HEADER CELL CYCLE 09-OCT-23 8QRY TITLE CRYSTAL STRUCTURE OF THE YEAST SPINDLE BODY COMPONENT SPC98 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPINDLE POLE BODY COMPONENT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SPC98; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS YEAST CELL DIVISION, YEAST SPINDLE POLE BODY, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR D.BELLINI,S.YATSKEVICH,D.BARFORD REVDAT 2 16-OCT-24 8QRY 1 JRNL REVDAT 1 03-APR-24 8QRY 0 JRNL AUTH T.DENDOOVEN,S.YATSKEVICH,A.BURT,Z.A.CHEN,D.BELLINI, JRNL AUTH 2 J.RAPPSILBER,J.V.KILMARTIN,D.BARFORD JRNL TITL STRUCTURE OF THE NATIVE GAMMA-TUBULIN RING COMPLEX CAPPING JRNL TITL 2 SPINDLE MICROTUBULES. JRNL REF NAT.STRUCT.MOL.BIOL. V. 31 1134 2024 JRNL REFN ESSN 1545-9985 JRNL PMID 38609662 JRNL DOI 10.1038/S41594-024-01281-Y REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.17.1_3660: ???) 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 7294 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 331 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 37.2600 - 2.3600 1.00 3595 175 0.2372 0.3054 REMARK 3 2 2.3600 - 1.8700 0.97 3368 156 0.2415 0.2927 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.620 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 : 0.008 777 REMARK 3 ANGLE : 1.045 1055 REMARK 3 CHIRALITY : 0.057 127 REMARK 3 PLANARITY : 0.009 132 REMARK 3 DIHEDRAL : 6.936 99 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 8QRY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1292133877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-21 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) : 1.5 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7339 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 65.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS B4: PEG 3350/PEG 1K/MPD REMARK 280 (1:1:1) 37.5%, MES/IMIDAZOLE 0.1M PH 6.5, MORPHEUS HALIDES 90 MM, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 14.15200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.78450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.64200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.78450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.15200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.64200 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 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 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 CB THR A 39 O HOH A 128 1.83 REMARK 500 O HOH A 139 O HOH A 142 2.07 REMARK 500 CB THR A 43 O HOH A 106 2.12 REMARK 500 OD1 ASP A 30 O HOH A 101 2.12 REMARK 500 OD1 ASP A 84 O HOH A 102 2.12 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 ALA A 42 -130.33 55.51 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8QRY A 1 95 UNP A0A8H4BVY6_YEASX DBREF2 8QRY A A0A8H4BVY6 1 95 SEQADV 8QRY ALA A 0 UNP A0A8H4BVY EXPRESSION TAG SEQRES 1 A 96 ALA MET GLU LEU GLU PRO THR LEU PHE GLY ILE ILE GLU SEQRES 2 A 96 ALA LEU ALA PRO GLN LEU LEU SER GLN SER HIS LEU GLN SEQRES 3 A 96 THR PHE VAL SER ASP VAL VAL ASN LEU LEU ARG SER SER SEQRES 4 A 96 THR LYS SER ALA THR GLN LEU GLY PRO LEU ILE ASP PHE SEQRES 5 A 96 TYR LYS LEU GLN SER LEU ASP SER PRO GLU THR THR ILE SEQRES 6 A 96 MET TRP HIS LYS ILE GLU LYS PHE LEU ASP ALA LEU PHE SEQRES 7 A 96 GLY ILE GLN ASN THR ASP ASP MET VAL LYS TYR LEU SER SEQRES 8 A 96 VAL PHE GLN SER LEU FORMUL 2 HOH *44(H2 O) HELIX 1 AA1 GLU A 2 ALA A 15 1 14 HELIX 2 AA2 SER A 20 ARG A 36 1 17 HELIX 3 AA3 GLN A 44 LEU A 54 1 11 HELIX 4 AA4 SER A 59 PHE A 77 1 19 HELIX 5 AA5 ASN A 81 GLN A 93 1 13 CRYST1 28.304 45.284 65.569 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 0.035331 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015251 0.00000 TER 763 LEU A 95 HETATM 764 O HOH A 101 -8.367 -13.546 10.094 1.00 27.10 O HETATM 765 O HOH A 102 -10.493 8.225 -6.441 1.00 23.38 O HETATM 766 O HOH A 103 1.408 4.325 14.637 1.00 28.89 O HETATM 767 O HOH A 104 -0.803 -0.361 21.677 1.00 22.47 O HETATM 768 O HOH A 105 -21.228 0.561 18.108 1.00 25.15 O HETATM 769 O HOH A 106 -20.876 -5.434 9.674 1.00 29.29 O HETATM 770 O HOH A 107 -4.309 -5.525 -3.921 1.00 20.65 O HETATM 771 O HOH A 108 -10.311 -5.133 23.130 1.00 23.86 O HETATM 772 O HOH A 109 -15.630 2.881 -9.933 1.00 27.04 O HETATM 773 O HOH A 110 -0.443 6.270 14.151 1.00 17.30 O HETATM 774 O HOH A 111 -18.242 -11.536 16.753 1.00 14.64 O HETATM 775 O HOH A 112 -1.106 -8.030 23.844 1.00 23.39 O HETATM 776 O HOH A 113 -19.563 -0.691 4.572 1.00 24.15 O HETATM 777 O HOH A 114 -1.208 5.212 8.346 1.00 17.34 O HETATM 778 O HOH A 115 -18.255 8.358 25.257 1.00 18.39 O HETATM 779 O HOH A 116 -17.763 4.605 1.524 1.00 23.31 O HETATM 780 O HOH A 117 2.166 1.016 10.518 1.00 18.65 O HETATM 781 O HOH A 118 -8.931 -14.057 13.322 1.00 18.64 O HETATM 782 O HOH A 119 -9.181 -2.661 24.528 1.00 19.69 O HETATM 783 O HOH A 120 -16.220 -13.287 10.428 1.00 20.01 O HETATM 784 O HOH A 121 -3.539 8.651 10.809 1.00 19.22 O HETATM 785 O HOH A 122 -11.858 11.241 20.512 1.00 17.41 O HETATM 786 O HOH A 123 -15.149 3.298 -4.932 1.00 30.09 O HETATM 787 O HOH A 124 0.016 11.678 10.566 1.00 23.99 O HETATM 788 O HOH A 125 0.307 -9.894 15.955 1.00 20.24 O HETATM 789 O HOH A 126 -4.668 0.817 19.581 1.00 15.08 O HETATM 790 O HOH A 127 -15.672 -9.727 4.330 1.00 29.72 O HETATM 791 O HOH A 128 -20.401 -11.070 -2.280 1.00 31.83 O HETATM 792 O HOH A 129 -7.177 11.057 15.699 1.00 18.79 O HETATM 793 O HOH A 130 -7.006 3.751 24.971 1.00 17.75 O HETATM 794 O HOH A 131 -15.007 7.809 -6.321 1.00 32.75 O HETATM 795 O HOH A 132 -13.100 7.483 31.970 1.00 30.43 O HETATM 796 O HOH A 133 -6.156 10.365 19.368 1.00 20.93 O HETATM 797 O HOH A 134 -4.444 16.302 12.731 1.00 27.65 O HETATM 798 O HOH A 135 -23.392 -3.925 17.394 1.00 33.57 O HETATM 799 O HOH A 136 -0.192 -10.989 14.021 1.00 24.06 O HETATM 800 O HOH A 137 -0.709 12.701 5.517 1.00 31.75 O HETATM 801 O HOH A 138 -1.396 7.374 10.111 1.00 18.17 O HETATM 802 O HOH A 139 -11.412 10.628 0.104 1.00 25.94 O HETATM 803 O HOH A 140 0.526 7.344 12.118 1.00 20.50 O HETATM 804 O HOH A 141 -0.456 8.085 16.147 1.00 17.66 O HETATM 805 O HOH A 142 -10.779 12.572 -0.220 1.00 27.02 O HETATM 806 O HOH A 143 -6.996 15.773 3.708 1.00 34.00 O HETATM 807 O HOH A 144 -2.472 10.320 20.101 1.00 22.67 O MASTER 221 0 0 5 0 0 0 6 806 1 0 8 END