10 20 30 40 50 60 70 80 1IKK - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 03-MAY-01 1IKK
TITLE INTRINSIC BENDING AND DEFORMABILITY AT THE T-A STEP OF TITLE 2 CCTTTAAAGG: A COMPARATIVE ANALYSIS OF T-A AND A-T STEPS TITLE 3 WITHIN A-TRACTS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*TP*TP*TP*AP*AP*AP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IT WAS SYNTHESIZED ON A EPPENDORF ECOSYN SOURCE 4 D300 SYNTHESIZER
KEYWDS B-DNA DOUBLE HELIX, A-TRACT CONTAINING A T-A STEP
EXPDTA X-RAY DIFFRACTION
AUTHOR D.R.MACK,T.K.CHIU,R.E.DICKERSON
REVDAT 2 24-FEB-09 1IKK 1 VERSN REVDAT 1 05-OCT-01 1IKK 0
JRNL AUTH D.R.MACK,T.K.CHIU,R.E.DICKERSON JRNL TITL INTRINSIC BENDING AND DEFORMABILITY AT THE T-A JRNL TITL 2 STEP OF CCTTTAAAGG: A COMPARATIVE ANALYSIS OF T-A JRNL TITL 3 AND A-T STEPS WITHIN A-TRACTS. JRNL REF J.MOL.BIOL. V. 312 1037 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11580248 JRNL DOI 10.1006/JMBI.2001.4994
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.192 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.184 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 627 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6236 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 109 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 2.320 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1IKK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-01. REMARK 100 THE RCSB ID CODE IS RCSB013367.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-97 REMARK 200 TEMPERATURE (KELVIN) : 116 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 10.500 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.26800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NDB ENTRY BDJ036 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SPERMINE-HCL, MG(OAC)2, MPD, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K
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 17.77900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.25400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.36850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.25400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.77900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.36850 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 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' - C1' - N1 ANGL. DEV. = 8.2 DEGREES REMARK 500 DT A 4 N1 - C1' - C2' ANGL. DEV. = 9.2 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DT A 4 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 5 N1 - C1' - C2' ANGL. DEV. = 12.0 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = -10.6 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = -8.5 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = -7.8 DEGREES REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DT B 14 N1 - C1' - C2' ANGL. DEV. = 9.6 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = -9.8 DEGREES REMARK 500 DT B 15 O4' - C1' - N1 ANGL. DEV. = -9.5 DEGREES REMARK 500 DA B 17 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 17 N1 - C6 - N6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = -6.1 DEGREES REMARK 500 DG B 20 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES 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 B 21 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 134 O REMARK 620 2 HOH A 138 O 89.9 REMARK 620 3 HOH B 136 O 81.3 89.6 REMARK 620 4 HOH A 139 O 90.1 180.0 90.4 REMARK 620 5 HOH A 135 O 180.0 90.1 98.7 89.9 REMARK 620 6 HOH A 137 O 98.7 90.3 180.0 89.6 81.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 22 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 143 O REMARK 620 2 HOH A 144 O 90.1 REMARK 620 3 HOH A 140 O 98.9 89.9 REMARK 620 4 HOH B 145 O 89.9 180.0 90.1 REMARK 620 5 HOH A 141 O 81.1 90.1 180.0 89.9 REMARK 620 6 HOH A 142 O 180.0 89.9 81.1 90.1 98.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 23 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 150 O REMARK 620 2 HOH B 146 O 90.0 REMARK 620 3 HOH B 151 O 180.0 90.0 REMARK 620 4 HOH B 149 O 89.8 99.1 90.2 REMARK 620 5 HOH A 148 O 90.2 80.9 89.8 180.0 REMARK 620 6 HOH B 147 O 90.0 180.0 89.9 80.9 99.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 24 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 154 O REMARK 620 2 HOH B 152 O 80.8 REMARK 620 3 HOH B 156 O 90.0 89.9 REMARK 620 4 HOH B 155 O 180.0 99.2 90.0 REMARK 620 5 HOH B 157 O 90.0 90.1 180.0 90.0 REMARK 620 6 HOH B 153 O 99.2 180.0 90.2 80.8 89.8 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 21 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 22 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 23 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 24
DBREF 1IKK A 1 10 PDB 1IKK 1IKK 1 10 DBREF 1IKK B 11 20 PDB 1IKK 1IKK 11 20
SEQRES 1 A 10 DC DC DT DT DT DA DA DA DG DG SEQRES 1 B 10 DC DC DT DT DT DA DA DA DG DG
HET MG B 21 1 HET MG A 22 1 HET MG A 23 1 HET MG B 24 1
HETNAM MG MAGNESIUM ION
FORMUL 3 MG 4(MG 2+) FORMUL 7 HOH *133(H2 O)
LINK MG MG B 21 O HOH B 134 1555 1555 1.99 LINK MG MG B 21 O HOH A 138 1555 1555 2.03 LINK MG MG B 21 O HOH B 136 1555 1555 2.23 LINK MG MG B 21 O HOH A 139 1555 1555 2.03 LINK MG MG B 21 O HOH A 135 1555 1555 2.22 LINK MG MG B 21 O HOH A 137 1555 1555 1.99 LINK MG MG A 22 O HOH B 143 1555 1555 1.99 LINK MG MG A 22 O HOH A 144 1555 1555 2.03 LINK MG MG A 22 O HOH A 140 1555 1555 1.99 LINK MG MG A 22 O HOH B 145 1555 1555 2.03 LINK MG MG A 22 O HOH A 141 1555 1555 2.22 LINK MG MG A 22 O HOH A 142 1555 1555 2.23 LINK MG MG A 23 O HOH B 150 1555 1555 2.03 LINK MG MG A 23 O HOH B 146 1555 1555 1.99 LINK MG MG A 23 O HOH B 151 1555 1555 2.03 LINK MG MG A 23 O HOH B 149 1555 1555 1.99 LINK MG MG A 23 O HOH A 148 1555 1555 2.22 LINK MG MG A 23 O HOH B 147 1555 1555 2.23 LINK MG MG B 24 O HOH B 154 1555 1555 2.23 LINK MG MG B 24 O HOH B 152 1555 1555 1.99 LINK MG MG B 24 O HOH B 156 1555 1555 2.03 LINK MG MG B 24 O HOH B 155 1555 1555 1.99 LINK MG MG B 24 O HOH B 157 1555 1555 2.03 LINK MG MG B 24 O HOH B 153 1555 1555 2.23
SITE 1 AC1 6 HOH A 135 HOH A 137 HOH A 138 HOH A 139 SITE 2 AC1 6 HOH B 134 HOH B 136 SITE 1 AC2 6 HOH A 140 HOH A 141 HOH A 142 HOH A 144 SITE 2 AC2 6 HOH B 143 HOH B 145 SITE 1 AC3 6 HOH A 148 HOH B 146 HOH B 147 HOH B 149 SITE 2 AC3 6 HOH B 150 HOH B 151 SITE 1 AC4 6 HOH B 152 HOH B 153 HOH B 154 HOH B 155 SITE 2 AC4 6 HOH B 156 HOH B 157
CRYST1 35.558 38.737 32.508 90.00 90.00 90.00 P 21 21 21 8
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 0.028123 0.000000 0.000000 0.00000
SCALE2 0.000000 0.025815 0.000000 0.00000
SCALE3 0.000000 0.000000 0.030762 0.00000