HEADER STRUCTURAL PROTEIN 02-MAY-16 5JO8 TITLE CEP104 TOG DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEP104; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TOG DOMAIN, UNP RESIDUES 429-686; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: CEP104; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CENTRIOLAR PROTEIN, TOG DOMAIN, CEP104, MICROTUBULE BINDER, KEYWDS 2 STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.REZABKOVA,S.H.W.KRAATZ REVDAT 3 06-SEP-17 5JO8 1 REMARK REVDAT 2 07-SEP-16 5JO8 1 JRNL REVDAT 1 20-JUL-16 5JO8 0 JRNL AUTH L.REZABKOVA,S.H.KRAATZ,A.AKHMANOVA,M.O.STEINMETZ, JRNL AUTH 2 R.A.KAMMERER JRNL TITL BIOPHYSICAL AND STRUCTURAL CHARACTERIZATION OF THE JRNL TITL 2 CENTRIOLAR PROTEIN CEP104 INTERACTION NETWORK. JRNL REF J.BIOL.CHEM. V. 291 18496 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27402853 JRNL DOI 10.1074/JBC.M116.739771 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1965 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 55550 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.570 REMARK 3 FREE R VALUE TEST SET COUNT : 1982 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.7934 - 3.3737 0.92 3840 140 0.1876 0.1968 REMARK 3 2 3.3737 - 2.6779 0.94 3783 138 0.2163 0.2129 REMARK 3 3 2.6779 - 2.3394 0.95 3768 139 0.2378 0.2211 REMARK 3 4 2.3394 - 2.1255 1.00 3955 146 0.1931 0.2485 REMARK 3 5 2.1255 - 1.9732 0.99 3880 145 0.2041 0.2465 REMARK 3 6 1.9732 - 1.8568 0.98 3846 142 0.2334 0.3163 REMARK 3 7 1.8568 - 1.7638 1.00 3927 145 0.2258 0.2976 REMARK 3 8 1.7638 - 1.6871 1.00 3881 145 0.2258 0.2805 REMARK 3 9 1.6871 - 1.6221 1.00 3886 145 0.2381 0.2890 REMARK 3 10 1.6221 - 1.5661 0.89 3464 128 0.3043 0.3179 REMARK 3 11 1.5661 - 1.5172 0.97 3778 141 0.3023 0.3122 REMARK 3 12 1.5172 - 1.4738 0.99 3846 143 0.3206 0.3247 REMARK 3 13 1.4738 - 1.4350 1.00 3867 143 0.3717 0.3935 REMARK 3 14 1.4350 - 1.4000 1.00 3847 142 0.4068 0.4180 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2118 REMARK 3 ANGLE : 1.000 2867 REMARK 3 CHIRALITY : 0.069 334 REMARK 3 PLANARITY : 0.005 358 REMARK 3 DIHEDRAL : 11.465 816 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5JO8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000220840. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0, 0.96 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55668 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 16.40 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 16.50 REMARK 200 R MERGE FOR SHELL (I) : 2.76000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.050 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL, PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 1500, 0.1 M MMT PH 5.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.48000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.61000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.48000 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 515 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 538 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 REMARK 465 MET A 21 REMARK 465 ASP A 278 REMARK 465 GLY A 279 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 GLN A 116 -52.86 -123.30 REMARK 500 REMARK 500 REMARK: NULL DBREF 5JO8 A 22 279 UNP E1C2W2 E1C2W2_CHICK 429 686 SEQADV 5JO8 MET A 1 UNP E1C2W2 INITIATING METHIONINE SEQADV 5JO8 GLY A 2 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 SER A 3 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 SER A 4 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 HIS A 5 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 HIS A 6 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 HIS A 7 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 HIS A 8 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 HIS A 9 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 HIS A 10 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 SER A 11 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 SER A 12 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 GLY A 13 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 LEU A 14 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 VAL A 15 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 PRO A 16 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 ARG A 17 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 GLY A 18 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 SER A 19 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 HIS A 20 UNP E1C2W2 EXPRESSION TAG SEQADV 5JO8 MET A 21 UNP E1C2W2 EXPRESSION TAG SEQRES 1 A 279 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 279 LEU VAL PRO ARG GLY SER HIS MET GLU PRO GLU PRO LEU SEQRES 3 A 279 SER GLU LYS ALA LEU ARG GLU ALA SER PRO ALA ILE GLU SEQRES 4 A 279 VAL PHE GLY GLU ALA LEU VAL SER GLY ALA TYR SER LYS SEQRES 5 A 279 SER TRP SER TYR ARG GLU ASP ALA LEU LEU ALA VAL TYR SEQRES 6 A 279 LYS LYS LEU MET GLU MET SER VAL SER THR PRO LYS GLU SEQRES 7 A 279 ASP LEU ARG ASN MET LEU ARG ALA ALA ILE PHE LEU VAL SEQRES 8 A 279 ARG ARG ALA ILE LYS ASP ILE VAL SER SER VAL PHE GLN SEQRES 9 A 279 ALA SER LEU LYS LEU LEU LYS MET ILE ILE THR GLN TYR SEQRES 10 A 279 VAL PRO LYS HIS LYS LEU GLY LYS LEU GLU THR SER HIS SEQRES 11 A 279 CYS VAL GLU LYS THR LEU PRO GLY LEU LEU SER ARG THR SEQRES 12 A 279 GLY ASP SER SER SER ARG LEU ARG ILE VAL ALA ALA LYS SEQRES 13 A 279 PHE ILE GLN GLU MET ALA LEU TRP SER GLU VAL LYS PRO SEQRES 14 A 279 LEU GLN ILE VAL PRO VAL HIS LEU VAL GLN LEU LEU LYS SEQRES 15 A 279 PRO ASN SER PRO THR HIS LEU ALA MET SER ARG VAL GLU SEQRES 16 A 279 LEU VAL GLU CYS LEU LEU LYS GLU MET GLY THR GLU ASN SEQRES 17 A 279 SER GLY PHE THR ILE SER ASN VAL MET LYS PHE ALA THR SEQRES 18 A 279 GLY ALA LEU GLU HIS ARG VAL TYR GLU VAL ARG ASP VAL SEQRES 19 A 279 ALA LEU ARG ILE ILE PHE GLY MET TYR ARG LYS HIS LYS SEQRES 20 A 279 ALA ALA ILE LEU GLU TYR LEU PRO PRO ASP ASP ALA SER SEQRES 21 A 279 ILE ARG LYS THR VAL LEU TYR LYS THR LEU PHE ASP GLY SEQRES 22 A 279 PHE THR LYS ILE ASP GLY FORMUL 2 HOH *248(H2 O) HELIX 1 AA1 SER A 27 ALA A 34 1 8 HELIX 2 AA2 ALA A 34 GLY A 42 1 9 HELIX 3 AA3 GLY A 42 TYR A 50 1 9 HELIX 4 AA4 SER A 53 GLU A 70 1 18 HELIX 5 AA5 PRO A 76 ILE A 95 1 20 HELIX 6 AA6 VAL A 99 GLN A 116 1 18 HELIX 7 AA7 GLN A 116 LYS A 122 1 7 HELIX 8 AA8 GLY A 124 THR A 143 1 20 HELIX 9 AA9 SER A 147 TRP A 164 1 18 HELIX 10 AB1 VAL A 167 GLN A 171 5 5 HELIX 11 AB2 ILE A 172 VAL A 178 1 7 HELIX 12 AB3 PRO A 186 GLY A 205 1 20 HELIX 13 AB4 THR A 212 LEU A 224 1 13 HELIX 14 AB5 VAL A 228 HIS A 246 1 19 HELIX 15 AB6 HIS A 246 LEU A 254 1 9 HELIX 16 AB7 SER A 260 LYS A 263 5 4 HELIX 17 AB8 THR A 264 ILE A 277 1 14 CRYST1 48.360 57.220 102.960 90.00 90.00 90.00 P 2 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 0.020678 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017476 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009713 0.00000