Dbfetch
HEADER DNA 14-DEC-94 101D
TITLE REFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN ELECTRON
TITLE 2 DENSITY MAP INTERPRETATION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3');
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA
EXPDTA X-RAY DIFFRACTION
AUTHOR D.S.GOODSELL,M.L.KOPKA,R.E.DICKERSON
REVDAT 3 22-NOV-23 101D 1 REMARK LINK
REVDAT 2 24-FEB-09 101D 1 VERSN
REVDAT 1 27-FEB-95 101D 0
JRNL AUTH D.S.GOODSELL,M.L.KOPKA,R.E.DICKERSON
JRNL TITL REFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN
JRNL TITL 2 ELECTRON DENSITY MAP INTERPRETATION.
JRNL REF BIOCHEMISTRY V. 34 4983 1995
JRNL REFN ISSN 0006-2960
JRNL PMID 7711020
JRNL DOI 10.1021/BI00015A009
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH M.L.KOPKA,C.YOON,D.S.GOODSELL,P.PJURA,R.E.DICKERSON
REMARK 1 TITL BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND
REMARK 1 TITL 2 C-G-C-G-A-A-T-T-BRC-G-C-G
REMARK 1 REF J.MOL.BIOL. V. 183 553 1985
REMARK 1 REFN ISSN 0022-2836
REMARK 2
REMARK 2 RESOLUTION. 2.25 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NUCLSQ
REMARK 3 AUTHORS : WESTHOF,DUMAS,MORAS
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 2430
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : 0.163
REMARK 3 R VALUE (WORKING SET) : NULL
REMARK 3 FREE R VALUE : 0.252
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 0
REMARK 3 NUCLEIC ACID ATOMS : 488
REMARK 3 HETEROGEN ATOMS : 32
REMARK 3 SOLVENT ATOMS : 36
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 SUGAR-BASE BOND DISTANCE (A) : 0.024 ; 0.030
REMARK 3 SUGAR-BASE BOND ANGLE DISTANCE (A) : 0.040 ; 0.040
REMARK 3 PHOSPHATE BONDS DISTANCE (A) : 0.026 ; 0.040
REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A) : 0.057 ; 0.050
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : 0.014 ; 0.020
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.161 ; 0.150
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION CONTACT (A) : 0.093 ; 0.100
REMARK 3 MULTIPLE TORSION CONTACT (A) : 0.097 ; 0.100
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 SUGAR-BASE BONDS (A**2) : 4.282 ; 6.000
REMARK 3 SUGAR-BASE ANGLES (A**2) : 4.990 ; 6.000
REMARK 3 PHOSPHATE BONDS (A**2) : 5.693 ; 6.000
REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A**2) : 5.227 ; 6.000
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 101D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB.
REMARK 100 THE DEPOSITION ID IS D_1000170002.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.45
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 12.13500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.78500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.81000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.78500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.13500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.81000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
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 C1' -0.069
REMARK 500 DC A 1 O4' DC A 1 C1' 0.068
REMARK 500 DC A 1 O4' DC A 1 C4' -0.071
REMARK 500 DG A 2 N7 DG A 2 C8 -0.038
REMARK 500 DC A 3 C2' DC A 3 C1' -0.067
REMARK 500 DG A 4 C4' DG A 4 C3' 0.061
REMARK 500 DA A 6 C2' DA A 6 C1' -0.090
REMARK 500 DT A 7 O4' DT A 7 C1' 0.067
REMARK 500 DT A 7 O4' DT A 7 C4' -0.064
REMARK 500 DT A 8 O4' DT A 8 C1' 0.072
REMARK 500 DT A 8 O3' DT A 8 C3' -0.038
REMARK 500 DC A 11 C2' DC A 11 C1' -0.069
REMARK 500 DC A 11 O4' DC A 11 C1' 0.083
REMARK 500 DG B 14 C5' DG B 14 C4' 0.050
REMARK 500 DG B 14 O4' DG B 14 C1' 0.068
REMARK 500 DC B 15 O3' DC B 15 C3' -0.039
REMARK 500 DA B 17 N7 DA B 17 C8 -0.056
REMARK 500 DT B 19 O3' DT B 19 C3' -0.063
REMARK 500 DT B 20 C2' DT B 20 C1' -0.069
REMARK 500 DG B 24 O4' DG B 24 C4' -0.071
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 C5' - C4' - O4' ANGL. DEV. = 9.7 DEGREES
REMARK 500 DC A 1 C2 - N3 - C4 ANGL. DEV. = 4.1 DEGREES
REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -5.2 DEGREES
REMARK 500 DC A 1 C5 - C4 - N4 ANGL. DEV. = 7.4 DEGREES
REMARK 500 DG A 2 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES
REMARK 500 DG A 2 O5' - C5' - C4' ANGL. DEV. = -5.5 DEGREES
REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 19.2 DEGREES
REMARK 500 DC A 3 N3 - C4 - C5 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DG A 4 C5' - C4' - O4' ANGL. DEV. = 12.2 DEGREES
REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES
REMARK 500 DG A 4 C6 - N1 - C2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 DG A 4 N1 - C2 - N3 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DG A 4 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG A 4 N3 - C2 - N2 ANGL. DEV. = -5.3 DEGREES
REMARK 500 DG A 4 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DA A 5 C6 - N1 - C2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DA A 5 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES
REMARK 500 DA A 5 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES
REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES
REMARK 500 DA A 6 C6 - N1 - C2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DA A 6 C5 - C6 - N1 ANGL. DEV. = -3.0 DEGREES
REMARK 500 DA A 6 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES
REMARK 500 DT A 7 OP1 - P - OP2 ANGL. DEV. = -13.4 DEGREES
REMARK 500 DT A 7 O5' - P - OP2 ANGL. DEV. = 8.5 DEGREES
REMARK 500 DT A 7 O5' - C5' - C4' ANGL. DEV. = -7.7 DEGREES
REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES
REMARK 500 DT A 7 C2 - N3 - C4 ANGL. DEV. = -6.6 DEGREES
REMARK 500 DT A 7 N3 - C4 - C5 ANGL. DEV. = 5.6 DEGREES
REMARK 500 DT A 7 C3' - O3' - P ANGL. DEV. = 14.7 DEGREES
REMARK 500 DT A 8 N1 - C2 - N3 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DT A 8 C2 - N3 - C4 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DT A 8 N3 - C4 - C5 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DT A 8 N3 - C4 - O4 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DT A 8 C3' - O3' - P ANGL. DEV. = 24.0 DEGREES
REMARK 500 CBR A 9 C3' - O3' - P ANGL. DEV. = 15.6 DEGREES
REMARK 500 DG A 10 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES
REMARK 500 DG A 10 P - O5' - C5' ANGL. DEV. = 18.3 DEGREES
REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DG A 10 C6 - N1 - C2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 DG A 10 N1 - C2 - N3 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG A 10 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG A 10 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES
REMARK 500 DC A 11 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES
REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES
REMARK 500 DG A 12 OP1 - P - OP2 ANGL. DEV. = -13.0 DEGREES
REMARK 500 DG A 12 O5' - C5' - C4' ANGL. DEV. = -8.2 DEGREES
REMARK 500 DG A 12 O4' - C1' - C2' ANGL. DEV. = 3.7 DEGREES
REMARK 500 DG A 12 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DC B 13 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DC B 13 N3 - C4 - C5 ANGL. DEV. = -2.5 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 96 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 26 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 61 O
REMARK 620 2 HOH B 60 O 88.3
REMARK 620 3 HOH B 62 O 76.9 80.2
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NT B 25
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 26
DBREF 101D A 1 12 PDB 101D 101D 1 12
DBREF 101D B 13 24 PDB 101D 101D 13 24