HEADER ISOMERASE 24-NOV-23 8V2W TITLE CRYSTAL STRUCTURE OF THE ANCESTRAL TRIOSEPHOSPHATE ISOMERASE TITLE 2 RECONSTRUCTION OF THE LAST OPISTHOKONT COMMON ANCESTOR OBTAINED BY TITLE 3 BAYESIAN INFERENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIOSEPHOSPHATE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.3.1.1; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE FIRST 21 RESIDUES BELONG TO A HIS-TAG AND THROMBIN COMPND 7 CUTTING SITE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-28T(+) KEYWDS TRIOSE PHOSPHATE ISOMERASE, ANCESTRAL SEQUENCE RECONSTRUCTION, KEYWDS 2 ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.PEREZ-NINO,A.RODRIGUEZ-ROMERO,Y.GUERRA,D.A.FERNANDEZ-VELASCO REVDAT 1 04-SEP-24 8V2W 0 JRNL AUTH J.A.PEREZ-NINO,Y.GUERRA,A.J.DIAZ-SALAZAR,M.COSTAS, JRNL AUTH 2 A.RODRIGUEZ-ROMERO,D.A.FERNANDEZ-VELASCO JRNL TITL STABLE MONOMERS IN THE ANCESTRAL SEQUENCE RECONSTRUCTION OF JRNL TITL 2 THE LAST OPISTHOKONT COMMON ANCESTOR OF DIMERIC JRNL TITL 3 TRIOSEPHOSPHATE ISOMERASE. JRNL REF PROTEIN SCI. V. 33 E5134 2024 JRNL REFN ESSN 1469-896X JRNL PMID 39145435 JRNL DOI 10.1002/PRO.5134 REMARK 2 REMARK 2 RESOLUTION. 1.38 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 46451 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2333 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 31.9100 - 3.5500 1.00 2719 143 0.1417 0.1277 REMARK 3 2 3.5500 - 2.8200 1.00 2671 147 0.1473 0.1526 REMARK 3 3 2.8100 - 2.4600 1.00 2636 146 0.1553 0.1576 REMARK 3 4 2.4600 - 2.2300 1.00 2635 147 0.1526 0.1686 REMARK 3 5 2.2300 - 2.0700 1.00 2617 142 0.1534 0.1782 REMARK 3 6 2.0700 - 1.9500 1.00 2619 155 0.1563 0.1624 REMARK 3 7 1.9500 - 1.8500 1.00 2642 117 0.1517 0.1763 REMARK 3 8 1.8500 - 1.7700 1.00 2627 135 0.1632 0.1699 REMARK 3 9 1.7700 - 1.7100 1.00 2606 151 0.1637 0.2164 REMARK 3 10 1.7100 - 1.6500 1.00 2622 124 0.1743 0.1990 REMARK 3 11 1.6500 - 1.6000 0.99 2631 144 0.1796 0.2224 REMARK 3 12 1.6000 - 1.5500 0.99 2611 133 0.1843 0.2013 REMARK 3 13 1.5500 - 1.5100 0.99 2577 149 0.1931 0.2326 REMARK 3 14 1.5100 - 1.4700 0.99 2590 134 0.2037 0.2483 REMARK 3 15 1.4700 - 1.4400 0.98 2579 129 0.2266 0.2498 REMARK 3 16 1.4400 - 1.4100 0.98 2569 121 0.2518 0.2629 REMARK 3 17 1.4100 - 1.3800 0.83 2167 116 0.2719 0.2976 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.160 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 : 0.012 2120 REMARK 3 ANGLE : 1.267 2885 REMARK 3 CHIRALITY : 0.090 316 REMARK 3 PLANARITY : 0.008 382 REMARK 3 DIHEDRAL : 13.937 817 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 8V2W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1000274397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R 200K-A REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46451 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 31.912 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.47900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE PH 8.5, 15 % W/V PEG REMARK 280 1500, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 46.76250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.78950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.76250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.78950 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLN A 250 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 LYS A 12 -147.24 54.97 REMARK 500 VAL A 197 -77.32 -110.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 8V2W A -19 250 PDB 8V2W 8V2W -19 250 SEQRES 1 A 270 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 270 LEU VAL PRO ARG GLY SER HIS MET ALA ARG LYS PHE PHE SEQRES 3 A 270 VAL GLY GLY ASN TRP LYS MET ASN GLY SER LYS ALA SER SEQRES 4 A 270 ILE LYS SER LEU VAL GLU THR LEU ASN ALA SER LYS LEU SEQRES 5 A 270 ASP ASN LYS THR GLU VAL VAL VAL ALA PRO PRO ALA ILE SEQRES 6 A 270 TYR LEU PRO GLN VAL ARG GLN ALA LEU ARG LYS ASP ILE SEQRES 7 A 270 GLN VAL ALA ALA GLN ASN CYS TYR THR LYS ALA SER GLY SEQRES 8 A 270 ALA PHE THR GLY GLU ILE SER PRO GLU MET LEU LYS ASP SEQRES 9 A 270 LEU GLY ILE PRO TRP VAL ILE LEU GLY HIS SER GLU ARG SEQRES 10 A 270 ARG HIS ILE PHE GLY GLU SER ASP GLU PHE VAL ALA GLU SEQRES 11 A 270 LYS VAL LYS TYR ALA LEU ASP GLN GLY LEU LYS VAL ILE SEQRES 12 A 270 ALA CYS ILE GLY GLU THR LEU GLU GLU ARG GLU ALA GLY SEQRES 13 A 270 LYS THR MET GLU VAL CYS ALA ARG GLN LEU LYS ALA ILE SEQRES 14 A 270 ALA LYS LYS ILE SER GLU SER ASP TRP SER ASN VAL VAL SEQRES 15 A 270 ILE ALA TYR GLU PRO VAL TRP ALA ILE GLY THR GLY LYS SEQRES 16 A 270 VAL ALA THR PRO GLU GLN ALA GLN GLU VAL HIS ALA ALA SEQRES 17 A 270 ILE ARG LYS TRP LEU ALA GLU ASN VAL SER ALA GLU VAL SEQRES 18 A 270 ALA GLU SER THR ARG ILE ILE TYR GLY GLY SER VAL ASN SEQRES 19 A 270 GLY GLY ASN CYS ALA GLU LEU ALA LYS GLN PRO ASP ILE SEQRES 20 A 270 ASP GLY PHE LEU VAL GLY GLY ALA SER LEU LYS PRO GLU SEQRES 21 A 270 PHE VAL ASP ILE ILE ASN ALA ARG LYS GLN HET GOL A 301 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *291(H2 O) HELIX 1 AA1 SER A 16 ALA A 29 1 14 HELIX 2 AA2 PRO A 43 ILE A 45 5 3 HELIX 3 AA3 TYR A 46 LEU A 54 1 9 HELIX 4 AA4 SER A 78 LEU A 85 1 8 HELIX 5 AA5 HIS A 94 ILE A 100 1 7 HELIX 6 AA6 SER A 104 GLN A 118 1 15 HELIX 7 AA7 THR A 129 ALA A 135 1 7 HELIX 8 AA8 LYS A 137 ILE A 153 1 17 HELIX 9 AA9 GLU A 155 SER A 159 5 5 HELIX 10 AB1 PRO A 167 ILE A 171 5 5 HELIX 11 AB2 THR A 178 VAL A 197 1 20 HELIX 12 AB3 SER A 198 THR A 205 1 8 HELIX 13 AB4 ASN A 217 LYS A 223 1 7 HELIX 14 AB5 GLY A 233 PRO A 239 5 7 HELIX 15 AB6 GLU A 240 ASN A 246 1 7 SHEET 1 AA1 9 PHE A 5 ASN A 10 0 SHEET 2 AA1 9 THR A 36 ALA A 41 1 O ALA A 41 N GLY A 9 SHEET 3 AA1 9 GLN A 59 ALA A 62 1 O ALA A 61 N VAL A 40 SHEET 4 AA1 9 TRP A 89 LEU A 92 1 O ILE A 91 N ALA A 62 SHEET 5 AA1 9 LYS A 121 ILE A 126 1 O ILE A 123 N LEU A 92 SHEET 6 AA1 9 VAL A 161 TYR A 165 1 O VAL A 162 N ALA A 124 SHEET 7 AA1 9 ILE A 207 TYR A 209 1 O ILE A 208 N ILE A 163 SHEET 8 AA1 9 GLY A 229 VAL A 232 1 O GLY A 229 N TYR A 209 SHEET 9 AA1 9 PHE A 5 ASN A 10 1 N GLY A 8 O VAL A 232 CRYST1 93.525 47.579 64.308 90.00 126.00 90.00 C 1 2 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 0.010692 0.000000 0.007768 0.00000 SCALE2 0.000000 0.021018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019221 0.00000