10 20 30 40 50 60 70 80 2I2I - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 16-AUG-06 2I2I
TITLE CRYSTAL STRUCTURE OF THE DB293-D(CGCGAATTCGCG)2 COMPLEX.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: AT-RICH REGION IN THE GENOME OF ORGANISMS.
KEYWDS B-TYPE DNA DODECAMER WITH COMPOUND DB 293.
EXPDTA X-RAY DIFFRACTION
AUTHOR M.P.H.LEE,S.NEIDLE
REVDAT 2 24-FEB-09 2I2I 1 VERSN REVDAT 1 31-JUL-07 2I2I 0
JRNL AUTH M.P.H.LEE,S.NEIDLE JRNL TITL CRYSTAL STRUCTURE OF THE DB293-D(CGCGAATTCGCG)2 JRNL TITL 2 COMPLEX. JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.63 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) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 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) : 0.228 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.220 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.760 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 799 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8184 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.212 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.205 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 9.870 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 687 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6961 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 594.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2379 REMARK 3 NUMBER OF RESTRAINTS : 2537 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.015 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.007 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.063 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2I2I COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-06. REMARK 100 THE RCSB ID CODE IS RCSB039054.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 105.0 REMARK 200 PH : 7.00 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : OSMIC FOCUSING MIRROR SYSTEM REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8262 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 25.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.360 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.24900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 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: DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE. REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, DNA DODECAMER, REMARK 280 MPD, COMPOUND DB 293, SODIUM CACODYLATE BUFFER., PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, PH 7.00
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 12.08800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.87500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.88100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.87500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.08800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.88100 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. = -4.8 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG A 10 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = -5.2 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 DG B 22 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 95 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 98 DISTANCE = 5.27 ANGSTROMS
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 B 102 O REMARK 620 2 HOH B 104 O 88.8 REMARK 620 3 HOH A 102 O 89.1 177.8 REMARK 620 4 HOH A 100 O 91.3 91.0 89.5 REMARK 620 5 HOH B 103 O 89.5 90.6 88.9 178.2 REMARK 620 6 HOH A 101 O 179.0 90.6 91.5 89.6 89.7 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 A 26 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MBC A 25
DBREF 2I2I A 1 12 PDB 2I2I 2I2I 1 12 DBREF 2I2I B 13 24 PDB 2I2I 2I2I 13 24
SEQRES 1 A 12 DC DG DC DG DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA DT DT DC DG DC DG
HET MG A 26 1 HET MBC A 25 26
HETNAM MG MAGNESIUM ION HETNAM MBC 2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-FURYL)-1H- HETNAM 2 MBC BENZIMIDAZOLE-5-CARBOXIMIDAMIDE
HETSYN MBC DB 293
FORMUL 3 MG MG 2+ FORMUL 4 MBC C19 H16 N6 O FORMUL 5 HOH *81(H2 O)
LINK MG MG A 26 O HOH B 102 1555 1555 2.13 LINK MG MG A 26 O HOH B 104 1555 1555 2.11 LINK MG MG A 26 O HOH A 102 1555 1555 2.12 LINK MG MG A 26 O HOH A 100 1555 1555 2.12 LINK MG MG A 26 O HOH B 103 1555 1555 2.13 LINK MG MG A 26 O HOH A 101 1555 1555 2.13
SITE 1 AC1 6 HOH A 100 HOH A 101 HOH A 102 HOH B 102 SITE 2 AC1 6 HOH B 103 HOH B 104 SITE 1 AC2 10 DT A 7 DT A 8 DC A 9 HOH A 48 SITE 2 AC2 10 HOH A 55 DA B 17 DA B 18 DT B 19 SITE 3 AC2 10 DT B 20 DC B 21
CRYST1 24.176 39.762 65.750 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 0.041363 0.000000 0.000000 0.00000
SCALE2 0.000000 0.025150 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015209 0.00000