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