HEADER CYTOSOLIC PROTEIN 04-NOV-17 6EWH TITLE OREOCHROMIS NILOTICUS CEP120 SECOND C2 DOMAIN (C2B) G307S MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CENTROSOMAL PROTEIN 120; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OREOCHROMIS NILOTICUS; SOURCE 3 ORGANISM_COMMON: NILE TILAPIA; SOURCE 4 ORGANISM_TAXID: 8128; SOURCE 5 GENE: CEP120; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA KEYWDS CENTRIOLE CENTROSOME BASAL BODY CILIA, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.VAN BREUGEL,C.AL-JASSAR,M.YU REVDAT 3 08-MAY-24 6EWH 1 REMARK REVDAT 2 13-JUN-18 6EWH 1 JRNL REVDAT 1 02-MAY-18 6EWH 0 JRNL AUTH N.JOSEPH,C.AL-JASSAR,C.M.JOHNSON,A.ANDREEVA,D.D.BARNABAS, JRNL AUTH 2 S.M.V.FREUND,F.GERGELY,M.VAN BREUGEL JRNL TITL DISEASE-ASSOCIATED MUTATIONS IN CEP120 DESTABILIZE THE JRNL TITL 2 PROTEIN AND IMPAIR CILIOGENESIS. JRNL REF CELL REP V. 23 2805 2018 JRNL REFN ESSN 2211-1247 JRNL PMID 29847808 JRNL DOI 10.1016/J.CELREP.2018.04.100 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 35948 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3394 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 30.1710 - 4.3226 1.00 2687 142 0.1517 0.1536 REMARK 3 2 4.3226 - 3.4326 1.00 2719 119 0.1531 0.1597 REMARK 3 3 3.4326 - 2.9991 1.00 2687 138 0.1749 0.1827 REMARK 3 4 2.9991 - 2.7251 1.00 2697 125 0.1858 0.2451 REMARK 3 5 2.7251 - 2.5299 1.00 2724 128 0.1927 0.2362 REMARK 3 6 2.5299 - 2.3808 1.00 2690 135 0.1936 0.2610 REMARK 3 7 2.3808 - 2.2616 1.00 2656 160 0.1891 0.2053 REMARK 3 8 2.2616 - 2.1632 1.00 2700 151 0.1899 0.1895 REMARK 3 9 2.1632 - 2.0799 1.00 2711 130 0.2023 0.2281 REMARK 3 10 2.0799 - 2.0082 1.00 2658 162 0.1980 0.2256 REMARK 3 11 2.0082 - 1.9454 1.00 2660 157 0.1882 0.2564 REMARK 3 12 1.9454 - 1.8898 1.00 2724 132 0.1971 0.2391 REMARK 3 13 1.8898 - 1.8400 1.00 2680 141 0.2118 0.2282 REMARK 3 14 1.8400 - 1.7952 1.00 2711 140 0.2221 0.3060 REMARK 3 15 1.7952 - 1.7543 1.00 2651 146 0.2349 0.2781 REMARK 3 16 1.7543 - 1.7170 1.00 2684 138 0.2357 0.2606 REMARK 3 17 1.7170 - 1.6827 1.00 2713 140 0.2513 0.2654 REMARK 3 18 1.6827 - 1.6509 1.00 2650 158 0.2618 0.2578 REMARK 3 19 1.6509 - 1.6214 1.00 2709 125 0.2693 0.3265 REMARK 3 20 1.6214 - 1.5940 1.00 2648 155 0.2798 0.2809 REMARK 3 21 1.5940 - 1.5682 1.00 2702 154 0.3052 0.3227 REMARK 3 22 1.5682 - 1.5441 1.00 2713 150 0.3038 0.3561 REMARK 3 23 1.5441 - 1.5214 1.00 2633 151 0.3185 0.3511 REMARK 3 24 1.5214 - 1.5000 1.00 2677 117 0.3308 0.3373 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.70 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 : 0.005 1492 REMARK 3 ANGLE : 0.829 2054 REMARK 3 CHIRALITY : 0.078 252 REMARK 3 PLANARITY : 0.006 266 REMARK 3 DIHEDRAL : 15.015 576 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -4.8736 7.6894 -15.0564 REMARK 3 T TENSOR REMARK 3 T11: 0.2200 T22: 0.2152 REMARK 3 T33: 0.1877 T12: -0.0251 REMARK 3 T13: 0.0019 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 1.9190 L22: 1.2596 REMARK 3 L33: 0.9106 L12: -0.5730 REMARK 3 L13: -0.7547 L23: 0.2242 REMARK 3 S TENSOR REMARK 3 S11: -0.0459 S12: 0.0989 S13: -0.0902 REMARK 3 S21: 0.0609 S22: 0.0188 S23: 0.0285 REMARK 3 S31: 0.1218 S32: -0.1321 S33: 0.0000 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 6EWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007367. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36042 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 31.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA-MES, PH 6.1 29 % (V/V) PEG REMARK 280 -400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 18.22450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.68950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.62500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.68950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.22450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.62500 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 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: 10450 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 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 161 REMARK 465 PRO A 162 REMARK 465 HIS A 163 REMARK 465 MET A 164 REMARK 465 PRO A 165 REMARK 465 GLN A 347 REMARK 465 SER A 348 REMARK 465 VAL A 349 REMARK 465 GLY A 350 REMARK 465 ASN A 351 REMARK 465 LYS A 352 REMARK 465 GLU A 353 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 582 O HOH A 597 2.13 REMARK 500 O HOH A 411 O HOH A 415 2.15 REMARK 500 O HOH A 580 O HOH A 582 2.18 REMARK 500 O HOH A 500 O HOH A 545 2.18 REMARK 500 O HOH A 486 O HOH A 498 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 218 90.75 -66.07 REMARK 500 SER A 255 -165.44 -164.27 REMARK 500 ASP A 297 47.60 -144.57 REMARK 500 REMARK 500 REMARK: NULL DBREF 6EWH A 165 353 UNP I3K8D3 I3K8D3_ORENI 165 353 SEQADV 6EWH GLY A 161 UNP I3K8D3 EXPRESSION TAG SEQADV 6EWH PRO A 162 UNP I3K8D3 EXPRESSION TAG SEQADV 6EWH HIS A 163 UNP I3K8D3 EXPRESSION TAG SEQADV 6EWH MET A 164 UNP I3K8D3 EXPRESSION TAG SEQADV 6EWH SER A 307 UNP I3K8D3 GLY 307 ENGINEERED MUTATION SEQRES 1 A 193 GLY PRO HIS MET PRO GLU LYS LEU GLU ALA ILE LEU ILE SEQRES 2 A 193 PRO ASP GLN GLY TYR HIS GLN VAL GLY PRO ALA ASP LEU SEQRES 3 A 193 CYS THR ASP MET PHE VAL LEU SER VAL THR VAL ALA PHE SEQRES 4 A 193 ALA THR LYS LEU GLU GLN LEU VAL PRO SER THR MET LYS SEQRES 5 A 193 LEU SER ALA GLU GLY SER GLU PHE PHE PHE TYR TYR SER SEQRES 6 A 193 LEU LEU GLY ASN ASP ILE THR SER GLU PRO PHE HIS ASN SEQRES 7 A 193 LEU LEU SER PRO ASP PHE GLU PRO GLU ARG ALA SER VAL SEQRES 8 A 193 ARG ILE ARG SER SER LYS GLN ILE LEU LYS ALA PHE LEU SEQRES 9 A 193 SER GLN GLN PRO SER LEU GLN ILE HIS LEU CYS CYS GLY SEQRES 10 A 193 ASN HIS SER LEU GLY SER THR ASP VAL SER LEU SER ALA SEQRES 11 A 193 LEU ALA GLY ILE SER THR ASP LEU ASP ASN LYS ALA ALA SEQRES 12 A 193 THR VAL GLU SER ALA PHE ILE LEU GLN PRO PRO LYS ARG SEQRES 13 A 193 VAL LYS GLN THR LEU PRO ALA LEU PRO THR ASP LEU GLN SEQRES 14 A 193 PRO THR LEU GLY VAL ALA VAL THR LEU ARG ARG GLU GLU SEQRES 15 A 193 VAL ALA LEU GLN GLN SER VAL GLY ASN LYS GLU FORMUL 2 HOH *202(H2 O) HELIX 1 AA1 LYS A 202 VAL A 207 5 6 HELIX 2 AA2 SER A 209 ALA A 215 1 7 HELIX 3 AA3 SER A 256 GLN A 266 1 11 HELIX 4 AA4 SER A 287 ILE A 294 1 8 SHEET 1 AA1 6 ALA A 170 ILE A 173 0 SHEET 2 AA1 6 TYR A 178 VAL A 181 -1 O GLN A 180 N ILE A 171 SHEET 3 AA1 6 GLU A 247 SER A 255 1 O ARG A 254 N HIS A 179 SHEET 4 AA1 6 ASP A 189 THR A 201 -1 N PHE A 191 O ILE A 253 SHEET 5 AA1 6 THR A 331 ARG A 340 -1 O GLY A 333 N ALA A 198 SHEET 6 AA1 6 ALA A 303 ILE A 310 -1 N ALA A 303 O LEU A 338 SHEET 1 AA2 4 ASN A 229 THR A 232 0 SHEET 2 AA2 4 PHE A 220 LEU A 226 -1 N TYR A 224 O ILE A 231 SHEET 3 AA2 4 LEU A 270 CYS A 276 -1 O CYS A 275 N PHE A 221 SHEET 4 AA2 4 HIS A 279 VAL A 286 -1 O VAL A 286 N LEU A 270 CISPEP 1 LEU A 321 PRO A 322 0 -0.95 CISPEP 2 LEU A 321 PRO A 322 0 -0.06 CRYST1 36.449 67.250 89.379 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 0.027435 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011188 0.00000