HEADER SIGNALING PROTEIN 13-APR-18 6D2K TITLE CRYSTAL STRUCTURE OF THE FERM DOMAIN OF MOUSE FARP2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERM, ARHGEF AND PLECKSTRIN DOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FERM DOMAIN INCLUDING RHOGEF,FIR,FERM,RHOGEF AND PLECKSTRIN COMPND 5 DOMAIN-CONTAINING PROTEIN 2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: FARP2, KIAA0793; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MEMBRANE TARGETING, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.HE,X.ZHANG REVDAT 3 04-OCT-23 6D2K 1 REMARK REVDAT 2 01-JAN-20 6D2K 1 REMARK REVDAT 1 18-JUL-18 6D2K 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. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.5_2 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 37895 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1916 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 36.3910 - 3.7374 0.98 2874 156 0.1944 0.1947 REMARK 3 2 3.7374 - 2.9669 1.00 2762 145 0.1812 0.2369 REMARK 3 3 2.9669 - 2.5920 0.99 2729 143 0.1939 0.2154 REMARK 3 4 2.5920 - 2.3551 0.99 2702 143 0.1991 0.2217 REMARK 3 5 2.3551 - 2.1863 0.99 2688 139 0.1807 0.2069 REMARK 3 6 2.1863 - 2.0574 0.98 2662 142 0.1805 0.2126 REMARK 3 7 2.0574 - 1.9544 0.98 2626 140 0.1878 0.2103 REMARK 3 8 1.9544 - 1.8693 0.97 2591 140 0.1971 0.2466 REMARK 3 9 1.8693 - 1.7973 0.94 2535 133 0.2059 0.2356 REMARK 3 10 1.7973 - 1.7353 0.93 2494 134 0.2132 0.2709 REMARK 3 11 1.7353 - 1.6811 0.91 2454 126 0.2162 0.2810 REMARK 3 12 1.6811 - 1.6330 0.89 2368 130 0.2225 0.2543 REMARK 3 13 1.6330 - 1.5900 0.86 2307 122 0.2319 0.3169 REMARK 3 14 1.5900 - 1.5512 0.82 2187 123 0.2490 0.2424 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 : 0.40 REMARK 3 B_SOL : 60.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.130 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) : -0.44020 REMARK 3 B22 (A**2) : 6.37990 REMARK 3 B33 (A**2) : -5.93970 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 2445 REMARK 3 ANGLE : 1.031 3308 REMARK 3 CHIRALITY : 0.071 362 REMARK 3 PLANARITY : 0.004 420 REMARK 3 DIHEDRAL : 19.782 922 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: NULL REMARK 4 REMARK 4 6D2K 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_1000233895. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.97935 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37895 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 36.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.0200 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: 2HE7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE, 12 % REMARK 280 PEG 3350 (W/V), PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 19.70900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.11300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.38100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.11300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.70900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.38100 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 323 REMARK 465 ASP A 324 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 SER A 37 OG REMARK 470 ARG A 107 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 239 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 287 CG CD OE1 OE2 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 SER A 53 -4.86 82.35 REMARK 500 ARG A 110 -11.34 80.56 REMARK 500 ASN A 114 68.62 -152.43 REMARK 500 ARG A 277 -119.87 56.49 REMARK 500 HIS A 289 70.58 -101.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6D21 RELATED DB: PDB DBREF 6D2K A 38 324 UNP Q91VS8 FARP2_MOUSE 38 324 SEQADV 6D2K SER A 37 UNP Q91VS8 EXPRESSION TAG SEQRES 1 A 288 SER ARG MET GLN GLU LYS HIS MET ARG ILE ARG VAL LYS SEQRES 2 A 288 LEU LEU ASP SER THR VAL GLU LEU PHE ASP ILE GLU PRO SEQRES 3 A 288 LYS CYS ASP GLY GLN VAL LEU LEU THR GLN VAL TRP LYS SEQRES 4 A 288 HIS LEU ASN LEU ILE GLU CYS ASP TYR PHE GLY LEU GLU SEQRES 5 A 288 PHE LYS ASN VAL GLN SER TYR TRP ILE TRP LEU GLU PRO SEQRES 6 A 288 MET LYS PRO ILE ILE ARG GLN VAL ARG LYS PRO LYS ASN SEQRES 7 A 288 ALA VAL LEU ARG LEU ALA VAL LYS PHE PHE PRO PRO ASP SEQRES 8 A 288 PRO GLY GLN LEU GLN GLU GLU TYR THR ARG TYR LEU PHE SEQRES 9 A 288 ALA LEU GLN LEU LYS ARG ASP LEU LEU GLU GLU ARG LEU SEQRES 10 A 288 THR CYS THR ALA ASN THR ALA ALA LEU LEU ILE SER HIS SEQRES 11 A 288 LEU LEU GLN SER GLU ILE GLY ASP TYR ASP GLU THR LEU SEQRES 12 A 288 ASP ARG GLU HIS LEU LYS ALA ASN GLU TYR LEU PRO ASN SEQRES 13 A 288 GLN GLU LYS SER LEU GLU LYS ILE LEU ASP PHE HIS GLN SEQRES 14 A 288 ARG HIS THR GLY GLN THR PRO ALA GLU SER ASP PHE GLN SEQRES 15 A 288 VAL LEU GLU ILE ALA ARG LYS LEU GLU MET TYR GLY ILE SEQRES 16 A 288 ARG PHE HIS MET ALA SER ASP ARG GLU GLY THR LYS ILE SEQRES 17 A 288 ASN LEU ALA VAL SER HIS MET GLY VAL LEU VAL PHE GLN SEQRES 18 A 288 GLY THR THR LYS ILE ASN THR PHE ASN TRP SER LYS VAL SEQRES 19 A 288 ARG LYS LEU SER PHE LYS ARG LYS ARG PHE LEU ILE LYS SEQRES 20 A 288 LEU HIS PRO GLU VAL HIS GLY PRO TYR GLN ASP THR LEU SEQRES 21 A 288 GLU PHE LEU LEU GLY SER ARG ASP GLU CYS LYS ASN PHE SEQRES 22 A 288 TRP LYS ILE CYS VAL GLU TYR HIS THR PHE PHE ARG LEU SEQRES 23 A 288 SER ASP FORMUL 2 HOH *290(H2 O) HELIX 1 AA1 ASP A 65 ASN A 78 1 14 HELIX 2 AA2 GLU A 81 ASP A 83 5 3 HELIX 3 AA3 PRO A 104 ARG A 110 1 7 HELIX 4 AA4 ASP A 127 LEU A 131 5 5 HELIX 5 AA5 GLU A 133 GLU A 150 1 18 HELIX 6 AA6 THR A 156 GLY A 173 1 18 HELIX 7 AA7 ASP A 176 ASN A 187 1 12 HELIX 8 AA8 ASN A 192 LYS A 195 5 4 HELIX 9 AA9 SER A 196 GLN A 205 1 10 HELIX 10 AB1 ARG A 206 THR A 208 5 3 HELIX 11 AB2 THR A 211 ARG A 224 1 14 HELIX 12 AB3 SER A 268 VAL A 270 5 3 HELIX 13 AB4 SER A 302 ARG A 321 1 20 SHEET 1 AA1 5 VAL A 55 ILE A 60 0 SHEET 2 AA1 5 MET A 44 LYS A 49 -1 N MET A 44 O ILE A 60 SHEET 3 AA1 5 ALA A 115 VAL A 121 1 O LEU A 117 N LYS A 49 SHEET 4 AA1 5 PHE A 85 LYS A 90 -1 N GLU A 88 O ARG A 118 SHEET 5 AA1 5 TRP A 96 TRP A 98 -1 O ILE A 97 N PHE A 89 SHEET 1 AA2 7 THR A 260 ASN A 266 0 SHEET 2 AA2 7 GLY A 252 GLN A 257 -1 N GLN A 257 O THR A 260 SHEET 3 AA2 7 LYS A 243 SER A 249 -1 N ASN A 245 O PHE A 256 SHEET 4 AA2 7 HIS A 234 SER A 237 -1 N HIS A 234 O LEU A 246 SHEET 5 AA2 7 THR A 295 LEU A 300 -1 O LEU A 299 N SER A 237 SHEET 6 AA2 7 ARG A 279 LYS A 283 -1 N PHE A 280 O PHE A 298 SHEET 7 AA2 7 LYS A 272 LYS A 276 -1 N LYS A 272 O LYS A 283 CRYST1 39.418 72.762 94.226 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 0.025369 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013743 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010613 0.00000