HEADER TRANSCRIPTION 23-AUG-02 1MIJ TITLE CRYSTAL STRUCTURE OF THE HOMEO-PROSPERO DOMAIN OF D. TITLE 2 MELANOGASTER PROSPERO COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN PROSPERO; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HOMEO-PROSPERO DOMAIN (RESIDUES 1245-1396); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: PROS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS HOMEODOMAIN, DNA-BINDING DOMAIN, PROSPERO DOMAIN, 4-HELIX KEYWDS 2 BUNDLE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.M.RYTER,C.Q.DOE,B.W.MATTHEWS REVDAT 2 24-FEB-09 1MIJ 1 VERSN REVDAT 1 04-DEC-02 1MIJ 0 JRNL AUTH J.M.RYTER,C.Q.DOE,B.W.MATTHEWS JRNL TITL STRUCTURE OF THE DNA BINDING REGION OF PROSPERO JRNL TITL 2 REVEALS A NOVEL HOMEO-PROSPERO DOMAIN JRNL REF STRUCTURE V. 10 1541 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 12429095 JRNL DOI 10.1016/S0969-2126(02)00883-3 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 500.00 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) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 11045 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) : 0.216 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1081 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 : 1351 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 83 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 0.99 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) : 1.363 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.185 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.261 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.299 ; 2.500 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 : 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 : ION.PARAM REMARK 3 PARAMETER FILE 5 : 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 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MIJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-02. REMARK 100 THE RCSB ID CODE IS RCSB016937. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790, 0.9793, 0.9611 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 : 11045 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS, N-TETRADECYL BETA-D REMARK 280 -MALTOSIDE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 323K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 24.95000 REMARK 290 SMTRY3 2 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: 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 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 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 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 ASN A1338 53.42 -143.62 REMARK 500 REMARK 500 REMARK: NULL DBREF 1MIJ A 1245 1396 UNP P29617 PROS_DROME 1245 1396 SEQADV 1MIJ MSE A 1251 UNP P29617 MET 1251 MODIFIED RESIDUE SEQADV 1MIJ MSE A 1259 UNP P29617 MET 1259 MODIFIED RESIDUE SEQADV 1MIJ MSE A 1273 UNP P29617 MET 1273 MODIFIED RESIDUE SEQADV 1MIJ MSE A 1303 UNP P29617 MET 1303 MODIFIED RESIDUE SEQADV 1MIJ MSE A 1385 UNP P29617 MET 1385 MODIFIED RESIDUE SEQRES 1 A 152 SER SER THR LEU THR PRO MSE HIS LEU ARG LYS ALA LYS SEQRES 2 A 152 LEU MSE PHE PHE TRP VAL ARG TYR PRO SER SER ALA VAL SEQRES 3 A 152 LEU LYS MSE TYR PHE PRO ASP ILE LYS PHE ASN LYS ASN SEQRES 4 A 152 ASN THR ALA GLN LEU VAL LYS TRP PHE SER ASN PHE ARG SEQRES 5 A 152 GLU PHE TYR TYR ILE GLN MSE GLU LYS TYR ALA ARG GLN SEQRES 6 A 152 ALA VAL THR GLU GLY ILE LYS THR PRO ASP ASP LEU LEU SEQRES 7 A 152 ILE ALA GLY ASP SER GLU LEU TYR ARG VAL LEU ASN LEU SEQRES 8 A 152 HIS TYR ASN ARG ASN ASN HIS ILE GLU VAL PRO GLN ASN SEQRES 9 A 152 PHE ARG PHE VAL VAL GLU SER THR LEU ARG GLU PHE PHE SEQRES 10 A 152 ARG ALA ILE GLN GLY GLY LYS ASP THR GLU GLN SER TRP SEQRES 11 A 152 LYS LYS SER ILE TYR LYS ILE ILE SER ARG MSE ASP ASP SEQRES 12 A 152 PRO VAL PRO GLU TYR PHE LYS SER PRO MODRES 1MIJ MSE A 1251 MET SELENOMETHIONINE MODRES 1MIJ MSE A 1259 MET SELENOMETHIONINE MODRES 1MIJ MSE A 1273 MET SELENOMETHIONINE MODRES 1MIJ MSE A 1303 MET SELENOMETHIONINE MODRES 1MIJ MSE A 1385 MET SELENOMETHIONINE HET MSE A1251 16 HET MSE A1259 16 HET MSE A1273 16 HET MSE A1303 8 HET MSE A1385 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 HOH *83(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 LINK C PRO A1250 N AMSE A1251 1555 1555 1.33 LINK C PRO A1250 N BMSE A1251 1555 1555 1.33 LINK C AMSE A1251 N HIS A1252 1555 1555 1.33 LINK C BMSE A1251 N HIS A1252 1555 1555 1.33 LINK C LEU A1258 N AMSE A1259 1555 1555 1.33 LINK C LEU A1258 N BMSE A1259 1555 1555 1.33 LINK C AMSE A1259 N PHE A1260 1555 1555 1.33 LINK C BMSE A1259 N PHE A1260 1555 1555 1.33 LINK C LYS A1272 N BMSE A1273 1555 1555 1.33 LINK C LYS A1272 N AMSE A1273 1555 1555 1.33 LINK C BMSE A1273 N TYR A1274 1555 1555 1.33 LINK C AMSE A1273 N TYR A1274 1555 1555 1.33 LINK C GLN A1302 N MSE A1303 1555 1555 1.33 LINK C MSE A1303 N GLU A1304 1555 1555 1.33 LINK C BARG A1384 N MSE A1385 1555 1555 1.33 LINK C AARG A1384 N MSE A1385 1555 1555 1.33 LINK C MSE A1385 N ASP A1386 1555 1555 1.32 CRYST1 35.300 49.900 51.500 90.00 97.40 90.00 P 1 21 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 0.028329 0.000000 0.003679 0.00000 SCALE2 0.000000 0.020040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019581 0.00000