HEADER STRUCTURAL PROTEIN 25-MAY-22 8D00 TITLE STRUCTURE OF THE ARABIDOPSIS THALIANA SPIRAL2 TOG DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEIN TORTIFOLIA1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MICROTUBULE-ASSOCIATED PROTEIN SPIRAL2,PROTEIN CONVOLUTA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: TOR1, CN, SPR2, AT4G27060, T24A18.10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS KEYWDS TOG, HEAT, ALPHA-SOLENOID, MICROTUBULE-BINDING, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.C.SLEP,D.L.BOLHUIS REVDAT 1 29-NOV-23 8D00 0 JRNL AUTH Y.FAN,N.BILKEY,D.L.BOLHUIS,K.C.SLEP,R.DIXIT JRNL TITL A STRUCTURALLY DIVERGENT TOG DOMAIN STABILIZES MICROTUBULE JRNL TITL 2 MINUS ENDS IN ARABIDOPSIS JRNL REF PLANT CELL 2023 JRNL REFN ESSN 1532-298X REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.170 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 9163 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 917 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 38.3600 - 5.3500 0.98 1282 148 0.1925 0.2288 REMARK 3 2 5.3500 - 4.2500 0.96 1205 131 0.1909 0.2268 REMARK 3 3 4.2500 - 3.7100 0.99 1221 139 0.2064 0.2611 REMARK 3 4 3.7100 - 3.3700 0.98 1205 134 0.2215 0.2535 REMARK 3 5 3.3700 - 3.1300 0.96 1157 129 0.2540 0.2855 REMARK 3 6 3.1300 - 2.9500 0.89 1098 123 0.2745 0.4080 REMARK 3 7 2.9500 - 2.8000 0.90 1078 113 0.2756 0.3445 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.348 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.765 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.99 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 : 0.003 2288 REMARK 3 ANGLE : 0.535 3091 REMARK 3 CHIRALITY : 0.036 378 REMARK 3 PLANARITY : 0.005 384 REMARK 3 DIHEDRAL : 14.232 856 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): -9.7954 -5.8271 -41.1953 REMARK 3 T TENSOR REMARK 3 T11: 0.2286 T22: 0.1695 REMARK 3 T33: 0.2010 T12: -0.0284 REMARK 3 T13: -0.0002 T23: 0.0206 REMARK 3 L TENSOR REMARK 3 L11: 1.9022 L22: 0.3664 REMARK 3 L33: 0.6458 L12: -0.6377 REMARK 3 L13: 0.5466 L23: -0.1987 REMARK 3 S TENSOR REMARK 3 S11: -0.0662 S12: -0.0524 S13: -0.0838 REMARK 3 S21: 0.0726 S22: 0.0190 S23: 0.0777 REMARK 3 S31: 0.0712 S32: -0.0262 S33: -0.0008 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 8D00 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-21 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : SI 111. ROSENBAUM-ROCK DOUBLE REMARK 200 -CRYSTAL MONOCHROMATOR: LIQUID REMARK 200 NITROGEN COOLED; SAGITALLY REMARK 200 FOCUSING 2ND CRYSTAL, ROSENBAUM- REMARK 200 ROCK VERTICAL FOCUSING MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9490 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.16400 REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 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) : 0.84200 REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: ALPHAFOLD PREDICTION REMARK 200 REMARK 200 REMARK: RODS 50 X 50 X 400 MICRONS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 UL 15.7 MG/ML SPIRAL2 TOG DOMAIN REMARK 280 (RESIDUES 33-333) PROTEIN + 2 UL OF A 1 ML WELL SOLUTION (27.5% REMARK 280 W/V PEG3350, 150 MM AMMONIUM PHOSPHATE, 280 MM SODIUM IODIDE), REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 36.42150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.22800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 65.96900 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.42150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.22800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 65.96900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.42150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.22800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 65.96900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.42150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.22800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 65.96900 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: 160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14540 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 VAL A 328 REMARK 465 ASP A 329 REMARK 465 GLY A 330 REMARK 465 ALA A 331 REMARK 465 SER A 332 REMARK 465 ASP A 333 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 283 44.11 -106.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 8D00 A 33 333 UNP Q9T041 TOR1_ARATH 33 333 SEQADV 8D00 GLY A 29 UNP Q9T041 EXPRESSION TAG SEQADV 8D00 SER A 30 UNP Q9T041 EXPRESSION TAG SEQADV 8D00 HIS A 31 UNP Q9T041 EXPRESSION TAG SEQADV 8D00 MET A 32 UNP Q9T041 EXPRESSION TAG SEQRES 1 A 305 GLY SER HIS MET LEU THR SER PHE GLN ALA MET VAL GLU SEQRES 2 A 305 LEU LYS GLN LYS ILE LEU THR SER ILE SER LYS LEU ALA SEQRES 3 A 305 ASP ARG ASP THR TYR GLN ILE ALA VAL GLU ASP LEU GLU SEQRES 4 A 305 LYS THR ILE GLN SER LEU THR PRO GLU THR LEU PRO MET SEQRES 5 A 305 PHE LEU ASN CYS LEU TYR ASP SER CYS SER ASP PRO LYS SEQRES 6 A 305 PRO ALA VAL LYS LYS GLU CYS LEU HIS LEU LEU SER TYR SEQRES 7 A 305 VAL CYS SER LEU HIS CYS ASP SER THR ALA ALA HIS LEU SEQRES 8 A 305 THR LYS ILE ILE ALA GLN ILE VAL LYS ARG LEU LYS ASP SEQRES 9 A 305 SER ASP SER GLY VAL ARG ASP ALA CYS ARG ASP THR ILE SEQRES 10 A 305 GLY ALA LEU SER GLY ILE TYR LEU LYS GLY LYS GLU GLU SEQRES 11 A 305 GLY THR ASN THR GLY SER ALA SER LEU ALA VAL GLY LEU SEQRES 12 A 305 PHE VAL LYS PRO LEU PHE GLU ALA MET GLY GLU GLN ASN SEQRES 13 A 305 LYS VAL VAL GLN SER GLY ALA SER MET CYS MET ALA ARG SEQRES 14 A 305 MET VAL GLU SER ALA ALA SER PRO PRO VAL THR SER PHE SEQRES 15 A 305 GLN LYS LEU CYS PRO ARG ILE CYS LYS LEU LEU SER ASN SEQRES 16 A 305 SER SER PHE LEU ALA LYS ALA SER LEU LEU PRO VAL VAL SEQRES 17 A 305 SER SER LEU SER GLN VAL GLY ALA ILE ALA PRO GLN SER SEQRES 18 A 305 LEU GLU SER LEU LEU GLU SER ILE HIS ASP CYS LEU GLY SEQRES 19 A 305 SER THR ASP TRP VAL THR ARG LYS ALA ALA ALA GLU THR SEQRES 20 A 305 LEU THR ALA LEU ALA SER HIS SER SER GLY LEU ILE LYS SEQRES 21 A 305 GLU LYS THR ASP SER THR ILE THR VAL LEU GLU THR CYS SEQRES 22 A 305 ARG PHE ASP LYS ILE LYS PRO VAL ARG GLU SER VAL THR SEQRES 23 A 305 GLU ALA LEU GLN LEU TRP LYS LYS ILE SER GLY LYS TYR SEQRES 24 A 305 VAL ASP GLY ALA SER ASP HET IOD A 401 1 HETNAM IOD IODIDE ION FORMUL 2 IOD I 1- FORMUL 3 HOH *7(H2 O) HELIX 1 AA1 GLY A 29 LEU A 53 1 25 HELIX 2 AA2 TYR A 59 SER A 72 1 14 HELIX 3 AA3 THR A 77 CYS A 89 1 13 HELIX 4 AA4 LYS A 93 HIS A 111 1 19 HELIX 5 AA5 HIS A 111 ALA A 116 1 6 HELIX 6 AA6 HIS A 118 LEU A 130 1 13 HELIX 7 AA7 ASP A 134 LEU A 153 1 20 HELIX 8 AA8 GLY A 163 GLY A 181 1 19 HELIX 9 AA9 ASN A 184 ALA A 202 1 19 HELIX 10 AB1 PRO A 206 GLN A 211 1 6 HELIX 11 AB2 LEU A 213 ASN A 223 1 11 HELIX 12 AB3 ALA A 228 VAL A 242 1 15 HELIX 13 AB4 ALA A 246 GLN A 248 5 3 HELIX 14 AB5 SER A 249 GLY A 262 1 14 HELIX 15 AB6 ASP A 265 SER A 283 1 19 HELIX 16 AB7 SER A 284 ILE A 287 5 4 HELIX 17 AB8 THR A 291 ARG A 302 1 12 HELIX 18 AB9 ILE A 306 GLY A 325 1 20 CRYST1 72.843 78.456 131.938 90.00 90.00 90.00 I 2 2 2 8 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 0.013728 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007579 0.00000