HEADER STRUCTURAL PROTEIN 10-MAR-15 4YNH TITLE STRUCTURE OF THE C. ELEGANS SAS-5 IMPLICO DIMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPINDLE ASSEMBLY ABNORMAL PROTEIN 5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DIMERIZATION DOMAIN, UNP RESIDUES 210-265; COMPND 5 SYNONYM: SAS-5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: SAS-5, F35B12.5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS SAS-5, CENTRIOLE, DIMERIZATION DOMAIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.B.ROGALA,I.VAKONAKIS,G.N.HATZOPOULOS REVDAT 2 26-AUG-15 4YNH 1 JRNL REVDAT 1 10-JUN-15 4YNH 0 JRNL AUTH K.B.ROGALA,N.J.DYNES,G.N.HATZOPOULOS,J.YAN,S.K.PONG, JRNL AUTH 2 C.V.ROBINSON,C.M.DEANE,P.GONCZY,I.VAKONAKIS JRNL TITL THE CAENORHABDITIS ELEGANS PROTEIN SAS-5 FORMS LARGE JRNL TITL 2 OLIGOMERIC ASSEMBLIES CRITICAL FOR CENTRIOLE FORMATION. JRNL REF ELIFE V. 4 07410 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26023830 JRNL DOI 10.7554/ELIFE.07410 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 44248 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2232 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 18.4888 - 2.5178 1.00 2714 150 0.1451 0.1730 REMARK 3 2 2.5178 - 1.9993 1.00 2684 130 0.1398 0.1451 REMARK 3 3 1.9993 - 1.7468 1.00 2651 144 0.1361 0.1497 REMARK 3 4 1.7468 - 1.5871 1.00 2661 133 0.1219 0.1458 REMARK 3 5 1.5871 - 1.4734 1.00 2626 154 0.1092 0.1333 REMARK 3 6 1.4734 - 1.3866 1.00 2630 145 0.1087 0.1350 REMARK 3 7 1.3866 - 1.3172 1.00 2632 145 0.1025 0.1228 REMARK 3 8 1.3172 - 1.2599 1.00 2633 133 0.1017 0.1189 REMARK 3 9 1.2599 - 1.2114 1.00 2628 137 0.0983 0.1248 REMARK 3 10 1.2114 - 1.1696 0.99 2627 115 0.1072 0.1374 REMARK 3 11 1.1696 - 1.1330 0.99 2595 139 0.1095 0.1327 REMARK 3 12 1.1330 - 1.1006 0.99 2620 143 0.1158 0.1421 REMARK 3 13 1.1006 - 1.0717 0.99 2614 121 0.1256 0.1330 REMARK 3 14 1.0717 - 1.0455 0.98 2558 153 0.1337 0.1564 REMARK 3 15 1.0455 - 1.0217 0.98 2584 163 0.1581 0.2085 REMARK 3 16 1.0217 - 1.0000 0.98 2559 127 0.1817 0.1804 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.63 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 : 0.007 1035 REMARK 3 ANGLE : 1.152 1420 REMARK 3 CHIRALITY : 0.057 157 REMARK 3 PLANARITY : 0.006 201 REMARK 3 DIHEDRAL : 12.549 420 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 4YNH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207757. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-12 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 : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 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 : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.235 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10800 REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.76300 REMARK 200 R SYM FOR SHELL (I) : 0.76300 REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES/IMIDAZOLE PH 6.4, 10% W/V REMARK 280 PEG 20,000, 20% V/V PEG MME 550, 0.1 M CARBOXYLIC ACIDS MIXTURE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 18.14500 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 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 -3 REMARK 465 PRO A 265 REMARK 465 SER B 264 REMARK 465 PRO B 265 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 OG SER B 214 O HOH B 301 2.12 REMARK 500 O HOH A 329 O HOH A 349 2.17 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 OH TYR A 263 O HOH B 321 1656 2.17 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 ASP B 240 94.49 -164.81 REMARK 500 REMARK 500 REMARK: NULL DBREF 4YNH A 210 265 UNP Q20010 SAS5_CAEEL 210 265 DBREF 4YNH B 210 265 UNP Q20010 SAS5_CAEEL 210 265 SEQADV 4YNH GLY A -3 UNP Q20010 EXPRESSION TAG SEQADV 4YNH PRO A -2 UNP Q20010 EXPRESSION TAG SEQADV 4YNH LEU A -1 UNP Q20010 EXPRESSION TAG SEQADV 4YNH GLY A 0 UNP Q20010 EXPRESSION TAG SEQADV 4YNH GLY B -3 UNP Q20010 EXPRESSION TAG SEQADV 4YNH PRO B -2 UNP Q20010 EXPRESSION TAG SEQADV 4YNH LEU B -1 UNP Q20010 EXPRESSION TAG SEQADV 4YNH GLY B 0 UNP Q20010 EXPRESSION TAG SEQRES 1 A 60 GLY PRO LEU GLY SER LYS ILE ALA SER ALA ARG GLU VAL SEQRES 2 A 60 ILE LYS ARG ASP GLY VAL ILE PRO PRO GLU ALA LEU THR SEQRES 3 A 60 ILE ILE GLU GLN ARG LEU ARG SER ASP PRO MET PHE ARG SEQRES 4 A 60 GLN GLN ILE ASP ASN VAL LEU ALA ASP ALA GLU CYS ASP SEQRES 5 A 60 ALA ASN ARG ALA ALA TYR SER PRO SEQRES 1 B 60 GLY PRO LEU GLY SER LYS ILE ALA SER ALA ARG GLU VAL SEQRES 2 B 60 ILE LYS ARG ASP GLY VAL ILE PRO PRO GLU ALA LEU THR SEQRES 3 B 60 ILE ILE GLU GLN ARG LEU ARG SER ASP PRO MET PHE ARG SEQRES 4 B 60 GLN GLN ILE ASP ASN VAL LEU ALA ASP ALA GLU CYS ASP SEQRES 5 B 60 ALA ASN ARG ALA ALA TYR SER PRO FORMUL 3 HOH *124(H2 O) HELIX 1 AA1 PRO A -2 GLY A 223 1 17 HELIX 2 AA2 PRO A 226 ASP A 240 1 15 HELIX 3 AA3 ASP A 240 ASN A 259 1 20 HELIX 4 AA4 PRO B -2 GLY B 223 1 17 HELIX 5 AA5 PRO B 226 ARG B 238 1 13 HELIX 6 AA6 ASP B 240 ARG B 260 1 21 CRYST1 27.180 36.290 42.600 90.00 97.50 90.00 P 1 21 1 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 0.036792 0.000000 0.004844 0.00000 SCALE2 0.000000 0.027556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023677 0.00000