10 20 30 40 50 60 70 80 2O4A - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION/DNA 04-DEC-06 2O4A
TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL CUT DOMAIN OF SATB1 TITLE 2 BOUND TO MATRIX ATTACHMENT REGION DNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN SATB1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL CUT DOMAIN (RESIDUES 368-452); COMPND 5 SYNONYM: SPECIAL AT-RICH SEQUENCE-BINDING PROTEIN 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*DGP*DCP*DTP*DAP*DAP*DTP*DAP*DTP*DAP*DTP*DGP*DC)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(*DGP*DCP*DAP*DTP*DAP*DTP*DAP*DTP*DTP*DAP*DGP*DC)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES
KEYWDS PROTEIN-DNA COMPLEX, TRANSCRIPTION, TRANSCRIPTION/DNA KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR K.YAMASAKI,T.AKIBA,K.HARATA
REVDAT 2 24-FEB-09 2O4A 1 VERSN REVDAT 1 14-AUG-07 2O4A 0
JRNL AUTH K.YAMASAKI,T.AKIBA,T.YAMASAKI,K.HARATA JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF THE MATRIX JRNL TITL 2 ATTACHMENT REGION OF DNA BY TRANSCRIPTION FACTOR JRNL TITL 3 SATB1. JRNL REF NUCLEIC ACIDS RES. V. 35 5073 2007 JRNL REFN ISSN 0305-1048 JRNL PMID 17652321 JRNL DOI 10.1093/NAR/GKM504
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 477657.400 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.3 REMARK 3 NUMBER OF REFLECTIONS : 14958 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1522 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 57.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1494 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 163 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 696 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.04000 REMARK 3 B22 (A**2) : -1.46000 REMARK 3 B33 (A**2) : -2.58000 REMARK 3 B12 (A**2) : 5.05000 REMARK 3 B13 (A**2) : 2.73000 REMARK 3 B23 (A**2) : 5.10000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.28 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.04 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.14 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.230 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.940 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.950 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.910 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.44 REMARK 3 BSOL : 67.46 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2O4A COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-06. REMARK 100 THE RCSB ID CODE IS RCSB040668.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14958 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 22.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 55.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.27500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: PDB ENTRY 2O49 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 20000, 0.05M TRISHCL, 0.01M REMARK 280 MAGNESIUM SULFATE, 20% ETHYLENE GLYCOL, PH 8.00, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, A 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 364 REMARK 465 SER A 365 REMARK 465 HIS A 366 REMARK 465 MET A 367 REMARK 465 ASN A 368 REMARK 465 THR A 369 REMARK 465 LYS A 454 REMARK 465 ARG A 455 REMARK 465 LYS A 456
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 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 398 23.67 -144.65 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YSE RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF ESSENTIALLY THE SAME PROTEIN REMARK 900 DOMAIN IN A FREE STATE REMARK 900 RELATED ID: 2O49 RELATED DB: PDB
DBREF 2O4A A 368 452 UNP Q01826 SATB1_HUMAN 368 452 DBREF 2O4A B 1 12 PDB 2O4A 2O4A 1 12 DBREF 2O4A C 1 12 PDB 2O4A 2O4A 1 12
SEQADV 2O4A GLY A 364 UNP Q01826 CLONING ARTIFACT SEQADV 2O4A SER A 365 UNP Q01826 CLONING ARTIFACT SEQADV 2O4A HIS A 366 UNP Q01826 CLONING ARTIFACT SEQADV 2O4A MET A 367 UNP Q01826 CLONING ARTIFACT SEQADV 2O4A ARG A 453 UNP Q01826 CLONING ARTIFACT SEQADV 2O4A LYS A 454 UNP Q01826 CLONING ARTIFACT SEQADV 2O4A ARG A 455 UNP Q01826 CLONING ARTIFACT SEQADV 2O4A LYS A 456 UNP Q01826 CLONING ARTIFACT
SEQRES 1 A 93 GLY SER HIS MET ASN THR GLU VAL SER SER GLU ILE TYR SEQRES 2 A 93 GLN TRP VAL ARG ASP GLU LEU LYS ARG ALA GLY ILE SER SEQRES 3 A 93 GLN ALA VAL PHE ALA ARG VAL ALA PHE ASN ARG THR GLN SEQRES 4 A 93 GLY LEU LEU SER GLU ILE LEU ARG LYS GLU GLU ASP PRO SEQRES 5 A 93 LYS THR ALA SER GLN SER LEU LEU VAL ASN LEU ARG ALA SEQRES 6 A 93 MET GLN ASN PHE LEU GLN LEU PRO GLU ALA GLU ARG ASP SEQRES 7 A 93 ARG ILE TYR GLN ASP GLU ARG GLU ARG SER LEU ARG LYS SEQRES 8 A 93 ARG LYS SEQRES 1 B 12 DG DC DT DA DA DT DA DT DA DT DG DC SEQRES 1 C 12 DG DC DA DT DA DT DA DT DT DA DG DC
FORMUL 4 HOH *108(H2 O)
HELIX 1 1 GLU A 374 GLY A 387 1 14 HELIX 2 2 SER A 389 ASN A 399 1 11 HELIX 3 3 THR A 401 GLU A 412 1 12 HELIX 4 4 SER A 419 GLN A 434 1 16 HELIX 5 5 PRO A 436 ARG A 453 1 18
CRYST1 32.659 38.318 40.709 71.34 82.50 66.63 P 1 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 0.030619 -0.013231 -0.000139 0.00000
SCALE2 0.000000 0.028430 -0.008766 0.00000
SCALE3 0.000000 0.000000 0.025928 0.00000