HEADER PROTEIN BINDING 10-JUL-07 2QK2 TITLE STRUCTURAL BASIS OF MICROTUBULE PLUS END TRACKING BY XMAP215, CLIP-170 TITLE 2 AND EB1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LP04448P; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TOG DOMAIN 2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: MSPS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS MINI SPINDLES, MSPS, XMAP215, DIS1, STU2, HEAT REPEAT, MICROTUBULE KEYWDS 2 PLUS END, +TIP, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.C.SLEP,R.D.VALE REVDAT 4 18-OCT-17 2QK2 1 REMARK REVDAT 3 28-APR-10 2QK2 1 REMARK REVDAT 2 24-FEB-09 2QK2 1 VERSN REVDAT 1 02-OCT-07 2QK2 0 JRNL AUTH K.C.SLEP,R.D.VALE JRNL TITL STRUCTURAL BASIS OF MICROTUBULE PLUS END TRACKING BY JRNL TITL 2 XMAP215, CLIP-170, AND EB1. JRNL REF MOL.CELL V. 27 976 2007 JRNL REFN ISSN 1097-2765 JRNL PMID 17889670 JRNL DOI 10.1016/J.MOLCEL.2007.07.023 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 43880 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 10% REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : 4291 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 : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.11 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 587 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE : 0.2300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 70 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 : 1851 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 161 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.72600 REMARK 3 B22 (A**2) : 5.26700 REMARK 3 B33 (A**2) : 2.46000 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.382 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.115 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.724 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.118 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 55.20 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 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2QK2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000043696. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.97963, 0.97974, 1.00801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45149 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18500 REMARK 200 R SYM FOR SHELL (I) : 0.18500 REMARK 200 FOR SHELL : 4.300 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 (%): 67.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.25 M SODIUM MALONATE, PROTEIN REMARK 280 CONCENTRATION 15 MG/ML , PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 39.27800 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 39.27800 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 45.68500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.70700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.68500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.70700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.27800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.68500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.70700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.27800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.68500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.70700 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 300 REMARK: MSPS IS A MONOMER. THE N-TERMINAL TWO-THIRDS IS REMARK 300 CHARACTERIZED BY FIVE ARRAYED TOG DOMAINS. THIS STRUCTURE IS THE REMARK 300 SECOND OF THE FIVE TOG DOMAINS. 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 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 505 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 ALA A 352 -128.00 49.69 REMARK 500 THR A 392 -148.46 -137.61 REMARK 500 VAL A 503 -91.16 -58.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QJX RELATED DB: PDB REMARK 900 RELATED ID: 2QJZ RELATED DB: PDB REMARK 900 RELATED ID: 2QK0 RELATED DB: PDB REMARK 900 RELATED ID: 2QK1 RELATED DB: PDB DBREF 2QK2 A 267 505 UNP Q4QQC0 Q4QQC0_DROME 267 505 SEQADV 2QK2 GLY A 264 UNP Q4QQC0 EXPRESSION TAG SEQADV 2QK2 SER A 265 UNP Q4QQC0 EXPRESSION TAG SEQADV 2QK2 HIS A 266 UNP Q4QQC0 EXPRESSION TAG SEQRES 1 A 242 GLY SER HIS MSE ASP LEU LEU ASP PRO VAL ASP ILE LEU SEQRES 2 A 242 SER LYS MSE PRO LYS ASP PHE TYR ASP LYS LEU GLU GLU SEQRES 3 A 242 LYS LYS TRP THR LEU ARG LYS GLU SER LEU GLU VAL LEU SEQRES 4 A 242 GLU LYS LEU LEU THR ASP HIS PRO LYS LEU GLU ASN GLY SEQRES 5 A 242 GLU TYR GLY ALA LEU VAL SER ALA LEU LYS LYS VAL ILE SEQRES 6 A 242 THR LYS ASP SER ASN VAL VAL LEU VAL ALA MSE ALA GLY SEQRES 7 A 242 LYS CYS LEU ALA LEU LEU ALA LYS GLY LEU ALA LYS ARG SEQRES 8 A 242 PHE SER ASN TYR ALA SER ALA CYS VAL PRO SER LEU LEU SEQRES 9 A 242 GLU LYS PHE LYS GLU LYS LYS PRO ASN VAL VAL THR ALA SEQRES 10 A 242 LEU ARG GLU ALA ILE ASP ALA ILE TYR ALA SER THR SER SEQRES 11 A 242 LEU GLU ALA GLN GLN GLU SER ILE VAL GLU SER LEU SER SEQRES 12 A 242 ASN LYS ASN PRO SER VAL LYS SER GLU THR ALA LEU PHE SEQRES 13 A 242 ILE ALA ARG ALA LEU THR ARG THR GLN PRO THR ALA LEU SEQRES 14 A 242 ASN LYS LYS LEU LEU LYS LEU LEU THR THR SER LEU VAL SEQRES 15 A 242 LYS THR LEU ASN GLU PRO ASP PRO THR VAL ARG ASP SER SEQRES 16 A 242 SER ALA GLU ALA LEU GLY THR LEU ILE LYS LEU MSE GLY SEQRES 17 A 242 ASP LYS ALA VAL THR PRO LEU LEU ALA ASP VAL ASP PRO SEQRES 18 A 242 LEU LYS MSE ALA LYS ILE LYS GLU CYS GLN GLU LYS ALA SEQRES 19 A 242 GLU ILE LYS ILE LYS VAL ALA GLY MODRES 2QK2 MSE A 267 MET SELENOMETHIONINE MODRES 2QK2 MSE A 279 MET SELENOMETHIONINE MODRES 2QK2 MSE A 339 MET SELENOMETHIONINE MODRES 2QK2 MSE A 470 MET SELENOMETHIONINE MODRES 2QK2 MSE A 487 MET SELENOMETHIONINE HET MSE A 267 8 HET MSE A 279 8 HET MSE A 339 8 HET MSE A 470 8 HET MSE A 487 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 HOH *161(H2 O) HELIX 1 1 GLY A 264 LEU A 269 1 6 HELIX 2 2 ILE A 275 MSE A 279 5 5 HELIX 3 3 ASP A 282 GLU A 288 1 7 HELIX 4 4 LYS A 291 HIS A 309 1 19 HELIX 5 5 TYR A 317 ASP A 331 1 15 HELIX 6 6 ASN A 333 ALA A 352 1 20 HELIX 7 7 PHE A 355 LYS A 369 1 15 HELIX 8 8 PHE A 370 GLU A 372 5 3 HELIX 9 9 LYS A 374 ALA A 390 1 17 HELIX 10 10 SER A 393 LEU A 405 1 13 HELIX 11 11 ASN A 409 THR A 425 1 17 HELIX 12 12 ARG A 426 THR A 427 5 2 HELIX 13 13 GLN A 428 LEU A 432 5 5 HELIX 14 14 ASN A 433 ASN A 449 1 17 HELIX 15 15 ASP A 452 GLY A 471 1 20 HELIX 16 16 GLY A 471 THR A 476 1 6 HELIX 17 17 PRO A 477 ALA A 480 5 4 HELIX 18 18 ASP A 483 ALA A 497 1 15 LINK C HIS A 266 N MSE A 267 1555 1555 1.33 LINK C MSE A 267 N ASP A 268 1555 1555 1.33 LINK C LYS A 278 N MSE A 279 1555 1555 1.32 LINK C MSE A 279 N PRO A 280 1555 1555 1.34 LINK C ALA A 338 N MSE A 339 1555 1555 1.33 LINK C MSE A 339 N ALA A 340 1555 1555 1.33 LINK C LEU A 469 N MSE A 470 1555 1555 1.33 LINK C MSE A 470 N GLY A 471 1555 1555 1.33 LINK C LYS A 486 N MSE A 487 1555 1555 1.33 LINK C MSE A 487 N ALA A 488 1555 1555 1.33 CRYST1 91.370 113.414 78.556 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 0.010945 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008817 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012730 0.00000