HEADER ISOMERASE 24-NOV-23 8V2X TITLE CRYSTAL STRUCTURE OF THE RECONSTRUCTION OF THE WORST CASE OF THE TITLE 2 ANCESTRAL TRIOSEPHOSPHATE ISOMERASE OF THE LAST OPISTHOKONT COMMON TITLE 3 ANCESTOR OBTAINED BY 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 AMINOACIDS CORRESPOND TO THE HISITIDINE COMPND 7 TAG BUT IS NOT PRESENT IN THE ELECTRONIC DENSITY 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-BORREGO,D.A.FERNANDEZ- AUTHOR 2 VELASCO REVDAT 1 04-SEP-24 8V2X 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. 1.43 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 58029 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2917 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 36.5000 - 3.9400 1.00 2907 147 0.1527 0.1363 REMARK 3 2 3.9400 - 3.1300 1.00 2764 132 0.1550 0.1510 REMARK 3 3 3.1300 - 2.7400 1.00 2739 150 0.1699 0.1768 REMARK 3 4 2.7400 - 2.4900 1.00 2697 165 0.1764 0.1596 REMARK 3 5 2.4900 - 2.3100 1.00 2684 152 0.1750 0.1736 REMARK 3 6 2.3100 - 2.1700 1.00 2700 142 0.1731 0.1815 REMARK 3 7 2.1700 - 2.0600 1.00 2690 137 0.1817 0.1988 REMARK 3 8 2.0600 - 1.9700 1.00 2685 138 0.1841 0.1962 REMARK 3 9 1.9700 - 1.9000 1.00 2674 125 0.1787 0.1880 REMARK 3 10 1.9000 - 1.8300 0.99 2641 144 0.1954 0.2045 REMARK 3 11 1.8300 - 1.7700 0.99 2621 146 0.2067 0.1942 REMARK 3 12 1.7700 - 1.7200 0.98 2612 141 0.1969 0.1981 REMARK 3 13 1.7200 - 1.6800 0.98 2600 148 0.1924 0.2140 REMARK 3 14 1.6800 - 1.6400 0.97 2584 119 0.1968 0.2223 REMARK 3 15 1.6400 - 1.6000 0.97 2573 142 0.1962 0.1855 REMARK 3 16 1.6000 - 1.5700 0.96 2554 128 0.1980 0.2146 REMARK 3 17 1.5700 - 1.5300 0.95 2529 138 0.2004 0.2184 REMARK 3 18 1.5300 - 1.5100 0.95 2508 144 0.2177 0.2319 REMARK 3 19 1.5100 - 1.4800 0.94 2496 116 0.2199 0.2031 REMARK 3 20 1.4800 - 1.4500 0.94 2477 132 0.2193 0.2391 REMARK 3 21 1.4500 - 1.4300 0.90 2377 131 0.2312 0.2156 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.460 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 2096 REMARK 3 ANGLE : 1.039 2857 REMARK 3 CHIRALITY : 0.093 320 REMARK 3 PLANARITY : 0.012 379 REMARK 3 DIHEDRAL : 13.630 798 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 8V2X 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_1000274852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-18 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 58029 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 46.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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 (%): 54.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3350 , 0.2 M NAF, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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+1/2,-Z+1/2 REMARK 290 4555 -X,-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 29.76750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.39450 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.76750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.39450 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 GLN A 250 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 249 CG CD CE NZ 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 -148.64 55.94 REMARK 500 ASN A 99 -66.95 -91.80 REMARK 500 VAL A 197 -71.49 -115.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 8V2X A -19 250 PDB 8V2X 8V2X -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 THR GLN GLU SER SEQRES 4 A 270 ILE LYS SER LEU VAL GLU THR LEU ASN ALA ASN ASN LEU SEQRES 5 A 270 ASP ASN LYS VAL GLU VAL VAL ILE ALA PRO PRO ALA VAL SEQRES 6 A 270 TYR LEU PRO GLN VAL ARG GLN GLN LEU ARG LYS ASP ILE SEQRES 7 A 270 GLN VAL ALA ALA GLN ASN CYS TYR THR LYS GLY 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 ASN ILE PHE GLY GLU SER ASP GLU LEU VAL ALA GLU SEQRES 11 A 270 LYS VAL LYS HIS ALA LEU GLU ALA GLY LEU LYS VAL ILE SEQRES 12 A 270 PHE CYS ILE GLY GLU THR LEU GLU GLU ARG GLU ALA GLY SEQRES 13 A 270 LYS THR THR GLU VAL VAL ALA ARG GLN LEU LYS ALA ILE SEQRES 14 A 270 ALA LYS LYS ILE SER GLU SER ASP TRP SER LYS 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 SER 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 SER 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 LYS LYS GLN FORMUL 2 HOH *330(H2 O) HELIX 1 AA1 THR A 16 ASN A 30 1 15 HELIX 2 AA2 PRO A 43 VAL 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 ALA 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 6 ASN A 10 0 SHEET 2 AA1 9 GLU A 37 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 ILE 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 ALA A 164 N PHE A 124 SHEET 7 AA1 9 ILE A 207 GLY A 210 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 6 ASN A 10 1 N ASN A 10 O VAL A 232 CRYST1 46.205 59.535 114.789 90.00 90.00 90.00 P 2 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 0.021643 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016797 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008712 0.00000