HEADER PROTEIN BINDING 18-JUL-17 5OI7 TITLE HUMAN CEP85 - COILED COIL DOMAIN 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CENTROSOMAL PROTEIN OF 85 KDA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CEP85,COILED-COIL DOMAIN-CONTAINING PROTEIN 21; COMPND 5 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: CEP85, CCDC21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C41 KEYWDS CENTROSOMES, CENTRIOLE, CEP85, STIL, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.VAN BREUGEL REVDAT 3 17-JAN-24 5OI7 1 REMARK REVDAT 2 09-MAY-18 5OI7 1 JRNL REVDAT 1 18-APR-18 5OI7 0 JRNL AUTH Y.LIU,G.D.GUPTA,D.D.BARNABAS,F.G.AGIRCAN,S.MEHMOOD,D.WU, JRNL AUTH 2 E.COYAUD,C.M.JOHNSON,S.H.MCLAUGHLIN,A.ANDREEVA,S.M.V.FREUND, JRNL AUTH 3 C.V.ROBINSON,S.W.T.CHEUNG,B.RAUGHT,L.PELLETIER,M.VAN BREUGEL JRNL TITL DIRECT BINDING OF CEP85 TO STIL ENSURES ROBUST PLK4 JRNL TITL 2 ACTIVATION AND EFFICIENT CENTRIOLE ASSEMBLY. JRNL REF NAT COMMUN V. 9 1731 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29712910 JRNL DOI 10.1038/S41467-018-04122-X REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21329 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2011 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 36.9849 - 4.0244 0.99 2756 119 0.2025 0.2059 REMARK 3 2 4.0244 - 3.1949 1.00 2716 163 0.1571 0.2030 REMARK 3 3 3.1949 - 2.7912 1.00 2760 150 0.1772 0.2244 REMARK 3 4 2.7912 - 2.5361 1.00 2731 134 0.1826 0.2140 REMARK 3 5 2.5361 - 2.3543 1.00 2740 153 0.1826 0.2074 REMARK 3 6 2.3543 - 2.2155 1.00 2718 154 0.1810 0.2407 REMARK 3 7 2.2155 - 2.1046 1.00 2746 149 0.1934 0.2475 REMARK 3 8 2.1046 - 2.0130 1.00 2723 146 0.2237 0.2814 REMARK 3 9 2.0130 - 1.9355 1.00 2737 158 0.2507 0.2955 REMARK 3 10 1.9355 - 1.8687 1.00 2735 131 0.2611 0.2704 REMARK 3 11 1.8687 - 1.8103 1.00 2756 130 0.2787 0.3518 REMARK 3 12 1.8103 - 1.7585 1.00 2762 125 0.2866 0.3327 REMARK 3 13 1.7585 - 1.7122 1.00 2700 159 0.3154 0.3532 REMARK 3 14 1.7122 - 1.6705 0.97 2664 140 0.3336 0.3485 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) : 27.300 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 : 0.002 1487 REMARK 3 ANGLE : 0.538 1994 REMARK 3 CHIRALITY : 0.029 220 REMARK 3 PLANARITY : 0.002 270 REMARK 3 DIHEDRAL : 12.160 960 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 5OI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005854. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21341 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 36.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.20200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 1.55200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2Q6Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA-HEPES, PH 7.7 200 MM NA REMARK 280 -CITRATE 36 % (V/V) MPD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 18.96500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.94000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 64.06500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.96500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.94000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.06500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.96500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.94000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.06500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.96500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 36.94000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.06500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 799 O HOH B 829 2.04 REMARK 500 O HOH B 904 O HOH B 913 2.06 REMARK 500 O HOH B 802 O HOH B 863 2.12 REMARK 500 O HOH A 799 O HOH B 898 2.13 REMARK 500 OE1 GLU B 616 O HOH B 801 2.13 REMARK 500 O HOH A 797 O HOH B 911 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 786 O HOH B 810 4554 2.03 REMARK 500 O HOH A 703 O HOH A 709 3554 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 701 DBREF 5OI7 A 570 656 UNP Q6P2H3 CEP85_HUMAN 570 656 DBREF 5OI7 B 570 656 UNP Q6P2H3 CEP85_HUMAN 570 656 SEQADV 5OI7 GLY A 569 UNP Q6P2H3 EXPRESSION TAG SEQADV 5OI7 GLY B 569 UNP Q6P2H3 EXPRESSION TAG SEQRES 1 A 88 GLY GLU SER TRP GLN LYS ARG TYR ASP SER LEU GLN LYS SEQRES 2 A 88 ILE VAL GLU LYS GLN GLN GLN LYS MET ASP GLN LEU ARG SEQRES 3 A 88 SER GLN VAL GLN SER LEU GLU GLN GLU VAL ALA GLN GLU SEQRES 4 A 88 GLU GLY THR SER GLN ALA LEU ARG GLU GLU ALA GLN ARG SEQRES 5 A 88 ARG ASP SER ALA LEU GLN GLN LEU ARG THR ALA VAL LYS SEQRES 6 A 88 GLU LEU SER VAL GLN ASN GLN ASP LEU ILE GLU LYS ASN SEQRES 7 A 88 LEU THR LEU GLN GLU HIS LEU ARG GLN ALA SEQRES 1 B 88 GLY GLU SER TRP GLN LYS ARG TYR ASP SER LEU GLN LYS SEQRES 2 B 88 ILE VAL GLU LYS GLN GLN GLN LYS MET ASP GLN LEU ARG SEQRES 3 B 88 SER GLN VAL GLN SER LEU GLU GLN GLU VAL ALA GLN GLU SEQRES 4 B 88 GLU GLY THR SER GLN ALA LEU ARG GLU GLU ALA GLN ARG SEQRES 5 B 88 ARG ASP SER ALA LEU GLN GLN LEU ARG THR ALA VAL LYS SEQRES 6 B 88 GLU LEU SER VAL GLN ASN GLN ASP LEU ILE GLU LYS ASN SEQRES 7 B 88 LEU THR LEU GLN GLU HIS LEU ARG GLN ALA HET MPD B 701 22 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 MPD C6 H14 O2 FORMUL 4 HOH *227(H2 O) HELIX 1 AA1 SER A 571 LEU A 653 1 83 HELIX 2 AA2 SER B 571 ARG B 654 1 84 SITE 1 AC1 4 TRP A 572 HOH A 773 GLN B 606 GLY B 609 CRYST1 37.930 73.880 128.130 90.00 90.00 90.00 I 2 2 2 16 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 0.026364 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007805 0.00000