HEADER TRANSCRIPTION REGULATION/DNA 09-OCT-04 1XPX TITLE STRUCTURAL BASIS OF PROSPERO-DNA INTERACTION; IMPLICATIONS FOR TITLE 2 TRANSCRIPTION REGULATION IN DEVELOPING CELLS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3'; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*T)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROTEIN PROSPERO; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: HOMEO-PROSPERO DOMAIN (RESIDUES 1245-1401); COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 7 ORGANISM_COMMON: FRUIT FLY; SOURCE 8 ORGANISM_TAXID: 7227; SOURCE 9 GENE: PROS; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HOMEODOMAIN, PROTEIN-DNA BINDING, PROSPERO, NEURAL CELL DEVELOPMENT, KEYWDS 2 TRANSCRIPTION REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.S.YOUSEF,B.W.MATTHEWS REVDAT 3 14-FEB-24 1XPX 1 REMARK REVDAT 2 24-FEB-09 1XPX 1 VERSN REVDAT 1 03-MAY-05 1XPX 0 JRNL AUTH M.S.YOUSEF,B.W.MATTHEWS JRNL TITL STRUCTURAL BASIS OF PROSPERO-DNA INTERACTION: IMPLICATIONS JRNL TITL 2 FOR TRANSCRIPTION REGULATIONIN DEVELOPING CELLS. JRNL REF STRUCTURE V. 13 601 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 15837198 JRNL DOI 10.1016/J.STR.2005.01.023 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.M.RYTER,C.Q.DOE,B.W.MATTHEWS REMARK 1 TITL STRUCTURE OF THE DNA BINDING REGION OF PROSPERO REVEALS A REMARK 1 TITL 2 NOVEL HOMEO-PROSPERO DOMAIN. REMARK 1 REF STRUCTURE V. 10 1541 2002 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 12429095 REMARK 1 DOI 10.1016/S0969-2126(02)00883-3 REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 5532 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) : 0.217 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 317 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 : 1240 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 15 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 1XPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6354 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 113.33050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.35400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.35400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 169.99575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.35400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.35400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.66525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.35400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.35400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 169.99575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.35400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.35400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 56.66525 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 113.33050 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: D, 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 THR A 1241 REMARK 465 PRO A 1242 REMARK 465 LEU A 1243 REMARK 465 HIS A 1244 REMARK 465 GLY A 1314 REMARK 465 ILE A 1315 REMARK 465 LYS A 1316 REMARK 465 THR A 1317 REMARK 465 PRO A 1318 REMARK 465 ASP A 1319 REMARK 465 ASP A 1320 REMARK 465 LEU A 1321 REMARK 465 LEU A 1322 REMARK 465 ILE A 1323 REMARK 465 ALA A 1324 REMARK 465 GLY A 1325 REMARK 465 ASP A 1326 REMARK 465 LEU A 1402 REMARK 465 GLU A 1403 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 LYS A1282 -48.25 -29.16 REMARK 500 ASN A1283 -83.48 -67.07 REMARK 500 ASN A1284 -34.70 -38.80 REMARK 500 ARG A1339 -51.30 -23.87 REMARK 500 ASN A1341 40.77 35.65 REMARK 500 LYS A1368 13.47 -69.34 REMARK 500 TYR A1392 1.41 -65.70 REMARK 500 GLU A1400 -133.90 -56.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC C 404 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. DBREF 1XPX A 1241 1403 UNP P29617 PROS_DROME 1241 1403 DBREF 1XPX D 300 309 PDB 1XPX 1XPX 300 309 DBREF 1XPX C 404 413 PDB 1XPX 1XPX 404 413 SEQRES 1 D 10 DA DG DC DA DT DG DC DC DT DG SEQRES 1 C 10 DC DA DG DG DC DA DT DG DC DT SEQRES 1 A 163 THR PRO LEU HIS SER SER THR LEU THR PRO MET HIS LEU SEQRES 2 A 163 ARG LYS ALA LYS LEU MET PHE PHE TRP VAL ARG TYR PRO SEQRES 3 A 163 SER SER ALA VAL LEU LYS MET TYR PHE PRO ASP ILE LYS SEQRES 4 A 163 PHE ASN LYS ASN ASN THR ALA GLN LEU VAL LYS TRP PHE SEQRES 5 A 163 SER ASN PHE ARG GLU PHE TYR TYR ILE GLN MET GLU LYS SEQRES 6 A 163 TYR ALA ARG GLN ALA VAL THR GLU GLY ILE LYS THR PRO SEQRES 7 A 163 ASP ASP LEU LEU ILE ALA GLY ASP SER GLU LEU TYR ARG SEQRES 8 A 163 VAL LEU ASN LEU HIS TYR ASN ARG ASN ASN HIS ILE GLU SEQRES 9 A 163 VAL PRO GLN ASN PHE ARG PHE VAL VAL GLU SER THR LEU SEQRES 10 A 163 ARG GLU PHE PHE ARG ALA ILE GLN GLY GLY LYS ASP THR SEQRES 11 A 163 GLU GLN SER TRP LYS LYS SER ILE TYR LYS ILE ILE SER SEQRES 12 A 163 ARG MET ASP ASP PRO VAL PRO GLU TYR PHE LYS SER PRO SEQRES 13 A 163 ASN PHE LEU GLU GLN LEU GLU FORMUL 4 HOH *15(H2 O) HELIX 1 1 THR A 1249 PHE A 1260 1 12 HELIX 2 2 SER A 1267 PHE A 1275 1 9 HELIX 3 3 ASN A 1281 GLU A 1313 1 33 HELIX 4 4 SER A 1327 ASN A 1338 1 12 HELIX 5 5 PRO A 1346 GLY A 1366 1 21 HELIX 6 6 GLY A 1367 GLU A 1371 5 5 HELIX 7 7 LYS A 1375 ARG A 1384 1 10 HELIX 8 8 PRO A 1390 SER A 1395 5 6 HELIX 9 9 ASN A 1397 GLN A 1401 5 5 CRYST1 44.708 44.708 226.661 90.00 90.00 90.00 P 43 21 2 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 0.022367 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004412 0.00000