HEADER STRUCTURAL PROTEIN 06-JAN-14 3WOY TITLE CRYSTAL STRUCTURE OF CLASP2 TOG DOMAIN (TOG2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLIP-ASSOCIATING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 60-310; COMPND 5 SYNONYM: CYTOPLASMIC LINKER-ASSOCIATED PROTEIN 2, PROTEIN ORBIT COMPND 6 HOMOLOG 2, HORBIT2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CLASP2, KIAA0627; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEAT REPEAT, MICROTUBULE BINDING, TUBULIN, UNKNOWN, MICROTUBULE, KEYWDS 2 STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.HAYASHI,T.MAKI REVDAT 3 20-MAR-24 3WOY 1 REMARK REVDAT 2 17-OCT-18 3WOY 1 JRNL REVDAT 1 27-MAY-15 3WOY 0 JRNL AUTH T.MAKI,A.D.GRIMALDI,S.FUCHIGAMI,I.KAVERINA,I.HAYASHI JRNL TITL CLASP2 HAS TWO DISTINCT TOG DOMAINS THAT CONTRIBUTE JRNL TITL 2 DIFFERENTLY TO MICROTUBULE DYNAMICS JRNL REF J. MOL. BIOL. V. 427 2379 2015 JRNL REFN ESSN 1089-8638 JRNL PMID 26003921 JRNL DOI 10.1016/J.JMB.2015.05.012 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 172351.580 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 18642 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) : 0.183 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1836 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2624 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 299 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1954 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 212 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.04000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : 0.36 REMARK 3 BSOL : 59.01 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3WOY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000096609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-09; 10-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A; BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97901, 0.97931, 0.96408; 1.0 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; SI 111 CHANNEL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R; ADSC QUANTUM REMARK 200 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44169 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 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: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM TRIS, 3%(W/V) PEG10K , PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 104.71533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.35767 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 52.35767 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 104.71533 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 60 REMARK 465 GLY A 61 REMARK 465 ALA A 62 REMARK 465 LYS A 309 REMARK 465 SER A 310 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WOZ RELATED DB: PDB DBREF 3WOY A 60 310 UNP O75122 CLAP2_HUMAN 60 310 SEQRES 1 A 251 GLY GLY ALA GLY ALA VAL ASP GLU ASP ASP PHE ILE LYS SEQRES 2 A 251 ALA PHE THR ASP VAL PRO SER ILE GLN ILE TYR SER SER SEQRES 3 A 251 ARG GLU LEU GLU GLU THR LEU ASN LYS ILE ARG GLU ILE SEQRES 4 A 251 LEU SER ASP ASP LYS HIS ASP TRP ASP GLN ARG ALA ASN SEQRES 5 A 251 ALA LEU LYS LYS ILE ARG SER LEU LEU VAL ALA GLY ALA SEQRES 6 A 251 ALA GLN TYR ASP CYS PHE PHE GLN HIS LEU ARG LEU LEU SEQRES 7 A 251 ASP GLY ALA LEU LYS LEU SER ALA LYS ASP LEU ARG SER SEQRES 8 A 251 GLN VAL VAL ARG GLU ALA CYS ILE THR VAL ALA HIS LEU SEQRES 9 A 251 SER THR VAL LEU GLY ASN LYS PHE ASP HIS GLY ALA GLU SEQRES 10 A 251 ALA ILE VAL PRO THR LEU PHE ASN LEU VAL PRO ASN SER SEQRES 11 A 251 ALA LYS VAL MET ALA THR SER GLY CYS ALA ALA ILE ARG SEQRES 12 A 251 PHE ILE ILE ARG HIS THR HIS VAL PRO ARG LEU ILE PRO SEQRES 13 A 251 LEU ILE THR SER ASN CYS THR SER LYS SER VAL PRO VAL SEQRES 14 A 251 ARG ARG ARG SER PHE GLU PHE LEU ASP LEU LEU LEU GLN SEQRES 15 A 251 GLU TRP GLN THR HIS SER LEU GLU ARG HIS ALA ALA VAL SEQRES 16 A 251 LEU VAL GLU THR ILE LYS LYS GLY ILE HIS ASP ALA ASP SEQRES 17 A 251 ALA GLU ALA ARG VAL GLU ALA ARG LYS THR TYR MET GLY SEQRES 18 A 251 LEU ARG ASN HIS PHE PRO GLY GLU ALA GLU THR LEU TYR SEQRES 19 A 251 ASN SER LEU GLU PRO SER TYR GLN LYS SER LEU GLN THR SEQRES 20 A 251 TYR LEU LYS SER FORMUL 2 HOH *212(H2 O) HELIX 1 1 GLY A 63 ASP A 76 1 14 HELIX 2 2 SER A 84 ASP A 101 1 18 HELIX 3 3 ASP A 105 ALA A 122 1 18 HELIX 4 4 GLY A 123 GLN A 126 5 4 HELIX 5 5 TYR A 127 LEU A 137 1 11 HELIX 6 6 LEU A 137 ALA A 145 1 9 HELIX 7 7 ARG A 149 GLY A 168 1 20 HELIX 8 8 PHE A 171 VAL A 186 1 16 HELIX 9 9 ALA A 190 THR A 208 1 19 HELIX 10 10 ARG A 212 CYS A 221 1 10 HELIX 11 11 SER A 225 TRP A 243 1 19 HELIX 12 12 GLN A 244 GLU A 249 1 6 HELIX 13 13 HIS A 251 HIS A 264 1 14 HELIX 14 14 ASP A 267 PHE A 285 1 19 HELIX 15 15 PHE A 285 SER A 295 1 11 HELIX 16 16 GLU A 297 LEU A 304 1 8 CRYST1 58.812 58.812 157.073 90.00 90.00 120.00 P 32 2 1 6 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 0.017003 0.009817 0.000000 0.00000 SCALE2 0.000000 0.019634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006366 0.00000