HEADER STRUCTURAL PROTEIN 25-MAY-20 6Z4A TITLE STRUCTURE OF THE HUMAN SAS-6 N-TERMINAL DOMAIN, F131E MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HSSAS-6; 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: SASS6, SAS6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PFLOAT2 KEYWDS CENTROSOME, CENTRIOLE, CARTWHEEL, ALPHA/BETA PROTEIN, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.C.BUSCH,I.VAKONAKIS REVDAT 3 07-FEB-24 6Z4A 1 REMARK REVDAT 2 01-MAR-23 6Z4A 1 JRNL REVDAT 1 09-SEP-20 6Z4A 0 JRNL AUTH J.M.C.BUSCH,M.T.MATSOUKAS,M.MUSGAARD,G.A.SPYROULIAS, JRNL AUTH 2 P.C.BIGGIN,I.VAKONAKIS JRNL TITL IDENTIFICATION OF COMPOUNDS THAT BIND THE CENTRIOLAR PROTEIN JRNL TITL 2 SAS-6 AND INHIBIT ITS OLIGOMERIZATION. JRNL REF J.BIOL.CHEM. V. 295 17922 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32873708 JRNL DOI 10.1074/JBC.RA120.014780 REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 26340 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 REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.730 REMARK 3 FREE R VALUE TEST SET COUNT : 1247 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.47 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.62 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 527 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2961 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 501 REMARK 3 BIN R VALUE (WORKING SET) : 0.2935 REMARK 3 BIN FREE R VALUE : 0.3472 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.93 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1219 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.32630 REMARK 3 B22 (A**2) : -1.48370 REMARK 3 B33 (A**2) : -0.84260 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.210 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.076 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.080 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.085 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.078 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2569 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4678 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 578 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 418 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2569 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 167 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2721 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.75 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.12 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 10.9670 74.0722 13.6684 REMARK 3 T TENSOR REMARK 3 T11: -0.0097 T22: -0.0213 REMARK 3 T33: -0.0120 T12: -0.0012 REMARK 3 T13: -0.0017 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 1.2382 L22: 0.2747 REMARK 3 L33: 0.0000 L12: -0.0377 REMARK 3 L13: 0.3993 L23: -0.1295 REMARK 3 S TENSOR REMARK 3 S11: 0.0080 S12: 0.0330 S13: -0.0302 REMARK 3 S21: -0.0068 S22: -0.0075 S23: 0.0280 REMARK 3 S31: 0.0001 S32: 0.0161 S33: -0.0005 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Z4A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108838. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26380 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 21.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 1.11800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 2Y3V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES 30% W/V PEG 6000 REMARK 280 CRYOPROTECTED BY ADDITION OF 20% V/V GLYCEROL, PH 7, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 29.79500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.56500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.79500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.56500 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: 190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9120 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 LYS A 150 REMARK 465 LYS A 151 REMARK 465 PHE A 152 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 A 117 -153.53 -139.44 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 GOL A 201 DBREF 6Z4A A 1 152 UNP Q6UVJ0 SAS6_HUMAN 1 152 SEQADV 6Z4A GLY A -1 UNP Q6UVJ0 EXPRESSION TAG SEQADV 6Z4A PRO A 0 UNP Q6UVJ0 EXPRESSION TAG SEQADV 6Z4A GLU A 131 UNP Q6UVJ0 PHE 131 ENGINEERED MUTATION SEQRES 1 A 154 GLY PRO MET SER GLN VAL LEU PHE HIS GLN LEU VAL PRO SEQRES 2 A 154 LEU GLN VAL LYS CYS LYS ASP CYS GLU GLU ARG ARG VAL SEQRES 3 A 154 SER ILE ARG MET SER ILE GLU LEU GLN SER VAL SER ASN SEQRES 4 A 154 PRO VAL HIS ARG LYS ASP LEU VAL ILE ARG LEU THR ASP SEQRES 5 A 154 ASP THR ASP PRO PHE PHE LEU TYR ASN LEU VAL ILE SER SEQRES 6 A 154 GLU GLU ASP PHE GLN SER LEU LYS PHE GLN GLN GLY LEU SEQRES 7 A 154 LEU VAL ASP PHE LEU ALA PHE PRO GLN LYS PHE ILE ASP SEQRES 8 A 154 LEU LEU GLN GLN CYS THR GLN GLU HIS ALA LYS GLU ILE SEQRES 9 A 154 PRO ARG PHE LEU LEU GLN LEU VAL SER PRO ALA ALA ILE SEQRES 10 A 154 LEU ASP ASN SER PRO ALA PHE LEU ASN VAL VAL GLU THR SEQRES 11 A 154 ASN PRO GLU LYS HIS LEU THR HIS LEU SER LEU LYS LEU SEQRES 12 A 154 LEU PRO GLY ASN ASP VAL GLU ILE LYS LYS PHE HET GOL A 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *93(H2 O) HELIX 1 AA1 ASP A 66 GLY A 75 1 10 HELIX 2 AA2 ASP A 79 LEU A 81 5 3 HELIX 3 AA3 ALA A 82 GLU A 97 1 16 SHEET 1 AA1 8 MET A 1 LYS A 15 0 SHEET 2 AA1 8 GLU A 20 VAL A 35 -1 O GLU A 21 N VAL A 14 SHEET 3 AA1 8 ARG A 41 ASP A 50 -1 O ASP A 43 N GLN A 33 SHEET 4 AA1 8 ASP A 53 SER A 63 -1 O ILE A 62 N LEU A 44 SHEET 5 AA1 8 LEU A 134 PRO A 143 -1 O LEU A 142 N ASN A 59 SHEET 6 AA1 8 ALA A 121 GLU A 127 -1 N GLU A 127 O LEU A 134 SHEET 7 AA1 8 PHE A 105 VAL A 110 -1 N GLN A 108 O ASN A 124 SHEET 8 AA1 8 MET A 1 LYS A 15 1 N LYS A 15 O LEU A 109 CISPEP 1 ASN A 37 PRO A 38 0 5.56 SITE 1 AC1 9 ASP A 43 VAL A 61 SER A 63 GLU A 97 SITE 2 AC1 9 LYS A 100 ILE A 102 ARG A 104 HOH A 307 SITE 3 AC1 9 HOH A 315 CRYST1 59.590 65.130 38.060 90.00 90.00 90.00 P 21 21 2 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 0.016781 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015354 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026274 0.00000