK 500 DC A 6 N1 DC A 6 C6 -0.100
REMARK 500 DC A 6 C5 DC A 6 C6 -0.106
REMARK 500 DC A 7 C3' DC A 7 C2' 0.077
REMARK 500 DT A 8 C5 DT A 8 C6 0.074
REMARK 500 DT A 8 C5 DT A 8 C7 0.075
REMARK 500 DA B 9 C8 DA B 9 N9 -0.107
REMARK 500 DG B 10 C8 DG B 10 N9 -0.064
REMARK 500 DC B 12 C4' DC B 12 C3' -0.080
REMARK 500 DC B 12 C3' DC B 12 C2' 0.102
REMARK 500 DC B 12 C2' DC B 12 C1' 0.064
REMARK 500 DG B 13 C8 DG B 13 N9 -0.046
REMARK 500 DC B 14 O4' DC B 14 C1' -0.086
REMARK 500 DC B 14 O4' DC B 14 C4' -0.130
REMARK 500 DC B 14 C1' DC B 14 N1 -0.115
REMARK 500 DC B 14 N1 DC B 14 C6 -0.105
REMARK 500 DC B 14 C5 DC B 14 C6 -0.106
REMARK 500 DC B 15 C3' DC B 15 C2' 0.085
REMARK 500 DT B 16 C5 DT B 16 C6 0.072
REMARK 500 DT B 16 C5 DT B 16 C7 0.069
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 DA A 1 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DA A 1 N7 - C8 - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES
REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 5.6 DEGREES
REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 DC A 4 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES
REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 11.2 DEGREES
REMARK 500 DG A 5 C5 - N7 - C8 ANGL. DEV. = -3.5 DEGREES
REMARK 500 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DG A 5 N3 - C4 - N9 ANGL. DEV. = -3.6 DEGREES
REMARK 500 DC A 6 C5' - C4' - O4' ANGL. DEV. = -12.6 DEGREES
REMARK 500 DC A 6 C6 - N1 - C2 ANGL. DEV. = 5.3 DEGREES
REMARK 500 DC A 6 C6 - N1 - C1' ANGL. DEV. = -12.1 DEGREES
REMARK 500 DC A 6 C2 - N1 - C1' ANGL. DEV. = 6.7 DEGREES
REMARK 500 DC A 6 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES
REMARK 500 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 DA B 9 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DA B 9 N7 - C8 - N9 ANGL. DEV. = 5.7 DEGREES
REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DG B 10 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES
REMARK 500 DG B 10 N7 - C8 - N9 ANGL. DEV. = 5.6 DEGREES
REMARK 500 DG B 11 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG B 11 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES
REMARK 500 DC B 12 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES
REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 12.6 DEGREES
REMARK 500 DG B 13 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DC B 14 C5' - C4' - O4' ANGL. DEV. = -12.2 DEGREES
REMARK 500 DC B 14 C6 - N1 - C2 ANGL. DEV. = 5.2 DEGREES
REMARK 500 DC B 14 N3 - C4 - C5 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DC B 14 C6 - N1 - C1' ANGL. DEV. = -11.8 DEGREES
REMARK 500 DC B 14 C3' - O3' - P ANGL. DEV. = 10.7 DEGREES
REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DT B 16 C5 - C6 - N1 ANGL. DEV. = -3.8 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 0.05 SIDE CHAIN
REMARK 500 DG B 11 0.05 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 A 9
DBREF 1HZ2 A 1 8 PDB 1HZ2 1HZ2 1 8
DBREF 1HZ2 B 9 16 PDB 1HZ2 1HZ2 9 16
SEQRES 1 A 8 DA DG DG DC DG DC DC DT
SEQRES 1 B 8 DA DG DG DC DG DC DC DT
HET TME A 9 9
HETNAM TME PROPANE
FORMUL 3 TME C3 H8
LINK N2 DG A 5 C3 TME A 9 1555 1555 1.46
LINK C1 TME A 9 N2 DG B 13 1555 1555 1.47
SITE 1 AC1 4 DG A 5 DC A 6 DG B 13 DC B 14
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