HEADER STRUCTURAL PROTEIN 21-MAY-21 7EVH TITLE ODINARCHAEOTA TUBULIN H393D MUTANT, IN A PSUEDO PROTOFILAMENT TITLE 2 ARRANGEMENT, BOUND TO 59% GDP, 41% PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUBULIN-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ODINARCHAEOTA ARCHAEON (STRAIN LCB_4); SOURCE 3 ORGANISM_TAXID: 1841599; SOURCE 4 STRAIN: LCB_4; SOURCE 5 GENE: CETZ, ODINLCB4_01330; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ASGARD, TUBULIN, GTP, FILAMENT, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.C.ROBINSON,C.AKIL,L.T.TRAN REVDAT 3 29-NOV-23 7EVH 1 REMARK REVDAT 2 15-JUN-22 7EVH 1 JRNL REVDAT 1 23-MAR-22 7EVH 0 JRNL AUTH C.AKIL,S.ALI,L.T.TRAN,J.GAILLARD,W.LI,K.HAYASHIDA,M.HIROSE, JRNL AUTH 2 T.KATO,A.OSHIMA,K.FUJISHIMA,L.BLANCHOIN,A.NARITA, JRNL AUTH 3 R.C.ROBINSON JRNL TITL STRUCTURE AND DYNAMICS OF ODINARCHAEOTA TUBULIN AND THE JRNL TITL 2 IMPLICATIONS FOR EUKARYOTIC MICROTUBULE EVOLUTION. JRNL REF SCI ADV V. 8 M2225 2022 JRNL REFN ESSN 2375-2548 JRNL PMID 35333570 JRNL DOI 10.1126/SCIADV.ABM2225 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.17.1 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 12599 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 625 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 2.7500 - 2.5000 0.49 0 28 0.2500 0.3240 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.59 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 3432 REMARK 3 ANGLE : 0.564 4653 REMARK 3 CHIRALITY : 0.042 529 REMARK 3 PLANARITY : 0.003 592 REMARK 3 DIHEDRAL : 19.332 1265 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 7EVH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1300022359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-20 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 : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13455 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 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: 6O2R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 1500, 0.1 M SPG (2 SUCCINIC REMARK 280 ACID: 7 SODIUM DIHYDROGEN PHOSPHATE), PH 9.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 20.15000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.05900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.67100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.05900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.15000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.67100 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 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 ASP A 213 REMARK 465 GLY A 424 REMARK 465 SER A 425 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 OD1 ASN A 203 N2 GDP A 501 1.30 REMARK 500 ND2 ASN A 226 O6 GDP A 501 1.30 REMARK 500 O LEU A 186 O HOH A 601 1.98 REMARK 500 OH TYR A 49 O HOH A 602 2.10 REMARK 500 O GLU A 262 O HOH A 603 2.18 REMARK 500 CG ASN A 226 O6 GDP A 501 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 TYR A 49 47.92 -90.77 REMARK 500 PHE A 222 -55.28 60.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7EVB RELATED DB: PDB REMARK 900 RELATED ID: 7EVC RELATED DB: PDB REMARK 900 RELATED ID: 7EVD RELATED DB: PDB REMARK 900 RELATED ID: 7EVE RELATED DB: PDB REMARK 900 RELATED ID: 7EVG RELATED DB: PDB DBREF1 7EVH A 1 423 UNP A0A1Q9N9N5_ODILC DBREF2 7EVH A A0A1Q9N9N5 1 423 SEQADV 7EVH GLY A 0 UNP A0A1Q9N9N EXPRESSION TAG SEQADV 7EVH ASP A 213 UNP A0A1Q9N9N GLN 213 CONFLICT SEQADV 7EVH ASP A 393 UNP A0A1Q9N9N HIS 393 ENGINEERED MUTATION SEQADV 7EVH GLY A 424 UNP A0A1Q9N9N EXPRESSION TAG SEQADV 7EVH SER A 425 UNP A0A1Q9N9N EXPRESSION TAG SEQRES 1 A 426 GLY MET PRO GLY ARG GLU ILE LEU VAL LEU HIS VAL GLY SEQRES 2 A 426 GLN GLY GLY ASN GLN ILE GLY TYR ASN PHE TRP LYS THR SEQRES 3 A 426 ILE CYS GLU GLU HIS ASN ILE ASP ILE ARG SER ASN GLN SEQRES 4 A 426 ARG LYS SER VAL GLU GLU ASP LYS VAL ASP TYR LYS SER SEQRES 5 A 426 VAL PHE LEU VAL GLU ALA PRO ASP GLY PHE HIS PRO ARG SEQRES 6 A 426 ALA LEU PHE ILE ASP LEU GLU PRO LEU ALA VAL GLU PHE SEQRES 7 A 426 LEU VAL LYS GLU MET LYS LEU GLY SER PHE PHE SER GLU SEQRES 8 A 426 ASP LEU MET VAL LEU SER TYR SER GLY ALA HIS ASN VAL SEQRES 9 A 426 TRP SER ILE GLY TYR GLN THR GLY LYS LYS LEU ILE PRO SEQRES 10 A 426 VAL ILE LEU GLU LYS ILE ARG ASP THR MET PRO GLU THR SEQRES 11 A 426 LEU GLN GLY PHE LEU ILE ILE HIS THR LEU GLY GLY GLY SEQRES 12 A 426 THR GLY SER GLY PHE GLY SER LEU LEU THR GLU THR LEU SEQRES 13 A 426 LYS LYS GLU PHE PRO GLY LYS GLY VAL LEU ASN PHE SER SEQRES 14 A 426 VAL LEU PRO SER GLU VAL ASN ASP VAL THR LEU ALA PRO SEQRES 15 A 426 TYR ASN THR VAL LEU SER LEU ASN HIS LEU SER ARG PHE SEQRES 16 A 426 SER ASP LEU VAL VAL LEU PHE ASP ASN THR ALA LEU ILE SEQRES 17 A 426 ARG ILE VAL LYS ASP ASP LEU ASN TYR PRO VAL ILE LYS SEQRES 18 A 426 GLN PHE SER ASP LEU ASN PHE LEU ILE GLY ARG VAL MET SEQRES 19 A 426 ALA SER ILE THR ALA SER LEU ARG PHE PRO GLY PRO LEU SEQRES 20 A 426 ASN MET ASP LEU MET GLU MET ALA HIS ASN LEU VAL ALA SEQRES 21 A 426 LEU PRO GLU THR LYS PHE ILE ILE PRO SER VAL ALA PRO SEQRES 22 A 426 LEU THR LYS GLU GLU SER GLU MET SER THR GLU LEU ASP SEQRES 23 A 426 LEU VAL GLU ARG CYS PHE ASP PRO THR HIS TYR MET VAL SEQRES 24 A 426 ASN CYS SER GLY GLN GLY LYS THR ILE SER SER VAL LEU SEQRES 25 A 426 MET PHE ARG GLY ASN ILE ALA ILE GLU ASN ALA PHE SER SEQRES 26 A 426 ILE MET THR ASP ILE LYS SER ASN VAL ALA PHE ALA PRO SEQRES 27 A 426 GLY VAL HIS PRO ASP LEU GLY LEU LYS TYR GLY ILE CYS SEQRES 28 A 426 GLU SER ALA PRO VAL ASP PHE ASP LYS GLU VAL THR LEU SEQRES 29 A 426 LEU SER ASN ASN THR ILE ILE SER GLU VAL PHE ASN ARG SEQRES 30 A 426 VAL LEU GLU ARG PHE ASP SER LEU PHE ASN ARG ASP TRP SEQRES 31 A 426 TYR THR SER ASP TYR VAL ASN ALA GLY THR SER LYS SER SEQRES 32 A 426 ASN LEU LYS GLU ALA ARG ASP ASN PHE ASP ARG ILE ILE SEQRES 33 A 426 LYS ILE TYR LYS GLU ILE GLU GLY GLY SER HET GDP A 501 28 HET PO4 A 502 5 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM PO4 PHOSPHATE ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *45(H2 O) HELIX 1 AA1 GLY A 12 HIS A 30 1 19 HELIX 2 AA2 TYR A 49 VAL A 52 5 4 HELIX 3 AA3 PRO A 72 LYS A 80 1 9 HELIX 4 AA4 SER A 89 ASP A 91 5 3 HELIX 5 AA5 VAL A 103 LYS A 113 1 11 HELIX 6 AA6 LEU A 114 MET A 126 1 13 HELIX 7 AA7 GLY A 142 PHE A 159 1 18 HELIX 8 AA8 LEU A 179 SER A 195 1 17 HELIX 9 AA9 ASN A 203 ASP A 212 1 10 HELIX 10 AB1 ASP A 224 ILE A 236 1 13 HELIX 11 AB2 THR A 237 PHE A 242 1 6 HELIX 12 AB3 ASP A 249 ASN A 256 1 8 HELIX 13 AB4 THR A 274 MET A 280 1 7 HELIX 14 AB5 THR A 282 PHE A 291 1 10 HELIX 15 AB6 ASP A 292 TYR A 296 5 5 HELIX 16 AB7 ALA A 318 VAL A 333 1 16 HELIX 17 AB8 ILE A 369 ASN A 386 1 18 HELIX 18 AB9 THR A 391 ALA A 397 1 7 HELIX 19 AC1 SER A 400 GLY A 423 1 24 SHEET 1 AA110 MET A 93 LEU A 95 0 SHEET 2 AA110 ALA A 65 ASP A 69 1 N ASP A 69 O VAL A 94 SHEET 3 AA110 GLU A 5 VAL A 11 1 N HIS A 10 O ILE A 68 SHEET 4 AA110 LEU A 130 THR A 138 1 O LEU A 134 N LEU A 9 SHEET 5 AA110 GLY A 163 LEU A 170 1 O GLY A 163 N PHE A 133 SHEET 6 AA110 LEU A 197 ASP A 202 1 O PHE A 201 N LEU A 170 SHEET 7 AA110 PHE A 265 ALA A 271 1 O ILE A 266 N VAL A 198 SHEET 8 AA110 LYS A 359 ASN A 367 -1 O VAL A 361 N ALA A 271 SHEET 9 AA110 THR A 306 GLY A 315 -1 N ARG A 314 O GLU A 360 SHEET 10 AA110 LEU A 345 CYS A 350 1 O CYS A 350 N PHE A 313 SHEET 1 AA2 2 LEU A 54 ALA A 57 0 SHEET 2 AA2 2 GLY A 60 PRO A 63 -1 O HIS A 62 N VAL A 55 CISPEP 1 ALA A 271 PRO A 272 0 4.39 CRYST1 40.300 93.342 100.118 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 0.024814 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009988 0.00000