HEADER PROTEIN BINDING 05-JUN-15 5A48 TITLE CRYSTAL STRUCTURE OF THE LOTUS DOMAIN (AA 139-240) OF DROSOPHILA TITLE 2 OSKAR IN P65 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATERNAL EFFECT PROTEIN OSKAR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LOTUS DOMAIN, RESIDUES 139-240; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN BINDING, OST-HTH DOMAIN, WINGED HELIX-TURN-HELIX, DIMER, KEYWDS 2 VASA INTERACTION, GERM PLASM, EXPDTA X-RAY DIFFRACTION AUTHOR M.JESKE,S.GLATT,A.EPHRUSSI,C.W.MUELLER REVDAT 3 12-AUG-15 5A48 1 JRNL REVDAT 2 29-JUL-15 5A48 1 JRNL REVDAT 1 22-JUL-15 5A48 0 JRNL AUTH M.JESKE,M.BORDI,S.GLATT,S.MULLER,V.RYBIN,C.W.MULLER, JRNL AUTH 2 A.EPHRUSSI JRNL TITL THE CRYSTAL STRUCTURE OF THE DROSOPHILA GERMLINE INDUCER JRNL TITL 2 OSKAR IDENTIFIES TWO DOMAINS WITH DISTINCT VASA HELICASE- JRNL TITL 3 AND RNA-BINDING ACTIVITIES. JRNL REF CELL REP. V. 12 587 2015 JRNL REFN ISSN 2211-1247 JRNL PMID 26190108 JRNL DOI 10.1016/J.CELREP.2015.06.055 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.350 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.038 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.36 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.82 REMARK 3 NUMBER OF REFLECTIONS : 7330 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1882 REMARK 3 R VALUE (WORKING SET) : 0.1858 REMARK 3 FREE R VALUE : 0.2338 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 368 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 46.0467 - 3.3897 1.00 2349 121 0.1645 0.2062 REMARK 3 2 3.3897 - 2.6906 1.00 2318 123 0.2011 0.2495 REMARK 3 3 2.6906 - 2.3505 0.99 2295 124 0.2476 0.3133 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.31 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.62 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 1448 REMARK 3 ANGLE : 0.710 1964 REMARK 3 CHIRALITY : 0.050 233 REMARK 3 PLANARITY : 0.002 251 REMARK 3 DIHEDRAL : 12.811 542 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE OCCUPANCY OF SIDE CHAIN ATOMS, FOR WHICH ELECTRON REMARK 3 DENSITY WAS POOR, IS SET TO 0. REMARK 4 REMARK 4 5A48 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUN-15. REMARK 100 THE PDBE ID CODE IS EBI-63965. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7333 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.35 REMARK 200 RESOLUTION RANGE LOW (A) : 50.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.49 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.4 REMARK 200 R MERGE (I) : 0.23 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.66 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: 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: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.30667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.65333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.98000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.32667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 91.63333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -0.6 KCAL/MOL 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 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 137 REMARK 465 SER A 222 REMARK 465 LEU A 223 REMARK 465 LYS A 224 REMARK 465 ASN A 225 REMARK 465 GLY A 226 REMARK 465 HIS A 227 REMARK 465 LEU A 228 REMARK 465 LEU A 229 REMARK 465 ASP A 230 REMARK 465 MET A 231 REMARK 465 VAL A 232 REMARK 465 LEU A 233 REMARK 465 ASN A 234 REMARK 465 GLN A 235 REMARK 465 LYS A 236 REMARK 465 GLU A 237 REMARK 465 ARG A 238 REMARK 465 THR A 239 REMARK 465 SER A 240 REMARK 465 GLY B 137 REMARK 465 ASN B 234 REMARK 465 GLN B 235 REMARK 465 LYS B 236 REMARK 465 GLU B 237 REMARK 465 ARG B 238 REMARK 465 THR B 239 REMARK 465 SER B 240 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 MET A 139 SD CE REMARK 470 GLN A 169 CG CD OE1 NE2 REMARK 470 LYS A 220 CG CD CE NZ REMARK 470 GLU B 152 CG CD OE1 OE2 REMARK 470 GLN B 169 CG CD OE1 NE2 REMARK 470 LYS B 224 CB CG CD CE NZ REMARK 470 ASN B 225 CG OD1 ND2 REMARK 470 LEU B 233 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLU A 143 O HOH A 2001 2.00 REMARK 500 O ASN B 225 O HOH B 2033 2.05 REMARK 500 O HOH B 2019 O HOH B 2020 1.97 REMARK 500 O HOH B 2020 O HOH B 2025 2.08 REMARK 500 O HOH B 2021 O HOH B 2028 1.98 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 ASN A 204 -6.63 80.32 REMARK 500 LYS A 220 79.82 -68.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A49 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LOTUS DOMAIN (AA 139-222) REMARK 900 OF DROSOPHILA OSKAR IN C222 REMARK 900 RELATED ID: 5A4A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OSK DOMAIN OF DROSOPHILA REMARK 900 OSKAR DBREF 5A48 A 139 240 UNP P25158 OSKA_DROME 139 240 DBREF 5A48 B 139 240 UNP P25158 OSKA_DROME 139 240 SEQADV 5A48 GLY A 137 UNP P25158 EXPRESSION TAG SEQADV 5A48 HIS A 138 UNP P25158 EXPRESSION TAG SEQADV 5A48 GLY B 137 UNP P25158 EXPRESSION TAG SEQADV 5A48 HIS B 138 UNP P25158 EXPRESSION TAG SEQRES 1 A 104 GLY HIS MET THR ILE ILE GLU SER ASN TYR ILE SER VAL SEQRES 2 A 104 ARG GLU GLU TYR PRO ASP ILE ASP SER GLU VAL ARG ALA SEQRES 3 A 104 ILE LEU LEU SER HIS ALA GLN ASN GLY ILE THR ILE SER SEQRES 4 A 104 SER ILE LYS SER GLU TYR ARG LYS LEU THR GLY ASN PRO SEQRES 5 A 104 PHE PRO LEU HIS ASP ASN VAL THR ASP PHE LEU LEU THR SEQRES 6 A 104 ILE PRO ASN VAL THR ALA GLU CYS SER GLU SER GLY LYS SEQRES 7 A 104 ARG ILE PHE ASN LEU LYS ALA SER LEU LYS ASN GLY HIS SEQRES 8 A 104 LEU LEU ASP MET VAL LEU ASN GLN LYS GLU ARG THR SER SEQRES 1 B 104 GLY HIS MET THR ILE ILE GLU SER ASN TYR ILE SER VAL SEQRES 2 B 104 ARG GLU GLU TYR PRO ASP ILE ASP SER GLU VAL ARG ALA SEQRES 3 B 104 ILE LEU LEU SER HIS ALA GLN ASN GLY ILE THR ILE SER SEQRES 4 B 104 SER ILE LYS SER GLU TYR ARG LYS LEU THR GLY ASN PRO SEQRES 5 B 104 PHE PRO LEU HIS ASP ASN VAL THR ASP PHE LEU LEU THR SEQRES 6 B 104 ILE PRO ASN VAL THR ALA GLU CYS SER GLU SER GLY LYS SEQRES 7 B 104 ARG ILE PHE ASN LEU LYS ALA SER LEU LYS ASN GLY HIS SEQRES 8 B 104 LEU LEU ASP MET VAL LEU ASN GLN LYS GLU ARG THR SER FORMUL 3 HOH *68(H2 O) HELIX 1 1 ASN A 145 TYR A 153 1 9 HELIX 2 2 ASP A 155 SER A 166 1 12 HELIX 3 3 THR A 173 GLY A 186 1 14 HELIX 4 4 ASN A 194 LEU A 200 1 7 HELIX 5 5 ASN B 145 TYR B 153 1 9 HELIX 6 6 ASP B 155 HIS B 167 1 13 HELIX 7 7 THR B 173 GLY B 186 1 14 HELIX 8 8 ASN B 194 LEU B 200 1 7 SHEET 1 AA 4 ARG A 215 LEU A 219 0 SHEET 2 AA 4 VAL A 205 CYS A 209 -1 O THR A 206 N ASN A 218 SHEET 3 AA 4 VAL B 205 CYS B 209 -1 O VAL B 205 N CYS A 209 SHEET 4 AA 4 ARG B 215 LEU B 219 -1 O ILE B 216 N GLU B 208 CRYST1 53.160 53.160 109.960 90.00 90.00 120.00 P 65 12 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 0.018811 0.010861 0.000000 0.00000 SCALE2 0.000000 0.021721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009094 0.00000