HEADER CELL CYCLE 15-MAR-12 4E61 TITLE CRYSTAL STRUCTURE OF THE EB1-LIKE MOTIF OF BIM1P COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN BIM1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, EB1-LIKE MOTIF (UNP RESIDUES 182-282); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 STRAIN: BY4741 MATA; SOURCE 6 GENE: BIM1, YER016W; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PGEX-6P-1 KEYWDS EB1-LIKE MOTIF, COILED-COIL, SPINDLE ORIENTATION, MITOSIS, KAR9P, KEYWDS 2 PHOSPHORYLATION, MITOTIC SPINDLE, MICROTUBULES, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR D.HUELS,Z.STORCHOVA,D.NIESSING REVDAT 5 03-APR-24 4E61 1 REMARK REVDAT 4 28-FEB-24 4E61 1 SEQADV REVDAT 3 15-NOV-17 4E61 1 REMARK REVDAT 2 13-JUN-12 4E61 1 JRNL REVDAT 1 11-APR-12 4E61 0 JRNL AUTH D.HULS,Z.STORCHOVA,D.NIESSING JRNL TITL POST-TRANSLATIONAL MODIFICATIONS REGULATE ASSEMBLY OF EARLY JRNL TITL 2 SPINDLE ORIENTATION COMPLEX IN YEAST. JRNL REF J.BIOL.CHEM. V. 287 16238 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22461628 JRNL DOI 10.1074/JBC.M112.347872 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT 2.X REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8832 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 418 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1363 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL 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 : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : NULL ; NULL ; NULL REMARK 3 BOND ANGLES : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS : NULL ; NULL ; NULL 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 : NULL ; NULL ; NULL 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 : NULL ; NULL ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.098 REMARK 3 BOND ANGLES (DEGREES) : 1.18 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4E61 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071213. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.254330 REMARK 200 MONOCHROMATOR : SI111 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 : 8832 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 13.120 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 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: SHELXD, SHELX C REMARK 200 STARTING MODEL: NOT FULLY REFINED MODEL AFTER STRUCTURE REMARK 200 DETERMINATION BY SAD WITH POTASSIUM TETRANITROPLATINATE(II)- REMARK 200 SOAKED CRYSTALS. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 8.0, 20% PEG 5000MME, REMARK 280 40% GAMMA-BUTYRLACTONE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.25000 REMARK 290 SMTRY3 2 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: 3970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 PHE A 69 REMARK 465 ASN A 70 REMARK 465 ASP A 71 REMARK 465 GLU A 72 REMARK 465 THR A 73 REMARK 465 ILE A 74 REMARK 465 THR A 75 REMARK 465 GLY A 76 REMARK 465 HIS A 77 REMARK 465 GLY A 78 REMARK 465 ASN A 79 REMARK 465 GLY A 80 REMARK 465 ASN A 81 REMARK 465 GLY A 82 REMARK 465 ASN A 106 REMARK 465 VAL B 66 REMARK 465 TYR B 67 REMARK 465 LYS B 68 REMARK 465 PHE B 69 REMARK 465 ASN B 70 REMARK 465 ASP B 71 REMARK 465 GLU B 72 REMARK 465 THR B 73 REMARK 465 ILE B 74 REMARK 465 THR B 75 REMARK 465 GLY B 76 REMARK 465 HIS B 77 REMARK 465 GLY B 78 REMARK 465 ASN B 79 REMARK 465 GLY B 80 REMARK 465 ASN B 81 REMARK 465 GLU B 101 REMARK 465 GLY B 102 REMARK 465 PHE B 103 REMARK 465 GLU B 104 REMARK 465 MET B 105 REMARK 465 ASN B 106 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 GLU A 42 CG CD OE1 OE2 REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 GLU A 104 CG CD OE1 OE2 REMARK 470 MET A 105 CG SD CE REMARK 470 LYS B 15 CD CE NZ 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 TYR A 67 30.33 -141.83 REMARK 500 ASN B 63 -85.28 -51.11 REMARK 500 GLU B 64 -61.20 -99.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 4E61 A 6 106 UNP P40013 BIM1_YEAST 182 282 DBREF 4E61 B 6 106 UNP P40013 BIM1_YEAST 182 282 SEQADV 4E61 GLY A 1 UNP P40013 EXPRESSION TAG SEQADV 4E61 PRO A 2 UNP P40013 EXPRESSION TAG SEQADV 4E61 LEU A 3 UNP P40013 EXPRESSION TAG SEQADV 4E61 GLY A 4 UNP P40013 EXPRESSION TAG SEQADV 4E61 SER A 5 UNP P40013 EXPRESSION TAG SEQADV 4E61 GLY B 1 UNP P40013 EXPRESSION TAG SEQADV 4E61 PRO B 2 UNP P40013 EXPRESSION TAG SEQADV 4E61 LEU B 3 UNP P40013 EXPRESSION TAG SEQADV 4E61 GLY B 4 UNP P40013 EXPRESSION TAG SEQADV 4E61 SER B 5 UNP P40013 EXPRESSION TAG SEQRES 1 A 106 GLY PRO LEU GLY SER LEU VAL ALA ILE GLN ALA GLU LEU SEQRES 2 A 106 THR LYS SER GLN GLU THR ILE GLY SER LEU ASN GLU GLU SEQRES 3 A 106 ILE GLU GLN TYR LYS GLY THR VAL SER THR LEU GLU ILE SEQRES 4 A 106 GLU ARG GLU PHE TYR PHE ASN LYS LEU ARG ASP ILE GLU SEQRES 5 A 106 ILE LEU VAL HIS THR THR GLN ASP LEU ILE ASN GLU GLY SEQRES 6 A 106 VAL TYR LYS PHE ASN ASP GLU THR ILE THR GLY HIS GLY SEQRES 7 A 106 ASN GLY ASN GLY GLY ALA LEU LEU ARG PHE VAL LYS LYS SEQRES 8 A 106 VAL GLU SER ILE LEU TYR ALA THR ALA GLU GLY PHE GLU SEQRES 9 A 106 MET ASN SEQRES 1 B 106 GLY PRO LEU GLY SER LEU VAL ALA ILE GLN ALA GLU LEU SEQRES 2 B 106 THR LYS SER GLN GLU THR ILE GLY SER LEU ASN GLU GLU SEQRES 3 B 106 ILE GLU GLN TYR LYS GLY THR VAL SER THR LEU GLU ILE SEQRES 4 B 106 GLU ARG GLU PHE TYR PHE ASN LYS LEU ARG ASP ILE GLU SEQRES 5 B 106 ILE LEU VAL HIS THR THR GLN ASP LEU ILE ASN GLU GLY SEQRES 6 B 106 VAL TYR LYS PHE ASN ASP GLU THR ILE THR GLY HIS GLY SEQRES 7 B 106 ASN GLY ASN GLY GLY ALA LEU LEU ARG PHE VAL LYS LYS SEQRES 8 B 106 VAL GLU SER ILE LEU TYR ALA THR ALA GLU GLY PHE GLU SEQRES 9 B 106 MET ASN HELIX 1 1 GLY A 1 GLU A 64 1 64 HELIX 2 2 ALA A 84 GLY A 102 1 19 HELIX 3 3 PRO B 2 GLU B 64 1 63 HELIX 4 4 GLY B 83 ALA B 98 1 16 CRYST1 28.000 42.500 100.500 90.00 90.30 90.00 P 1 21 1 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 0.035714 0.000000 0.000187 0.00000 SCALE2 0.000000 0.023529 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009950 0.00000