HEADER CYTOSOLIC PROTEIN 09-SEP-19 6KWZ TITLE CRYSTAL STRUCTURE OF FRAGMIN F3 DOMAIN WITH CALCIUM ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACTIN-BINDING PROTEIN FRAGMIN P; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSARUM POLYCEPHALUM; SOURCE 3 ORGANISM_COMMON: SLIME MOLD; SOURCE 4 ORGANISM_TAXID: 5791; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FRAGMIN, GELSOLIN FAMILY PROTEIN, CALCIUM REGULATION, ACTIN FILAMENT KEYWDS 2 SEVERING, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.TAKEDA REVDAT 3 22-NOV-23 6KWZ 1 REMARK REVDAT 2 15-APR-20 6KWZ 1 JRNL REVDAT 1 01-JAN-20 6KWZ 0 JRNL AUTH S.TAKEDA,I.FUJIWARA,Y.SUGIMOTO,T.ODA,A.NARITA,Y.MAEDA JRNL TITL NOVEL INTER-DOMAIN CA2+-BINDING SITE IN THE GELSOLIN JRNL TITL 2 SUPERFAMILY PROTEIN FRAGMIN. JRNL REF J.MUSCLE RES.CELL.MOTIL. V. 41 153 2020 JRNL REFN ISSN 0142-4319 JRNL PMID 31863323 JRNL DOI 10.1007/S10974-019-09571-5 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3459: ??? 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) : 35.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 26655 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1333 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 35.5960 - 3.3413 1.00 2693 142 0.1609 0.1858 REMARK 3 2 3.3413 - 2.6524 1.00 2587 136 0.1847 0.1940 REMARK 3 3 2.6524 - 2.3172 1.00 2549 135 0.1882 0.2195 REMARK 3 4 2.3172 - 2.1053 1.00 2522 132 0.1757 0.2049 REMARK 3 5 2.1053 - 1.9545 1.00 2513 133 0.1768 0.1960 REMARK 3 6 1.9545 - 1.8392 1.00 2511 132 0.1971 0.2341 REMARK 3 7 1.8392 - 1.7471 1.00 2514 133 0.2261 0.3032 REMARK 3 8 1.7471 - 1.6711 1.00 2473 130 0.2591 0.2794 REMARK 3 9 1.6711 - 1.6067 1.00 2509 132 0.3032 0.3678 REMARK 3 10 1.6067 - 1.5513 0.99 2451 128 0.3617 0.3567 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.60 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6KWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013791. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AICHISR REMARK 200 BEAMLINE : BL2S1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.12 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26672 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 35.596 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.587 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.06 REMARK 200 R MERGE FOR SHELL (I) : 1.31200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.560 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3FFK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MES-NAOH (PH 6.0), 20% PEG 3350, 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 23.32400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.94500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.53800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.94500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.32400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.53800 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: 1380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 46.64800 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -27.53800 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -34.94500 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 ALA B 317 -19.96 -140.15 REMARK 500 PHE B 370 30.72 -93.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 308 O REMARK 620 2 ASP A 309 OD1 80.3 REMARK 620 3 GLU A 331 OE1 81.7 94.2 REMARK 620 4 GLU A 331 OE2 127.5 77.5 53.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 308 O REMARK 620 2 ASP B 309 OD1 79.6 REMARK 620 3 GLU B 331 OE1 83.8 91.2 REMARK 620 4 GLU B 331 OE2 129.1 76.5 52.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 401 DBREF 6KWZ A 276 371 UNP Q94707 Q94707_PHYPO 276 371 DBREF 6KWZ B 276 371 UNP Q94707 Q94707_PHYPO 276 371 SEQADV 6KWZ GLY A 274 UNP Q94707 EXPRESSION TAG SEQADV 6KWZ PRO A 275 UNP Q94707 EXPRESSION TAG SEQADV 6KWZ GLY B 274 UNP Q94707 EXPRESSION TAG SEQADV 6KWZ PRO B 275 UNP Q94707 EXPRESSION TAG SEQRES 1 A 98 GLY PRO PRO ALA VAL LEU LEU ARG LEU SER ASP ALA SER SEQRES 2 A 98 GLY LYS PHE GLU PHE THR GLU VAL ALA ARG GLY LEU LYS SEQRES 3 A 98 VAL LYS ARG ASN LEU LEU ASP SER ASN ASP VAL PHE VAL SEQRES 4 A 98 LEU TYR THR GLY ALA GLU VAL PHE ALA TRP VAL GLY LYS SEQRES 5 A 98 HIS ALA SER VAL GLY GLU LYS LYS LYS ALA LEU SER PHE SEQRES 6 A 98 ALA GLN GLU TYR VAL GLN LYS ALA GLY LEU PRO ILE HIS SEQRES 7 A 98 THR PRO VAL ALA ARG ILE LEU GLU GLY GLY GLU ASN GLU SEQRES 8 A 98 VAL PHE GLU ASP PHE PHE ASP SEQRES 1 B 98 GLY PRO PRO ALA VAL LEU LEU ARG LEU SER ASP ALA SER SEQRES 2 B 98 GLY LYS PHE GLU PHE THR GLU VAL ALA ARG GLY LEU LYS SEQRES 3 B 98 VAL LYS ARG ASN LEU LEU ASP SER ASN ASP VAL PHE VAL SEQRES 4 B 98 LEU TYR THR GLY ALA GLU VAL PHE ALA TRP VAL GLY LYS SEQRES 5 B 98 HIS ALA SER VAL GLY GLU LYS LYS LYS ALA LEU SER PHE SEQRES 6 B 98 ALA GLN GLU TYR VAL GLN LYS ALA GLY LEU PRO ILE HIS SEQRES 7 B 98 THR PRO VAL ALA ARG ILE LEU GLU GLY GLY GLU ASN GLU SEQRES 8 B 98 VAL PHE GLU ASP PHE PHE ASP HET CA A 401 1 HET CA B 401 1 HETNAM CA CALCIUM ION FORMUL 3 CA 2(CA 2+) FORMUL 5 HOH *262(H2 O) HELIX 1 AA1 LEU A 298 VAL A 300 5 3 HELIX 2 AA2 LYS A 301 LEU A 305 5 5 HELIX 3 AA3 SER A 328 GLY A 347 1 20 HELIX 4 AA4 ASN A 363 ASP A 371 1 9 HELIX 5 AA5 LEU B 298 VAL B 300 5 3 HELIX 6 AA6 LYS B 301 LEU B 305 5 5 HELIX 7 AA7 SER B 328 GLY B 347 1 20 HELIX 8 AA8 ASN B 363 PHE B 370 1 8 SHEET 1 AA1 5 GLU A 290 ARG A 296 0 SHEET 2 AA1 5 VAL A 278 SER A 283 -1 N ARG A 281 O THR A 292 SHEET 3 AA1 5 VAL A 310 TYR A 314 -1 O VAL A 310 N LEU A 282 SHEET 4 AA1 5 VAL A 319 VAL A 323 -1 O TRP A 322 N PHE A 311 SHEET 5 AA1 5 VAL A 354 LEU A 358 1 O ALA A 355 N ALA A 321 SHEET 1 AA2 5 GLU B 290 ARG B 296 0 SHEET 2 AA2 5 VAL B 278 SER B 283 -1 N ARG B 281 O THR B 292 SHEET 3 AA2 5 VAL B 310 TYR B 314 -1 O TYR B 314 N VAL B 278 SHEET 4 AA2 5 VAL B 319 VAL B 323 -1 O TRP B 322 N PHE B 311 SHEET 5 AA2 5 VAL B 354 LEU B 358 1 O ALA B 355 N ALA B 321 LINK O ASN A 308 CA CA A 401 1555 1555 2.31 LINK OD1 ASP A 309 CA CA A 401 1555 1555 2.42 LINK OE1 GLU A 331 CA CA A 401 1555 1555 2.46 LINK OE2 GLU A 331 CA CA A 401 1555 1555 2.39 LINK O ASN B 308 CA CA B 401 1555 1555 2.33 LINK OD1 ASP B 309 CA CA B 401 1555 1555 2.38 LINK OE1 GLU B 331 CA CA B 401 1555 1555 2.45 LINK OE2 GLU B 331 CA CA B 401 1555 1555 2.46 SITE 1 AC1 6 ASN A 308 ASP A 309 GLU A 331 HOH A 555 SITE 2 AC1 6 HOH A 564 HOH A 598 SITE 1 AC2 6 ASN B 308 ASP B 309 GLU B 331 HOH B 512 SITE 2 AC2 6 HOH B 556 HOH B 594 CRYST1 46.648 55.076 69.890 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 0.021437 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018157 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014308 0.00000