HEADER STRUCTURAL PROTEIN 11-JAN-05 1YIG TITLE CRYSTAL STRUCTURE OF THE HUMAN EB1 C-TERMINAL DIMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EB1 C-TERMINAL DOMAIN; COMPND 5 SYNONYM: EB1; APC-BINDING PROTEIN EB1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MAPRE1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P2 KEYWDS COILED COIL; FOUR HELIX BUNDLE, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.C.SLEP,S.L.ROGERS,S.L.ELLIOTT,H.OHKURA,P.A.KOLODZIEJ,R.D.VALE REVDAT 3 20-OCT-21 1YIG 1 SEQADV LINK REVDAT 2 24-FEB-09 1YIG 1 VERSN REVDAT 1 08-MAR-05 1YIG 0 JRNL AUTH K.C.SLEP,S.L.ROGERS,S.L.ELLIOTT,H.OHKURA,P.A.KOLODZIEJ, JRNL AUTH 2 R.D.VALE JRNL TITL STRUCTURAL DETERMINANTS FOR EB1-MEDIATED RECRUITMENT OF APC JRNL TITL 2 AND SPECTRAPLAKINS TO THE MICROTUBULE PLUS END JRNL REF J.CELL BIOL. V. 168 587 2005 JRNL REFN ISSN 0021-9525 JRNL PMID 15699215 JRNL DOI 10.1083/JCB.200410114 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1407766.560 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.8 REMARK 3 NUMBER OF REFLECTIONS : 14228 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 SET) : 0.219 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1367 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 42.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1116 REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 131 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1042 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.88000 REMARK 3 B22 (A**2) : -0.86000 REMARK 3 B33 (A**2) : -10.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.88000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : -0.0 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.600 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 42.18 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YIG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97964, 0.97979, 1.12713 REMARK 200 MONOCHROMATOR : KOHZU: DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14472 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 31.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : 0.03000 REMARK 200 FOR THE DATA SET : 25.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 40.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.11000 REMARK 200 R SYM FOR SHELL (I) : 0.13300 REMARK 200 FOR SHELL : 6.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN STOCK = EB1 C-TERMINAL DOMAIN REMARK 280 @15 MG/ML, WELL = 22%, PEG 200 (V/V), 100 MM AMMONIUM ACETATE PH REMARK 280 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 18.66750 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 300 REMARK: THE TWO MOLECULES IN THE ASYMMETRIC UNIT (A AND B) CREATE REMARK 300 THE BIOLOGICAL ASSEMBLY: A COILED COIL, FOUR HELIX BUNDLE HOMODIMER 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: 3180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 GLY A 180 REMARK 465 PRO A 181 REMARK 465 LEU A 182 REMARK 465 GLY A 183 REMARK 465 SER A 184 REMARK 465 GLY A 185 REMARK 465 VAL A 186 REMARK 465 GLY A 187 REMARK 465 ASN A 188 REMARK 465 GLY A 189 REMARK 465 GLY B 180 REMARK 465 PRO B 181 REMARK 465 LEU B 182 REMARK 465 GLY B 183 REMARK 465 SER B 184 REMARK 465 GLY B 185 REMARK 465 VAL B 186 REMARK 465 GLY B 187 REMARK 465 ASN B 188 REMARK 465 GLY B 189 REMARK 465 GLU B 251 REMARK 465 GLY B 252 REMARK 465 PHE B 253 REMARK 465 VAL B 254 REMARK 465 ILE B 255 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YIB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EB1 C-TERMINAL DIMERIZATION DOMAIN, C2221 REMARK 900 CRYSTAL FORM DBREF 1YIG A 185 255 UNP Q15691 MARE1_HUMAN 184 254 DBREF 1YIG B 185 255 UNP Q15691 MARE1_HUMAN 184 254 SEQADV 1YIG GLY A 180 UNP Q15691 CLONING ARTIFACT SEQADV 1YIG PRO A 181 UNP Q15691 CLONING ARTIFACT SEQADV 1YIG LEU A 182 UNP Q15691 CLONING ARTIFACT SEQADV 1YIG GLY A 183 UNP Q15691 CLONING ARTIFACT SEQADV 1YIG SER A 184 UNP Q15691 CLONING ARTIFACT SEQADV 1YIG MSE A 197 UNP Q15691 MET 196 MODIFIED RESIDUE SEQADV 1YIG MSE A 243 UNP Q15691 VAL 242 ENGINEERED MUTATION SEQADV 1YIG GLY B 180 UNP Q15691 CLONING ARTIFACT SEQADV 1YIG PRO B 181 UNP Q15691 CLONING ARTIFACT SEQADV 1YIG LEU B 182 UNP Q15691 CLONING ARTIFACT SEQADV 1YIG GLY B 183 UNP Q15691 CLONING ARTIFACT SEQADV 1YIG SER B 184 UNP Q15691 CLONING ARTIFACT SEQADV 1YIG MSE B 197 UNP Q15691 MET 196 MODIFIED RESIDUE SEQADV 1YIG MSE B 243 UNP Q15691 VAL 242 ENGINEERED MUTATION SEQRES 1 A 76 GLY PRO LEU GLY SER GLY VAL GLY ASN GLY ASP ASP GLU SEQRES 2 A 76 ALA ALA GLU LEU MSE GLN GLN VAL ASN VAL LEU LYS LEU SEQRES 3 A 76 THR VAL GLU ASP LEU GLU LYS GLU ARG ASP PHE TYR PHE SEQRES 4 A 76 GLY LYS LEU ARG ASN ILE GLU LEU ILE CYS GLN GLU ASN SEQRES 5 A 76 GLU GLY GLU ASN ASP PRO VAL LEU GLN ARG ILE MSE ASP SEQRES 6 A 76 ILE LEU TYR ALA THR ASP GLU GLY PHE VAL ILE SEQRES 1 B 76 GLY PRO LEU GLY SER GLY VAL GLY ASN GLY ASP ASP GLU SEQRES 2 B 76 ALA ALA GLU LEU MSE GLN GLN VAL ASN VAL LEU LYS LEU SEQRES 3 B 76 THR VAL GLU ASP LEU GLU LYS GLU ARG ASP PHE TYR PHE SEQRES 4 B 76 GLY LYS LEU ARG ASN ILE GLU LEU ILE CYS GLN GLU ASN SEQRES 5 B 76 GLU GLY GLU ASN ASP PRO VAL LEU GLN ARG ILE MSE ASP SEQRES 6 B 76 ILE LEU TYR ALA THR ASP GLU GLY PHE VAL ILE MODRES 1YIG MSE A 197 MET SELENOMETHIONINE MODRES 1YIG MSE A 243 MET SELENOMETHIONINE MODRES 1YIG MSE B 197 MET SELENOMETHIONINE MODRES 1YIG MSE B 243 MET SELENOMETHIONINE HET MSE A 197 8 HET MSE A 243 8 HET MSE B 197 8 HET MSE B 243 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 HOH *29(H2 O) HELIX 1 1 ASP A 190 ASN A 231 1 42 HELIX 2 2 GLU A 232 ASN A 235 5 4 HELIX 3 3 ASP A 236 ALA A 248 1 13 HELIX 4 4 THR A 249 VAL A 254 5 6 HELIX 5 5 ASP B 190 ASN B 231 1 42 HELIX 6 6 GLU B 232 ASN B 235 5 4 HELIX 7 7 ASP B 236 TYR B 247 1 12 LINK C LEU A 196 N MSE A 197 1555 1555 1.33 LINK C MSE A 197 N GLN A 198 1555 1555 1.33 LINK C ILE A 242 N MSE A 243 1555 1555 1.33 LINK C MSE A 243 N ASP A 244 1555 1555 1.33 LINK C LEU B 196 N MSE B 197 1555 1555 1.33 LINK C MSE B 197 N GLN B 198 1555 1555 1.32 LINK C ILE B 242 N MSE B 243 1555 1555 1.33 LINK C MSE B 243 N ASP B 244 1555 1555 1.33 CRYST1 32.981 37.335 56.776 90.00 106.06 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 0.030320 0.000000 0.008729 0.00000 SCALE2 0.000000 0.026785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018328 0.00000 MASTER 249 0 4 7 0 0 0 6 0 0 0 12 END