HEADER RNA BINDING PROTEIN 07-NOV-17 6BK4 TITLE CRYSTAL STRUCTURE OF THE HR-1 DOMAIN OF DROSOPHILA CAPRIN IN THE TITLE 2 P212121 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPRIN HOMOLOG; COMPND 3 CHAIN: A, B; COMPND 4 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: CAPR, CG18811; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA-BINDING, ALPHA-HELICAL, FMRP PARNTER, CELLULAR PROLIFERATION, RNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHU,Y.WU,X.HUANG,Z.DU REVDAT 4 04-OCT-23 6BK4 1 REMARK REVDAT 3 01-JAN-20 6BK4 1 REMARK REVDAT 2 20-FEB-19 6BK4 1 REMARK REVDAT 1 07-NOV-18 6BK4 0 JRNL AUTH J.ZHU,Y.WU,X.HUANG,Z.DU JRNL TITL CRYSTAL STRUCTURE OF A DIMERIZATION DOMAIN OF DROSOPHILA JRNL TITL 2 CAPRIN: FURTHER SUPPORTS THE ASSEMBLY OF AN EVOLUTIONARILY JRNL TITL 3 CONSERVED RIBONUCLEOPROTEIN COMPLEX CONTAINING CAPRIN AND JRNL TITL 4 FMRP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 30061 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.650 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 36.2771 - 4.3360 0.96 2077 147 0.2407 0.2559 REMARK 3 2 4.3360 - 3.4425 1.00 2065 147 0.2018 0.2201 REMARK 3 3 3.4425 - 3.0076 1.00 2029 144 0.2175 0.2459 REMARK 3 4 3.0076 - 2.7327 1.00 2013 144 0.2079 0.2445 REMARK 3 5 2.7327 - 2.5369 1.00 2004 143 0.2032 0.2460 REMARK 3 6 2.5369 - 2.3873 1.00 1999 143 0.1962 0.2465 REMARK 3 7 2.3873 - 2.2678 1.00 2002 142 0.1962 0.2385 REMARK 3 8 2.2678 - 2.1691 1.00 1977 141 0.2021 0.2461 REMARK 3 9 2.1691 - 2.0856 1.00 1994 142 0.1981 0.2341 REMARK 3 10 2.0856 - 2.0136 1.00 1976 141 0.1995 0.2563 REMARK 3 11 2.0136 - 1.9507 1.00 1979 142 0.2141 0.2737 REMARK 3 12 1.9507 - 1.8949 1.00 1966 139 0.2385 0.2779 REMARK 3 13 1.8949 - 1.8450 1.00 1993 142 0.2543 0.2945 REMARK 3 14 1.8450 - 1.8000 1.00 1988 142 0.2725 0.3140 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.11 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 : 0.006 1659 REMARK 3 ANGLE : 0.687 2228 REMARK 3 CHIRALITY : 0.044 253 REMARK 3 PLANARITY : 0.003 290 REMARK 3 DIHEDRAL : 12.422 1012 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 43.6037 32.6668 32.3529 REMARK 3 T TENSOR REMARK 3 T11: 0.2058 T22: 0.2337 REMARK 3 T33: 0.2251 T12: -0.0084 REMARK 3 T13: -0.0098 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.9542 L22: 1.5225 REMARK 3 L33: 0.8065 L12: 0.1209 REMARK 3 L13: -0.2286 L23: 0.4693 REMARK 3 S TENSOR REMARK 3 S11: 0.0815 S12: -0.0883 S13: -0.1468 REMARK 3 S21: 0.0751 S22: -0.1461 S23: 0.0262 REMARK 3 S31: -0.0386 S32: -0.1980 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BK4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1000230882. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0-7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30126 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 36.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.49500 REMARK 200 R SYM FOR SHELL (I) : 0.49500 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4WBE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG2000, 0.1 M BISTRIS (PH6.8), 5% REMARK 280 GLYCEROL, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 26.52500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.70000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.02000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.70000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.52500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.02000 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 ALA A 186 REMARK 465 ARG A 187 REMARK 465 LYS A 188 REMARK 465 ASP A 189 REMARK 465 ASN A 190 REMARK 465 LEU A 191 REMARK 465 ALA A 192 REMARK 465 LYS A 193 REMARK 465 GLU A 254 REMARK 465 THR A 255 REMARK 465 ALA A 256 REMARK 465 ASP A 257 REMARK 465 ASP A 258 REMARK 465 VAL A 259 REMARK 465 LYS A 306 REMARK 465 TYR A 307 REMARK 465 TYR A 308 REMARK 465 LEU A 309 REMARK 465 ALA B 186 REMARK 465 ARG B 187 REMARK 465 LYS B 188 REMARK 465 ASP B 189 REMARK 465 ASN B 190 REMARK 465 LEU B 191 REMARK 465 ALA B 192 REMARK 465 LYS B 193 REMARK 465 GLU B 254 REMARK 465 THR B 255 REMARK 465 ALA B 256 REMARK 465 ASP B 257 REMARK 465 ASP B 258 REMARK 465 VAL B 259 REMARK 465 SER B 260 REMARK 465 ALA B 278 REMARK 465 ARG B 279 REMARK 465 PRO B 280 REMARK 465 LYS B 281 REMARK 465 SER B 282 REMARK 465 PHE B 283 REMARK 465 GLY B 284 REMARK 465 GLU B 285 REMARK 465 VAL B 286 REMARK 465 SER B 287 REMARK 465 PHE B 288 REMARK 465 GLU B 289 REMARK 465 LYS B 290 REMARK 465 LEU B 309 DBREF 6BK4 A 186 309 UNP Q9I7D3 CAPR1_DROME 186 309 DBREF 6BK4 B 186 309 UNP Q9I7D3 CAPR1_DROME 186 309 SEQRES 1 A 124 ALA ARG LYS ASP ASN LEU ALA LYS THR ILE ALA GLU THR SEQRES 2 A 124 ALA LYS ILE ARG GLU VAL LEU ILE ILE GLN ASN VAL LEU SEQRES 3 A 124 ASN CYS PHE ASN ASP ASP GLN VAL ARG SER ASP PHE LEU SEQRES 4 A 124 ASN GLY GLU ASN GLY ALA LYS LYS LEU GLU ASN THR GLU SEQRES 5 A 124 LEU GLU LEU LEU GLU LYS PHE PHE ILE GLU THR GLN THR SEQRES 6 A 124 ARG ARG PRO GLU THR ALA ASP ASP VAL SER PHE ILE ALA SEQRES 7 A 124 THR ALA GLN LYS SER ALA GLU LEU PHE TYR SER THR ILE SEQRES 8 A 124 ASN ALA ARG PRO LYS SER PHE GLY GLU VAL SER PHE GLU SEQRES 9 A 124 LYS LEU ARG SER LEU PHE GLN GLN ILE GLN ASP SER GLY SEQRES 10 A 124 TYR LEU ASP LYS TYR TYR LEU SEQRES 1 B 124 ALA ARG LYS ASP ASN LEU ALA LYS THR ILE ALA GLU THR SEQRES 2 B 124 ALA LYS ILE ARG GLU VAL LEU ILE ILE GLN ASN VAL LEU SEQRES 3 B 124 ASN CYS PHE ASN ASP ASP GLN VAL ARG SER ASP PHE LEU SEQRES 4 B 124 ASN GLY GLU ASN GLY ALA LYS LYS LEU GLU ASN THR GLU SEQRES 5 B 124 LEU GLU LEU LEU GLU LYS PHE PHE ILE GLU THR GLN THR SEQRES 6 B 124 ARG ARG PRO GLU THR ALA ASP ASP VAL SER PHE ILE ALA SEQRES 7 B 124 THR ALA GLN LYS SER ALA GLU LEU PHE TYR SER THR ILE SEQRES 8 B 124 ASN ALA ARG PRO LYS SER PHE GLY GLU VAL SER PHE GLU SEQRES 9 B 124 LYS LEU ARG SER LEU PHE GLN GLN ILE GLN ASP SER GLY SEQRES 10 B 124 TYR LEU ASP LYS TYR TYR LEU FORMUL 3 HOH *75(H2 O) HELIX 1 AA1 THR A 194 PHE A 214 1 21 HELIX 2 AA2 ASP A 216 GLY A 226 1 11 HELIX 3 AA3 GLU A 234 GLN A 249 1 16 HELIX 4 AA4 PHE A 261 ASN A 277 1 17 HELIX 5 AA5 PHE A 288 GLY A 302 1 15 HELIX 6 AA6 ILE B 195 ASN B 215 1 21 HELIX 7 AA7 ASP B 216 GLY B 226 1 11 HELIX 8 AA8 GLU B 234 GLN B 249 1 16 HELIX 9 AA9 ILE B 262 ASN B 277 1 16 HELIX 10 AB1 ARG B 292 GLY B 302 1 11 HELIX 11 AB2 GLY B 302 TYR B 308 1 7 SHEET 1 AA1 2 SER A 282 PHE A 283 0 SHEET 2 AA1 2 VAL A 286 SER A 287 -1 O VAL A 286 N PHE A 283 CRYST1 53.050 60.040 99.400 90.00 90.00 90.00 P 21 21 21 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 0.018850 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010060 0.00000