Header list of 1juu.pdb file
Complete list - b 23 2 Bytes
HEADER DNA 28-AUG-01 1JUU
TITLE NMR STRUCTURE OF A PARALLEL STRANDED DNA DUPLEX AT ATOMIC RESOLUTION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(P*CP*CP*AP*TP*AP*AP*TP*TP*TP*AP*CP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(P*CP*CP*TP*AP*TP*TP*AP*AP*AP*TP*CP*C)-3';
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THE DNA DUPLEX WAS SYNTHESIZED WITH AN APPLIED
SOURCE 4 BIOSYSTEMS MODEL 380B DNA SYNTHESIZER USING SOLID STATE
SOURCE 5 PHOSPHORAMIDATE CHEMISTRY;
SOURCE 6 MOL_ID: 2;
SOURCE 7 SYNTHETIC: YES
KEYWDS PARALLEL STRANDED, DNA DUPLEX, DNA
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR V.R.PARVATHY,S.R.BHAUMIK,K.V.R.CHARY,G.GOVIL,K.LIU,F.B.HOWARD,
AUTHOR 2 H.T.MILES
REVDAT 4 23-FEB-22 1JUU 1 REMARK
REVDAT 3 24-FEB-09 1JUU 1 VERSN
REVDAT 2 01-APR-03 1JUU 1 JRNL
REVDAT 1 03-APR-02 1JUU 0
JRNL AUTH V.R.PARVATHY,S.R.BHAUMIK,K.V.CHARY,G.GOVIL,K.LIU,F.B.HOWARD,
JRNL AUTH 2 H.T.MILES
JRNL TITL NMR STRUCTURE OF A PARALLEL-STRANDED DNA DUPLEX AT ATOMIC
JRNL TITL 2 RESOLUTION.
JRNL REF NUCLEIC ACIDS RES. V. 30 1500 2002
JRNL REFN ISSN 0305-1048
JRNL PMID 11917010
JRNL DOI 10.1093/NAR/30.7.1500
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DISCOVER 3.1, DISCOVER 3.1
REMARK 3 AUTHORS : MSI (DISCOVER), MSI (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE WAS CALCULATED USING 78 NOE
REMARK 3 CONSTRAINTS, 28 HYDROGEN BOND CONSTRAINTS, AND 162 DIHEDRAL
REMARK 3 ANGLE CONSTRAINTS.
REMARK 4
REMARK 4 1JUU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-01.
REMARK 100 THE DEPOSITION ID IS D_1000014208.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 5.5
REMARK 210 IONIC STRENGTH : 100MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 5 MM CONCENTRATION OF EACH
REMARK 210 DODECAMER STRAND, 0.05 M
REMARK 210 DEUTERATED SODIUM ACETATE BUFFER
REMARK 210 AND 0.1 M NACL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : COSY, NOESY, TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR
REMARK 210 DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 20
REMARK 210
REMARK 210 REMARK: STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR EXPERIMENTS.
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 1 DC A 1 C4 DC A 1 N4 0.099
REMARK 500 1 DC A 1 N1 DC A 1 C6 0.109
REMARK 500 1 DC A 1 C4 DC A 1 C5 -0.068
REMARK 500 1 DC A 2 C4 DC A 2 N4 0.099
REMARK 500 1 DC A 2 N1 DC A 2 C6 0.107
REMARK 500 1 DC A 2 C4 DC A 2 C5 -0.069
REMARK 500 1 DC A 11 C4 DC A 11 N4 0.103
REMARK 500 1 DC A 11 N1 DC A 11 C6 0.112
REMARK 500 1 DC A 11 C4 DC A 11 C5 -0.068
REMARK 500 1 DC A 12 C4 DC A 12 N4 0.098
REMARK 500 1 DC A 12 N1 DC A 12 C6 0.107
REMARK 500 1 DC A 12 C4 DC A 12 C5 -0.069
REMARK 500 1 DT B 5 C5 DT B 5 C7 0.040
REMARK 500 2 DC A 1 C4 DC A 1 N4 0.100
REMARK 500 2 DC A 1 N1 DC A 1 C6 0.110
REMARK 500 2 DC A 1 C4 DC A 1 C5 -0.069
REMARK 500 2 DC A 2 C4 DC A 2 N4 0.099
REMARK 500 2 DC A 2 N1 DC A 2 C6 0.109
REMARK 500 2 DC A 2 C4 DC A 2 C5 -0.068
REMARK 500 2 DT A 9 C5 DT A 9 C7 0.036
REMARK 500 2 DC A 11 C4 DC A 11 N4 0.103
REMARK 500 2 DC A 11 N1 DC A 11 C6 0.113
REMARK 500 2 DC A 11 C4 DC A 11 C5 -0.066
REMARK 500 2 DC A 12 C4 DC A 12 N4 0.098
REMARK 500 2 DC A 12 N1 DC A 12 C6 0.108
REMARK 500 2 DC A 12 C4 DC A 12 C5 -0.070
REMARK 500 2 DT B 5 C5 DT B 5 C7 0.040
REMARK 500 3 DC A 1 C4 DC A 1 N4 0.098
REMARK 500 3 DC A 1 N1 DC A 1 C6 0.109
REMARK 500 3 DC A 1 C4 DC A 1 C5 -0.067
REMARK 500 3 DC A 2 C4 DC A 2 N4 0.099
REMARK 500 3 DC A 2 N1 DC A 2 C6 0.108
REMARK 500 3 DC A 2 C4 DC A 2 C5 -0.068
REMARK 500 3 DT A 9 C5 DT A 9 C7 0.036
REMARK 500 3 DC A 11 C4 DC A 11 N4 0.103
REMARK 500 3 DC A 11 N1 DC A 11 C6 0.112
REMARK 500 3 DC A 11 C4 DC A 11 C5 -0.068
REMARK 500 3 DC A 12 C4 DC A 12 N4 0.098
REMARK 500 3 DC A 12 N1 DC A 12 C6 0.107
REMARK 500 3 DC A 12 C4 DC A 12 C5 -0.069
REMARK 500 3 DT B 5 C5 DT B 5 C7 0.040
REMARK 500 4 DC A 1 C4 DC A 1 N4 0.099
REMARK 500 4 DC A 1 N1 DC A 1 C6 0.109
REMARK 500 4 DC A 1 C4 DC A 1 C5 -0.069
REMARK 500 4 DC A 2 C4 DC A 2 N4 0.100
REMARK 500 4 DC A 2 N1 DC A 2 C6 0.107
REMARK 500 4 DC A 2 C4 DC A 2 C5 -0.068
REMARK 500 4 DC A 11 C4 DC A 11 N4 0.098
REMARK 500 4 DC A 11 N1 DC A 11 C6 0.111
REMARK 500 4 DC A 11 C4 DC A 11 C5 -0.068
REMARK 500
REMARK 500 THIS ENTRY HAS 262 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 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 1 DC A 1 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES
REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES
REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DC A 2 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES
REMARK 500 1 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES
REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES
REMARK 500 1 DT A 4 N3 - C2 - O2 ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 7 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 1 DT A 8 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES
REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES
REMARK 500 1 DT A 9 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DA A 10 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DA A 10 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DC A 11 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES
REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DT B 3 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DT B 3 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DA B 4 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 DA B 4 N1 - C6 - N6 ANGL. DEV. = -6.4 DEGREES
REMARK 500 1 DT B 5 O4' - C1' - C2' ANGL. DEV. = -7.6 DEGREES
REMARK 500 1 DT B 5 O4' - C1' - N1 ANGL. DEV. = 8.8 DEGREES
REMARK 500 1 DT B 5 N3 - C2 - O2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 DT B 6 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES
REMARK 500 1 DT B 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 DA B 7 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DA B 7 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES
REMARK 500 1 DA B 8 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DA B 8 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DA B 9 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DT B 10 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DT B 10 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 2 DC A 1 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DC A 2 C6 - N1 - C2 ANGL. DEV. = -2.9 DEGREES
REMARK 500 2 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 2 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES
REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 825 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 1 DA A 3 0.23 SIDE CHAIN
REMARK 500 1 DA A 5 0.06 SIDE CHAIN
REMARK 500 1 DA A 6 0.07 SIDE CHAIN
REMARK 500 1 DT A 7 0.10 SIDE CHAIN
REMARK 500 1 DC B 2 0.08 SIDE CHAIN
REMARK 500 1 DT B 3 0.08 SIDE CHAIN
REMARK 500 1 DA B 4 0.13 SIDE CHAIN
REMARK 500 1 DA B 7 0.07 SIDE CHAIN
REMARK 500 2 DA A 3 0.22 SIDE CHAIN
REMARK 500 2 DA A 5 0.06 SIDE CHAIN
REMARK 500 2 DA A 6 0.07 SIDE CHAIN
REMARK 500 2 DT A 7 0.10 SIDE CHAIN
REMARK 500 2 DC B 1 0.06 SIDE CHAIN
REMARK 500 2 DC B 2 0.08 SIDE CHAIN
REMARK 500 2 DT B 3 0.08 SIDE CHAIN
REMARK 500 2 DA B 4 0.13 SIDE CHAIN
REMARK 500 2 DA B 7 0.07 SIDE CHAIN
REMARK 500 3 DA A 3 0.23 SIDE CHAIN
REMARK 500 3 DA A 5 0.06 SIDE CHAIN
REMARK 500 3 DA A 6 0.08 SIDE CHAIN
REMARK 500 3 DT A 7 0.10 SIDE CHAIN
REMARK 500 3 DC B 2 0.08 SIDE CHAIN
REMARK 500 3 DT B 3 0.09 SIDE CHAIN
REMARK 500 3 DA B 4 0.13 SIDE CHAIN
REMARK 500 3 DA B 7 0.07 SIDE CHAIN
REMARK 500 4 DA A 3 0.22 SIDE CHAIN
REMARK 500 4 DA A 5 0.06 SIDE CHAIN
REMARK 500 4 DA A 6 0.08 SIDE CHAIN
REMARK 500 4 DT A 7 0.11 SIDE CHAIN
REMARK 500 4 DC B 2 0.09 SIDE CHAIN
REMARK 500 4 DT B 3 0.09 SIDE CHAIN
REMARK 500 4 DA B 4 0.12 SIDE CHAIN
REMARK 500 4 DA B 7 0.07 SIDE CHAIN
REMARK 500 5 DA A 3 0.23 SIDE CHAIN
REMARK 500 5 DA A 5 0.06 SIDE CHAIN
REMARK 500 5 DA A 6 0.08 SIDE CHAIN
REMARK 500 5 DT A 7 0.10 SIDE CHAIN
REMARK 500 5 DC B 2 0.07 SIDE CHAIN
REMARK 500 5 DT B 3 0.08 SIDE CHAIN
REMARK 500 5 DA B 4 0.14 SIDE CHAIN
REMARK 500 5 DA B 7 0.07 SIDE CHAIN
REMARK 500 6 DA A 3 0.22 SIDE CHAIN
REMARK 500 6 DA A 5 0.06 SIDE CHAIN
REMARK 500 6 DA A 6 0.08 SIDE CHAIN
REMARK 500 6 DT A 7 0.10 SIDE CHAIN
REMARK 500 6 DC B 1 0.06 SIDE CHAIN
REMARK 500 6 DC B 2 0.08 SIDE CHAIN
REMARK 500 6 DT B 3 0.08 SIDE CHAIN
REMARK 500 6 DA B 4 0.12 SIDE CHAIN
REMARK 500 6 DA B 7 0.08 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 171 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1JUU A 1 12 PDB 1JUU 1JUU 1 12
DBREF 1JUU B 1 12 PDB 1JUU 1JUU 1 12
SEQRES 1 A 12 DC DC DA DT DA DA DT DT DT DA DC DC
SEQRES 1 B 12 DC DC DT DA DT DT DA DA DA DT DC DC
CRYST1 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
MODEL 1
Complete list - b 23 2 Bytes