HEADER PROTEIN BINDING 09-JUL-07 2QK0 TITLE STRUCTURAL BASIS OF MICROTUBULE PLUS END TRACKING BY XMAP215, CLIP-170 TITLE 2 AND EB1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAP-GLY DOMAIN-CONTAINING LINKER PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CAP-GLY DOMAIN 1; COMPND 5 SYNONYM: RESTIN, CYTOPLASMIC LINKER PROTEIN 170 ALPHA-2, CLIP-170, COMPND 6 REED-STERNBERG INTERMEDIATE FILAMENT-ASSOCIATED PROTEIN, CYTOPLASMIC COMPND 7 LINKER PROTEIN 1; COMPND 8 ENGINEERED: YES; COMPND 9 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: CLIP1, CYLN1, RSN; 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: PET15B KEYWDS CLIP-170, CAP-GLY DOMAIN, MICROTUBULE PLUS END, +TIP, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.C.SLEP,R.D.VALE REVDAT 4 20-OCT-21 2QK0 1 SEQADV LINK REVDAT 3 18-OCT-17 2QK0 1 REMARK REVDAT 2 24-FEB-09 2QK0 1 VERSN REVDAT 1 02-OCT-07 2QK0 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. 2.00 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 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 7778 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 814 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 571 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.00700 REMARK 3 B22 (A**2) : -0.46000 REMARK 3 B33 (A**2) : -0.54800 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.204 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.637 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.276 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.325 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2QK0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000043694. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97964, 1.12713 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7855 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 4.60000 REMARK 200 FOR THE DATA SET : 37.6000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.07900 REMARK 200 R SYM FOR SHELL (I) : 7.90000 REMARK 200 FOR SHELL : 15.00 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 (%): 32.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M SODIUM MALONATE, 100 MM GLYCINE, REMARK 280 1.1 MM LANTHANUM CHLORIDE, PROTEIN CONCENTRATION 15 MG/ML, PH REMARK 280 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 13.62100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.90300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.26650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.90300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.62100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.26650 REMARK 290 SMTRY3 4 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: CLIP-170 IS A HOMODIMER FORMED VIA A LARGE CENTRAL COILED REMARK 300 COIL REGION NOT INCLUDED IN THIS CONSTRUCT. THIS CONSTRUCT EMBODIES REMARK 300 ONLY CAP-GLY DOMAIN 1. 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 VAL A 101 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: 2QK1 RELATED DB: PDB REMARK 900 RELATED ID: 2QK2 RELATED DB: PDB DBREF 2QK0 A 30 101 UNP P30622 CLIP1_HUMAN 57 128 SEQADV 2QK0 GLY A 28 UNP P30622 EXPRESSION TAG SEQADV 2QK0 SER A 29 UNP P30622 EXPRESSION TAG SEQADV 2QK0 MSE A 97 UNP P30622 LEU 124 ENGINEERED MUTATION SEQRES 1 A 74 GLY SER ASP PHE ARG VAL GLY GLU ARG VAL TRP VAL ASN SEQRES 2 A 74 GLY ASN LYS PRO GLY PHE ILE GLN PHE LEU GLY GLU THR SEQRES 3 A 74 GLN PHE ALA PRO GLY GLN TRP ALA GLY ILE VAL LEU ASP SEQRES 4 A 74 GLU PRO ILE GLY LYS ASN ASP GLY SER VAL ALA GLY VAL SEQRES 5 A 74 ARG TYR PHE GLN CYS GLU PRO LEU LYS GLY ILE PHE THR SEQRES 6 A 74 ARG PRO SER LYS MSE THR ARG LYS VAL MODRES 2QK0 MSE A 97 MET SELENOMETHIONINE HET MSE A 97 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *66(H2 O) HELIX 1 1 ARG A 93 SER A 95 5 3 SHEET 1 A 5 GLY A 89 THR A 92 0 SHEET 2 A 5 TRP A 60 LEU A 65 -1 N ILE A 63 O ILE A 90 SHEET 3 A 5 LYS A 43 GLY A 51 -1 N GLN A 48 O GLY A 62 SHEET 4 A 5 ARG A 36 VAL A 39 -1 N VAL A 37 O GLY A 45 SHEET 5 A 5 MSE A 97 THR A 98 -1 O THR A 98 N TRP A 38 SHEET 1 B 2 SER A 75 VAL A 76 0 SHEET 2 B 2 VAL A 79 ARG A 80 -1 O VAL A 79 N VAL A 76 LINK C LYS A 96 N MSE A 97 1555 1555 1.33 LINK C MSE A 97 N THR A 98 1555 1555 1.33 CRYST1 27.242 42.533 51.806 90.00 90.00 90.00 P 21 21 21 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 0.036708 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023511 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019303 0.00000 MASTER 207 0 1 1 7 0 0 6 0 0 0 6 END