HEADER TRANSCRIPTION 21-MAR-02 1L8R TITLE STRUCTURE OF THE RETINAL DETERMINATION PROTEIN DACHSHUND REVEALS A TITLE 2 DNA-BINDING MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: DACHSHUND; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DACHBOX-N; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS WINGED-HELIX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.S.KIM,R.ZHANG,S.E.BRAUNSTEIN,A.JOACHIMIAK,A.CVEKL,R.S.HEGDE REVDAT 4 30-OCT-24 1L8R 1 SEQADV LINK REVDAT 3 24-FEB-09 1L8R 1 VERSN REVDAT 2 01-APR-03 1L8R 1 JRNL REVDAT 1 26-JUN-02 1L8R 0 JRNL AUTH S.S.KIM,R.G.ZHANG,S.E.BRAUNSTEIN,A.JOACHIMIAK,A.CVEKL, JRNL AUTH 2 R.S.HEGDE JRNL TITL STRUCTURE OF THE RETINAL DETERMINATION PROTEIN DACHSHUND JRNL TITL 2 REVEALS A DNA BINDING MOTIF. JRNL REF STRUCTURE V. 10 787 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 12057194 JRNL DOI 10.1016/S0969-2126(02)00769-4 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 51275 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 5009 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1539 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 153 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 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1L8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000015747. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97981, 0.97904, 0.95366 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53166 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 25.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 10000, AMMONIUM SULPHATE, PH 7.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 277K 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, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 B 182 REMARK 465 SER B 183 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 LYS A 220 CG CD CE NZ REMARK 470 HIS A 221 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 220 CG CD CE NZ REMARK 470 HIS B 221 CB CG ND1 CD2 CE1 NE2 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 VAL A 223 -34.31 -141.41 REMARK 500 ASN A 281 54.26 -144.03 REMARK 500 LEU B 222 121.29 -38.41 REMARK 500 ASN B 281 57.90 -142.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 1L8R A 184 282 UNP Q9UI36 DACH1_HUMAN 184 282 DBREF 1L8R B 184 282 UNP Q9UI36 DACH1_HUMAN 184 282 SEQADV 1L8R GLY A 182 UNP Q9UI36 CLONING ARTIFACT SEQADV 1L8R SER A 183 UNP Q9UI36 CLONING ARTIFACT SEQADV 1L8R MSE A 190 UNP Q9UI36 MET 190 MODIFIED RESIDUE SEQADV 1L8R GLY B 182 UNP Q9UI36 CLONING ARTIFACT SEQADV 1L8R SER B 183 UNP Q9UI36 CLONING ARTIFACT SEQADV 1L8R MSE B 190 UNP Q9UI36 MET 190 MODIFIED RESIDUE SEQRES 1 A 101 GLY SER GLN ASN ASN GLU CYS LYS MSE VAL ASP LEU ARG SEQRES 2 A 101 GLY ALA LYS VAL ALA SER PHE THR VAL GLU GLY CYS GLU SEQRES 3 A 101 LEU ILE CYS LEU PRO GLN ALA PHE ASP LEU PHE LEU LYS SEQRES 4 A 101 HIS LEU VAL GLY GLY LEU HIS THR VAL TYR THR LYS LEU SEQRES 5 A 101 LYS ARG LEU GLU ILE THR PRO VAL VAL CYS ASN VAL GLU SEQRES 6 A 101 GLN VAL ARG ILE LEU ARG GLY LEU GLY ALA ILE GLN PRO SEQRES 7 A 101 GLY VAL ASN ARG CYS LYS LEU ILE SER ARG LYS ASP PHE SEQRES 8 A 101 GLU THR LEU TYR ASN ASP CYS THR ASN ALA SEQRES 1 B 101 GLY SER GLN ASN ASN GLU CYS LYS MSE VAL ASP LEU ARG SEQRES 2 B 101 GLY ALA LYS VAL ALA SER PHE THR VAL GLU GLY CYS GLU SEQRES 3 B 101 LEU ILE CYS LEU PRO GLN ALA PHE ASP LEU PHE LEU LYS SEQRES 4 B 101 HIS LEU VAL GLY GLY LEU HIS THR VAL TYR THR LYS LEU SEQRES 5 B 101 LYS ARG LEU GLU ILE THR PRO VAL VAL CYS ASN VAL GLU SEQRES 6 B 101 GLN VAL ARG ILE LEU ARG GLY LEU GLY ALA ILE GLN PRO SEQRES 7 B 101 GLY VAL ASN ARG CYS LYS LEU ILE SER ARG LYS ASP PHE SEQRES 8 B 101 GLU THR LEU TYR ASN ASP CYS THR ASN ALA MODRES 1L8R MSE A 190 MET SELENOMETHIONINE MODRES 1L8R MSE B 190 MET SELENOMETHIONINE HET MSE A 190 8 HET MSE B 190 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 HOH *153(H2 O) HELIX 1 1 SER A 183 GLU A 187 5 5 HELIX 2 2 LEU A 211 LEU A 219 1 9 HELIX 3 3 GLY A 225 LEU A 236 1 12 HELIX 4 4 ASN A 244 LEU A 254 1 11 HELIX 5 5 ARG A 269 ASN A 281 1 13 HELIX 6 6 LEU B 211 LEU B 219 1 9 HELIX 7 7 GLY B 224 LEU B 236 1 13 HELIX 8 8 ASN B 244 LEU B 254 1 11 HELIX 9 9 ARG B 269 ASN B 281 1 13 SHEET 1 A 5 LYS A 189 LEU A 193 0 SHEET 2 A 5 ALA A 196 VAL A 203 -1 O ALA A 196 N LEU A 193 SHEET 3 A 5 CYS A 206 CYS A 210 -1 O LEU A 208 N PHE A 201 SHEET 4 A 5 LYS A 265 SER A 268 -1 O ILE A 267 N ILE A 209 SHEET 5 A 5 VAL A 241 VAL A 242 -1 N VAL A 241 O LEU A 266 SHEET 1 B 5 CYS B 188 LEU B 193 0 SHEET 2 B 5 ALA B 196 VAL B 203 -1 O VAL B 198 N VAL B 191 SHEET 3 B 5 CYS B 206 CYS B 210 -1 O CYS B 206 N VAL B 203 SHEET 4 B 5 LYS B 265 SER B 268 -1 O ILE B 267 N ILE B 209 SHEET 5 B 5 VAL B 241 VAL B 242 -1 N VAL B 241 O LEU B 266 LINK C LYS A 189 N MSE A 190 1555 1555 1.33 LINK C MSE A 190 N VAL A 191 1555 1555 1.33 LINK C LYS B 189 N MSE B 190 1555 1555 1.33 LINK C MSE B 190 N VAL B 191 1555 1555 1.33 CRYST1 28.797 47.731 50.436 60.75 86.86 84.55 P 1 2 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 0.034726 -0.003313 -0.000336 0.00000 SCALE2 0.000000 0.021046 -0.011714 0.00000 SCALE3 0.000000 0.000000 0.022726 0.00000