HEADER STRUCTURAL PROTEIN 16-MAY-14 4UMG TITLE CRYSTAL STRUCTURE OF THE LIN-41 FILAMIN DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN LIN-41; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FILAMIN DOMAIN, RESIDUES 691-821; COMPND 5 SYNONYM: ABNORMAL CELL LINEAGE PROTEIN 41, LIN-41; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: LIN-41 ISOFORM B OF UNIPROT ENTRY Q9U489 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: POPINF KEYWDS STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.TOCCHINI,J.J.KEUSCH,S.B.MILLER,S.FINGER,H.GUT,M.STADLER,R.CIOSK REVDAT 2 08-MAY-24 4UMG 1 REMARK REVDAT 1 01-OCT-14 4UMG 0 JRNL AUTH C.TOCCHINI,J.J.KEUSCH,S.B.MILLER,S.FINGER,H.GUT,M.B.STADLER, JRNL AUTH 2 R.CIOSK JRNL TITL THE TRIM-NHL PROTEIN LIN-41 CONTROLS THE ONSET OF JRNL TITL 2 DEVELOPMENTAL PLASTICITY IN CAENORHABDITIS ELEGANS. JRNL REF PLOS GENET. V. 10 4533 2014 JRNL REFN ISSN 1553-7390 JRNL PMID 25167051 JRNL DOI 10.1371/JOURNAL.PGEN.1004533 REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.4 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13854 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 693 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2817 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2427 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2676 REMARK 3 BIN R VALUE (WORKING SET) : 0.2429 REMARK 3 BIN FREE R VALUE : 0.2387 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.01 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 762 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.23550 REMARK 3 B22 (A**2) : 1.04220 REMARK 3 B33 (A**2) : -2.27760 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.299 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.110 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.104 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.104 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.101 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 772 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1046 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 266 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 16 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 112 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 772 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 110 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 981 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.11 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.04 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.06 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -1.5506 -7.5568 -14.0256 REMARK 3 T TENSOR REMARK 3 T11: 0.0330 T22: 0.0179 REMARK 3 T33: -0.1128 T12: 0.1011 REMARK 3 T13: -0.0337 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 1.6034 L22: 2.0216 REMARK 3 L33: 0.8254 L12: -1.1795 REMARK 3 L13: -0.2879 L23: -0.4679 REMARK 3 S TENSOR REMARK 3 S11: -0.3263 S12: -0.2256 S13: -0.0100 REMARK 3 S21: 0.3231 S22: 0.1694 S23: -0.0150 REMARK 3 S31: -0.1679 S32: 0.0090 S33: 0.1569 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4UMG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1290060664. 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 : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13883 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.88000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1 M SODIUM MALONATE, 0.1 M HEPES PH REMARK 280 7.0, 0.5% JEFFAMINE ED-2001 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.65500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.65500 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.39000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.05500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.39000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.05500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.65500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.39000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.05500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.65500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.39000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 26.05500 REMARK 290 SMTRY3 8 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 GLY A 689 REMARK 465 PRO A 690 REMARK 465 SER A 730 REMARK 465 SER A 731 REMARK 465 ILE A 732 REMARK 465 ALA A 733 REMARK 465 ALA A 734 REMARK 465 THR A 735 REMARK 465 GLN A 736 REMARK 465 PRO A 737 REMARK 465 THR A 738 REMARK 465 SER A 739 REMARK 465 GLN A 740 REMARK 465 ALA A 741 REMARK 465 LEU A 742 REMARK 465 LEU A 743 REMARK 465 PRO A 744 REMARK 465 HIS A 745 REMARK 465 GLN A 746 REMARK 465 GLU A 747 REMARK 465 PRO A 748 REMARK 465 HIS A 749 REMARK 465 SER A 750 REMARK 465 HIS A 751 REMARK 465 LEU A 752 REMARK 465 GLU A 753 REMARK 465 GLN A 754 REMARK 465 ALA A 755 REMARK 465 MET A 756 REMARK 465 PRO A 757 REMARK 465 ARG A 821 DBREF 4UMG A 691 821 UNP Q9U489 LIN41_CAEEL 691 821 SEQADV 4UMG GLY A 689 UNP Q9U489 EXPRESSION TAG SEQADV 4UMG PRO A 690 UNP Q9U489 EXPRESSION TAG SEQRES 1 A 133 GLY PRO SER GLY PRO CYS ALA LYS ASN SER SER ILE VAL SEQRES 2 A 133 GLY ASP SER PHE LYS LYS ALA ILE ARG GLU ARG GLN THR SEQRES 3 A 133 VAL ILE TYR VAL GLN LEU ARG ASP ALA CYS GLY ASP LEU SEQRES 4 A 133 LEU SER SER SER ILE ALA ALA THR GLN PRO THR SER GLN SEQRES 5 A 133 ALA LEU LEU PRO HIS GLN GLU PRO HIS SER HIS LEU GLU SEQRES 6 A 133 GLN ALA MET PRO THR SER ASP VAL GLN ALA PHE VAL ILE SEQRES 7 A 133 SER PRO ASP GLY SER THR VAL GLU VAL THR MET THR PRO SEQRES 8 A 133 ARG GLU ASN GLY ILE VAL ALA LEU SER TYR TYR PRO SER SEQRES 9 A 133 ILE GLU GLY SER TYR THR LEU ASN ILE LEU VAL LYS GLY SEQRES 10 A 133 THR PRO ILE SER GLY CYS PRO THR THR MET ASP ILE ARG SEQRES 11 A 133 ARG GLY ARG FORMUL 2 HOH *81(H2 O) HELIX 1 1 CYS A 694 SER A 698 5 5 HELIX 2 2 ASP A 703 PHE A 705 5 3 SHEET 1 AA 4 SER A 699 ILE A 700 0 SHEET 2 AA 4 THR A 714 GLN A 719 -1 O GLN A 719 N SER A 699 SHEET 3 AA 4 ILE A 784 TYR A 789 -1 O VAL A 785 N VAL A 718 SHEET 4 AA 4 THR A 776 PRO A 779 -1 O THR A 776 N SER A 788 SHEET 1 AB 4 LYS A 707 ILE A 709 0 SHEET 2 AB 4 THR A 813 ARG A 818 1 O ASP A 816 N ALA A 708 SHEET 3 AB 4 GLY A 795 VAL A 803 -1 O GLY A 795 N ILE A 817 SHEET 4 AB 4 THR A 806 PRO A 807 1 O THR A 806 N VAL A 803 SHEET 1 AC 5 LYS A 707 ILE A 709 0 SHEET 2 AC 5 THR A 813 ARG A 818 1 O ASP A 816 N ALA A 708 SHEET 3 AC 5 GLY A 795 VAL A 803 -1 O GLY A 795 N ILE A 817 SHEET 4 AC 5 VAL A 761 ILE A 766 -1 O GLN A 762 N LEU A 802 SHEET 5 AC 5 THR A 772 VAL A 773 -1 O VAL A 773 N VAL A 765 SHEET 1 AD 2 THR A 806 PRO A 807 0 SHEET 2 AD 2 GLY A 795 VAL A 803 1 O VAL A 803 N THR A 806 CISPEP 1 CYS A 811 PRO A 812 0 0.36 CRYST1 44.780 52.110 101.310 90.00 90.00 90.00 C 2 2 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 0.022331 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019190 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009871 0.00000