HEADER DNA 26-SEP-04 1XJX TITLE THE CRYSTAL STRUCTURES OF THE DNA BINDING SITES OF THE RUNX1 TITLE 2 TRANSCRIPTION FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS A-DNA, DOUBLE HELIX, OVERHANGING BASES, RUNX1, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.KITAYNER,H.ROZENBERG,D.RABINOVICH,Z.SHAKKED REVDAT 4 03-APR-24 1XJX 1 REMARK REVDAT 3 13-MAR-24 1XJX 1 REMARK REVDAT 2 24-FEB-09 1XJX 1 VERSN REVDAT 1 15-MAR-05 1XJX 0 JRNL AUTH M.KITAYNER,H.ROZENBERG,D.RABINOVICH,Z.SHAKKED JRNL TITL STRUCTURES OF THE DNA-BINDING SITE OF RUNT-DOMAIN JRNL TITL 2 TRANSCRIPTION REGULATORS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 236 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 15735333 JRNL DOI 10.1107/S0907444904032378 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 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) : 0.166 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.162 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 210 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 4227 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)) : 0.157 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 195 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3905 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 330 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 432.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1744 REMARK 3 NUMBER OF RESTRAINTS : 5767 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.025 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.001 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.006 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.007 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.091 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : L.CLOWNEY ET REMARK 3 AL.,J.AM.CHEM.SOC.118(1996)509-518, A.GELBIN ET AL., REMARK 3 J.AM.CHEM.SOC.118(1996)519-529, G.PARKINSON ET AL.,ACTA REMARK 3 CRYST.D52(1996)57-64 REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 1XJX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030439. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC CONFOCAL MIRROR 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 : 4315 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 18.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03900 REMARK 200 FOR THE DATA SET : 39.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23600 REMARK 200 FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: ULTIMA REMARK 200 STARTING MODEL: FIBER A-DNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, MAGNESIUM CHLORIDE, SODIUM REMARK 280 CACODYLATE ACID, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 11.90000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.85000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 5.95000 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DT A 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT A 1 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT A 1 C7 C6 REMARK 470 DT B 10 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT B 10 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT B 10 C7 C6 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 2 C6 - N1 - C2 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG A 4 N1 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 4 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC A 5 C3' - O3' - P ANGL. DEV. = -9.9 DEGREES REMARK 500 DG A 7 C3' - O3' - P ANGL. DEV. = 12.2 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 9 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 11 N1 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 11 C5 - C6 - O6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 13 N3 - C4 - C5 ANGL. DEV. = -2.8 DEGREES REMARK 500 DC B 13 C5 - C4 - N4 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG B 15 C6 - N1 - C2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG B 15 N3 - C4 - C5 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG B 15 N3 - C4 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC B 16 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 18 N1 - C6 - O6 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 18 C5 - C6 - O6 ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XJY RELATED DB: PDB REMARK 900 THE SAME NUCLEIC ACID AT 2.0 ANGSTROM DBREF 1XJX A 1 9 PDB 1XJX 1XJX 1 9 DBREF 1XJX B 10 18 PDB 1XJX 1XJX 10 18 SEQRES 1 A 9 DT DC DT DG DC DG DG DT DC SEQRES 1 B 9 DT DG DA DC DC DG DC DA DG FORMUL 3 HOH *102(H2 O) CRYST1 41.032 41.032 23.800 90.00 90.00 90.00 P 43 4 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 0.024371 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.042017 0.00000