HEADER SIGNALING PROTEIN 13-APR-18 6D2Q TITLE CRYSTAL STRUCTURE OF THE FERM DOMAIN OF ZEBRAFISH FARP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERM, RHOGEF (ARHGEF) AND PLECKSTRIN DOMAIN PROTEIN 1 COMPND 3 (CHONDROCYTE-DERIVED); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: FARP1, SI:CH211-235F1.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MEMBRANE TARGETING, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.C.KUO,X.ZHANG REVDAT 3 04-OCT-23 6D2Q 1 REMARK REVDAT 2 01-JAN-20 6D2Q 1 REMARK REVDAT 1 18-JUL-18 6D2Q 0 JRNL AUTH Y.C.KUO,X.HE,A.J.COLEMAN,Y.J.CHEN,P.DASARI,J.LIOU, JRNL AUTH 2 T.BIEDERER,X.ZHANG JRNL TITL STRUCTURAL ANALYSES OF FERM DOMAIN-MEDIATED MEMBRANE JRNL TITL 2 LOCALIZATION OF FARP1. JRNL REF SCI REP V. 8 10477 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 29992992 JRNL DOI 10.1038/S41598-018-28692-4 REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 2.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 6910 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 690 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 40.7743 - 5.1178 0.98 1290 154 0.2113 0.2571 REMARK 3 2 5.1178 - 4.0633 1.00 1253 133 0.2033 0.2601 REMARK 3 3 4.0633 - 3.5500 1.00 1241 137 0.2270 0.2991 REMARK 3 4 3.5500 - 3.2256 0.99 1219 134 0.2592 0.3425 REMARK 3 5 3.2256 - 2.9945 0.98 1207 132 0.2883 0.3406 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.350 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 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 : 0.002 2280 REMARK 3 ANGLE : 0.471 3072 REMARK 3 CHIRALITY : 0.039 340 REMARK 3 PLANARITY : 0.003 391 REMARK 3 DIHEDRAL : 18.272 1384 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 14.1915 2.6237 12.8098 REMARK 3 T TENSOR REMARK 3 T11: 0.4435 T22: 0.4484 REMARK 3 T33: 0.5037 T12: 0.0134 REMARK 3 T13: -0.0651 T23: -0.0286 REMARK 3 L TENSOR REMARK 3 L11: 2.3898 L22: 1.8167 REMARK 3 L33: 3.1717 L12: -0.1837 REMARK 3 L13: 0.7002 L23: -0.9601 REMARK 3 S TENSOR REMARK 3 S11: 0.1865 S12: 0.0126 S13: -0.4096 REMARK 3 S21: -0.1421 S22: 0.1895 S23: 0.1520 REMARK 3 S31: 0.4801 S32: -0.3614 S33: -0.3464 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 6D2Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233908. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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) : 0.97926 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6910 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.990 REMARK 200 RESOLUTION RANGE LOW (A) : 40.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7500 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: PHENIX REMARK 200 STARTING MODEL: 6D2K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE PH 9.0, 16 % MPD (V/V), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 28.01550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.73100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.71800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.73100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.01550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.71800 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SER A 37 REMARK 465 PRO A 284 REMARK 465 ASP A 285 REMARK 465 LEU A 286 REMARK 465 ASN A 287 REMARK 465 SER A 288 REMARK 465 ASN A 289 REMARK 465 LEU A 320 REMARK 465 PHE A 321 REMARK 465 GLU A 322 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 HIS A 125 CG ND1 CD2 CE1 NE2 REMARK 470 THR A 126 OG1 CG2 REMARK 470 GLN A 127 CG CD OE1 NE2 REMARK 470 LEU A 129 CG CD1 CD2 REMARK 470 ARG A 282 CG CD NE CZ NH1 NH2 REMARK 470 CYS A 290 SG REMARK 470 GLN A 291 CG CD OE1 NE2 REMARK 470 ASP A 292 CG OD1 OD2 REMARK 470 ARG A 319 CG CD NE CZ NH1 NH2 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 GLU A 78 57.85 -109.11 REMARK 500 LEU A 128 96.63 -57.81 REMARK 500 LEU A 241 -154.10 -129.04 REMARK 500 ILE A 259 -64.93 -103.96 REMARK 500 ARG A 274 -99.75 53.91 REMARK 500 GLN A 291 -79.71 -72.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6D21 RELATED DB: PDB DBREF 6D2Q A 38 322 UNP E9QIC8 E9QIC8_DANRE 38 321 SEQADV 6D2Q SER A 37 UNP E9QIC8 EXPRESSION TAG SEQRES 1 A 285 SER GLY ARG GLN ILE SER ILE ARG VAL GLN MET LEU ASP SEQRES 2 A 285 ASP THR GLN GLU VAL PHE GLU VAL SER GLN ARG ALA PRO SEQRES 3 A 285 GLY LYS ALA LEU PHE ASP LEU VAL CYS SER HIS LEU ASN SEQRES 4 A 285 LEU VAL GLU GLY ASP TYR PHE GLY LEU GLU PHE GLN ASP SEQRES 5 A 285 GLN ARG LYS MET ILE VAL TRP LEU ASP LEU LEU LYS PRO SEQRES 6 A 285 ILE LEU LYS GLN ILE ARG ARG PRO LYS ASN ILE ILE LEU SEQRES 7 A 285 ARG PHE VAL VAL LYS PHE PHE PRO PRO ASP HIS THR GLN SEQRES 8 A 285 LEU LEU GLU GLU LEU THR ARG TYR LEU PHE ALA LEU GLN SEQRES 9 A 285 ILE LYS HIS ASP LEU ALA CYS GLY ARG LEU THR CYS ASN SEQRES 10 A 285 GLU SER SER ALA ALA LEU LEU VAL ALA HIS ILE VAL GLN SEQRES 11 A 285 SER GLU ILE GLY ASP PHE ASP GLU VAL GLN CYS LYS GLN SEQRES 12 A 285 HIS LEU LEU ASN ASN LYS TYR ILE PRO GLU GLN ASP THR SEQRES 13 A 285 LEU MET ASP LYS ILE ILE GLY TYR HIS ARG LYS HIS VAL SEQRES 14 A 285 GLY GLN THR PRO ALA GLU SER ASP TYR GLN LEU LEU GLU SEQRES 15 A 285 ILE ALA ARG ARG LEU GLU MET TYR GLY VAL ARG LEU HIS SEQRES 16 A 285 PRO ALA LYS ASP ARG GLU GLY THR ARG LEU SER LEU ALA SEQRES 17 A 285 VAL ALA HIS SER GLY VAL LEU VAL PHE GLN GLY HIS THR SEQRES 18 A 285 LYS ILE ASN ALA PHE ASN TRP SER LYS VAL ARG LYS LEU SEQRES 19 A 285 SER PHE LYS ARG LYS ARG PHE LEU ILE LYS LEU ARG PRO SEQRES 20 A 285 ASP LEU ASN SER ASN CYS GLN ASP THR LEU GLU PHE MET SEQRES 21 A 285 MET GLY SER ARG ASP CYS CYS LYS VAL PHE TRP LYS ILE SEQRES 22 A 285 CYS VAL GLU TYR HIS ALA PHE PHE ARG LEU PHE GLU HELIX 1 AA1 PRO A 62 ASN A 75 1 14 HELIX 2 AA2 GLU A 78 ASP A 80 5 3 HELIX 3 AA3 PRO A 101 ILE A 106 1 6 HELIX 4 AA4 GLU A 130 GLY A 148 1 19 HELIX 5 AA5 ASN A 153 GLY A 170 1 18 HELIX 6 AA6 ASP A 173 ASN A 184 1 12 HELIX 7 AA7 GLN A 190 THR A 192 5 3 HELIX 8 AA8 LEU A 193 ARG A 202 1 10 HELIX 9 AA9 THR A 208 ARG A 221 1 14 HELIX 10 AB1 SER A 300 ARG A 319 1 20 SHEET 1 AA1 5 GLN A 52 SER A 58 0 SHEET 2 AA1 5 GLN A 40 GLN A 46 -1 N VAL A 45 O GLU A 53 SHEET 3 AA1 5 ILE A 113 VAL A 118 1 O PHE A 116 N GLN A 46 SHEET 4 AA1 5 PHE A 82 GLN A 87 -1 N GLY A 83 O VAL A 117 SHEET 5 AA1 5 ILE A 93 TRP A 95 -1 O VAL A 94 N PHE A 86 SHEET 1 AA2 7 THR A 257 ASN A 263 0 SHEET 2 AA2 7 GLY A 249 GLN A 254 -1 N VAL A 252 O ILE A 259 SHEET 3 AA2 7 ARG A 240 VAL A 245 -1 N SER A 242 O PHE A 253 SHEET 4 AA2 7 HIS A 231 ASP A 235 -1 N ALA A 233 O LEU A 241 SHEET 5 AA2 7 THR A 293 MET A 298 -1 O MET A 297 N LYS A 234 SHEET 6 AA2 7 ARG A 276 LEU A 281 -1 N PHE A 277 O PHE A 296 SHEET 7 AA2 7 VAL A 267 LYS A 273 -1 N ARG A 268 O LYS A 280 CRYST1 56.031 59.436 97.462 90.00 90.00 90.00 P 21 21 21 4 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 0.017847 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010260 0.00000