Header list of 1rn9.pdb file
Complete list - 2 202 Bytes
HEADER DNA 01-DEC-03 1RN9
TITLE A SHORT LEXITROPSIN THAT RECOGNIZES THE DNA MINOR GROOVE AT 5'-ACTAGT-
TITLE 2 3': UNDERSTANDING THE ROLE OF ISOPROPYL-THIAZOLE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SYNTHESIZED ON SOLID PHASE
KEYWDS DOUBLE HELIX, DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR N.G.ANTHONY,B.F.JOHNSTON,A.I.KHALAF,S.P.MACKAY,J.A.PARKINSON,
AUTHOR 2 C.J.SUCKLING,R.D.WAIGH
REVDAT 4 02-MAR-22 1RN9 1 REMARK
REVDAT 3 24-FEB-09 1RN9 1 VERSN
REVDAT 2 05-OCT-04 1RN9 1 JRNL
REVDAT 1 24-AUG-04 1RN9 0
JRNL AUTH N.G.ANTHONY,B.F.JOHNSTON,A.I.KHALAF,S.P.MACKAY,
JRNL AUTH 2 J.A.PARKINSON,C.J.SUCKLING,R.D.WAIGH
JRNL TITL SHORT LEXITROPSIN THAT RECOGNIZES THE DNA MINOR GROOVE AT
JRNL TITL 2 5'-ACTAGT-3': UNDERSTANDING THE ROLE OF ISOPROPYL-THIAZOLE.
JRNL REF J.AM.CHEM.SOC. V. 126 11338 2004
JRNL REFN ISSN 0002-7863
JRNL PMID 15355117
JRNL DOI 10.1021/JA030658N
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SYBYL 6.3
REMARK 3 AUTHORS : TRIPOS INC.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: 514 NOE RESTRAINTS DEFINED FOR THE
REMARK 3 DECAMER DUPLEX
REMARK 4
REMARK 4 1RN9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-03.
REMARK 100 THE DEPOSITION ID IS D_1000020900.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 100MM NACL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 2.4MM DNA DUPLEX, 90% H2O, 10%
REMARK 210 D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY; 2D NOESY; DQF-COSY; 2D
REMARK 210 ROESY; P-H COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 400 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE; AMX
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MARDIGRAS 1.0, XWINNMR 3.0, VNMR
REMARK 210 6, SPARKY 3
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 : 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 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 DC A 1 C2 DC A 1 N3 0.088
REMARK 500 DC A 1 N3 DC A 1 C4 -0.067
REMARK 500 DG A 2 C2 DG A 2 N3 -0.051
REMARK 500 DG A 2 N3 DG A 2 C4 0.091
REMARK 500 DG A 2 C4 DG A 2 C5 -0.051
REMARK 500 DG A 2 C5 DG A 2 N7 0.050
REMARK 500 DG A 2 N7 DG A 2 C8 -0.046
REMARK 500 DG A 2 C8 DG A 2 N9 -0.068
REMARK 500 DG A 2 N9 DG A 2 C4 -0.064
REMARK 500 DA A 3 C5 DA A 3 N7 -0.046
REMARK 500 DA A 3 N7 DA A 3 C8 -0.046
REMARK 500 DA A 3 C8 DA A 3 N9 -0.067
REMARK 500 DC A 4 C2 DC A 4 N3 0.087
REMARK 500 DC A 4 N3 DC A 4 C4 -0.068
REMARK 500 DA A 6 C5 DA A 6 N7 -0.045
REMARK 500 DA A 6 N7 DA A 6 C8 -0.047
REMARK 500 DA A 6 C8 DA A 6 N9 -0.068
REMARK 500 DG A 7 C2 DG A 7 N3 -0.049
REMARK 500 DG A 7 N3 DG A 7 C4 0.091
REMARK 500 DG A 7 C4 DG A 7 C5 -0.049
REMARK 500 DG A 7 C6 DG A 7 N1 -0.042
REMARK 500 DG A 7 C5 DG A 7 N7 0.050
REMARK 500 DG A 7 N7 DG A 7 C8 -0.047
REMARK 500 DG A 7 C8 DG A 7 N9 -0.071
REMARK 500 DG A 7 N9 DG A 7 C4 -0.063
REMARK 500 DC A 9 C2 DC A 9 N3 0.089
REMARK 500 DC A 9 N3 DC A 9 C4 -0.065
REMARK 500 DG A 10 C2 DG A 10 N3 -0.051
REMARK 500 DG A 10 N3 DG A 10 C4 0.091
REMARK 500 DG A 10 C4 DG A 10 C5 -0.050
REMARK 500 DG A 10 C5 DG A 10 N7 0.049
REMARK 500 DG A 10 N7 DG A 10 C8 -0.047
REMARK 500 DG A 10 C8 DG A 10 N9 -0.071
REMARK 500 DG A 10 N9 DG A 10 C4 -0.064
REMARK 500 DC B 11 C2 DC B 11 N3 0.086
REMARK 500 DC B 11 N3 DC B 11 C4 -0.067
REMARK 500 DG B 12 C2 DG B 12 N3 -0.049
REMARK 500 DG B 12 N3 DG B 12 C4 0.092
REMARK 500 DG B 12 C4 DG B 12 C5 -0.050
REMARK 500 DG B 12 C5 DG B 12 N7 0.050
REMARK 500 DG B 12 N7 DG B 12 C8 -0.046
REMARK 500 DG B 12 C8 DG B 12 N9 -0.070
REMARK 500 DG B 12 N9 DG B 12 C4 -0.061
REMARK 500 DA B 13 C5 DA B 13 N7 -0.044
REMARK 500 DA B 13 N7 DA B 13 C8 -0.045
REMARK 500 DA B 13 C8 DA B 13 N9 -0.068
REMARK 500 DC B 14 C2 DC B 14 N3 0.087
REMARK 500 DC B 14 N3 DC B 14 C4 -0.066
REMARK 500 DA B 16 C5 DA B 16 N7 -0.045
REMARK 500 DA B 16 N7 DA B 16 C8 -0.044
REMARK 500
REMARK 500 THIS ENTRY HAS 68 BOND DEVIATIONS.
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' - C4' - C3' ANGL. DEV. = -2.7 DEGREES
REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DC A 1 C4 - C5 - C6 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES
REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 DC A 1 N3 - C4 - N4 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DG A 2 OP1 - P - OP2 ANGL. DEV. = -12.2 DEGREES
REMARK 500 DG A 2 C2 - N3 - C4 ANGL. DEV. = 8.9 DEGREES
REMARK 500 DG A 2 N3 - C4 - C5 ANGL. DEV. = -9.3 DEGREES
REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 DG A 2 C4 - C5 - N7 ANGL. DEV. = -9.3 DEGREES
REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DG A 2 N9 - C4 - C5 ANGL. DEV. = 6.1 DEGREES
REMARK 500 DG A 2 C6 - C5 - N7 ANGL. DEV. = 8.9 DEGREES
REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = -8.3 DEGREES
REMARK 500 DA A 3 OP1 - P - OP2 ANGL. DEV. = -11.7 DEGREES
REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 DA A 3 N1 - C2 - N3 ANGL. DEV. = -7.7 DEGREES
REMARK 500 DA A 3 C2 - N3 - C4 ANGL. DEV. = 7.6 DEGREES
REMARK 500 DA A 3 N3 - C4 - C5 ANGL. DEV. = -6.4 DEGREES
REMARK 500 DA A 3 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DA A 3 C4 - C5 - N7 ANGL. DEV. = -4.8 DEGREES
REMARK 500 DA A 3 C5 - N7 - C8 ANGL. DEV. = 5.5 DEGREES
REMARK 500 DA A 3 N3 - C4 - N9 ANGL. DEV. = 6.3 DEGREES
REMARK 500 DC A 4 OP1 - P - OP2 ANGL. DEV. = -11.3 DEGREES
REMARK 500 DC A 4 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES
REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DC A 4 N3 - C4 - C5 ANGL. DEV. = -4.7 DEGREES
REMARK 500 DC A 4 C4 - C5 - C6 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DC A 4 N1 - C2 - O2 ANGL. DEV. = 5.4 DEGREES
REMARK 500 DC A 4 N3 - C2 - O2 ANGL. DEV. = -7.3 DEGREES
REMARK 500 DC A 4 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES
REMARK 500 DT A 5 OP1 - P - OP2 ANGL. DEV. = -11.4 DEGREES
REMARK 500 DT A 5 N1 - C2 - N3 ANGL. DEV. = 4.8 DEGREES
REMARK 500 DT A 5 C2 - N3 - C4 ANGL. DEV. = -4.5 DEGREES
REMARK 500 DT A 5 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES
REMARK 500 DA A 6 OP1 - P - OP2 ANGL. DEV. = -12.0 DEGREES
REMARK 500 DA A 6 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 DA A 6 N1 - C2 - N3 ANGL. DEV. = -7.5 DEGREES
REMARK 500 DA A 6 C2 - N3 - C4 ANGL. DEV. = 7.3 DEGREES
REMARK 500 DA A 6 N3 - C4 - C5 ANGL. DEV. = -6.0 DEGREES
REMARK 500 DA A 6 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DA A 6 C4 - C5 - N7 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DA A 6 C5 - N7 - C8 ANGL. DEV. = 5.1 DEGREES
REMARK 500 DA A 6 N3 - C4 - N9 ANGL. DEV. = 5.9 DEGREES
REMARK 500 DA A 6 C3' - O3' - P ANGL. DEV. = 13.8 DEGREES
REMARK 500 DG A 7 OP1 - P - OP2 ANGL. DEV. = -13.7 DEGREES
REMARK 500 DG A 7 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 DG A 7 C2 - N3 - C4 ANGL. DEV. = 8.8 DEGREES
REMARK 500 DG A 7 N3 - C4 - C5 ANGL. DEV. = -9.3 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 153 ANGLE DEVIATIONS.
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 9 0.07 SIDE CHAIN
REMARK 500 DA B 16 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1RMX RELATED DB: PDB
REMARK 900 A SHORT LEXITROPSIN THAT RECOGNIZES THE DNA MINOR GROOVE AT 5'-
REMARK 900 ACTAGT-3': UNDERSTANDING THE ROLE OF ISOPROPYL-THIAZOLE
DBREF 1RN9 A 1 10 PDB 1RN9 1RN9 1 10
DBREF 1RN9 B 11 20 PDB 1RN9 1RN9 11 20
SEQRES 1 A 10 DC DG DA DC DT DA DG DT DC DG
SEQRES 1 B 10 DC DG DA DC DT DA DG DT DC 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
Complete list - 2 202 Bytes