HEADER TRANSFERASE 02-FEB-23 8G1H TITLE ANCESTRAL PROTEIN ANCTH OF PHOSPHOMETHYLPIRIMIDINE KINASES FAMILY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOMETHYLPYRIMIDINE KINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.4.7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANCESTRAL PROTEIN RECONSTRUCTION, 5-PHOSPHOHYDROXYMETHYL-2- KEYWDS 2 METHYLPIRIMIDINE KINASE, PHOSPHOMETHYLPIRIMIDINE KINASES FAMILY, KEYWDS 3 ENZYME EVOLUTION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PEREZ,S.MUNOZ,P.CEA,V.CASTRO-FERNANDEZ REVDAT 1 07-FEB-24 8G1H 0 JRNL AUTH M.PEREZ,S.MUNOZ,P.CEA,V.CASTRO-FERNANDEZ JRNL TITL ANCESTRAL PROTEIN ANCTH OF PHOSPHOMETHYLPYRIMIDINE KINASES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8023 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.750 REMARK 3 FREE R VALUE TEST SET COUNT : 461 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 44.0100 - 3.8900 1.00 2674 164 0.1883 0.1874 REMARK 3 2 3.8900 - 3.0900 1.00 2479 142 0.2134 0.2780 REMARK 3 3 3.0900 - 2.7000 1.00 2409 155 0.2326 0.2995 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) : 0.332 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.025 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.01 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 1929 REMARK 3 ANGLE : 0.731 2622 REMARK 3 CHIRALITY : 0.050 316 REMARK 3 PLANARITY : 0.006 342 REMARK 3 DIHEDRAL : 11.969 701 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 8G1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000269634. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS SIRIUS REMARK 200 BEAMLINE : MANACA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977180 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR - REMARK 200 WATER- COOLED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8030 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 44.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 34.10 REMARK 200 R MERGE (I) : 0.19260 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.27500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.050 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: 1UB0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONDITIONS: PROTEIN 26 MG/ML, REMARK 280 TRIS-HCL 25 MM, NACL 0.3 M, B-MERCAPTOETHANOL 5 MM, ATP 1 MM, REMARK 280 MGCL2 5 MM. RESERVOIR CONDITION: ETHYLENE GLYCOLS 0.12 M (0.3M REMARK 280 DIETHYLENE GLYCOL; 0.3M TRIETHYLENE GLYCOL; 0.3M TETRAETHYLENE REMARK 280 GLYCOL; 0.3M PENTAETHYLENE GLYCOL), SODIUM HEPES/ MOPS PH 7.5, REMARK 280 37.5% PRECIPITANTS (MPD, PEG 1000, PEG 3350), VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 84.97867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 169.95733 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 127.46800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 212.44667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.48933 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 84.97867 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 169.95733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 212.44667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 127.46800 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 42.48933 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 350 BIOMT1 2 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 42.48933 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7R8Z RELATED DB: PDB REMARK 900 RELATED ID: 7R8Y RELATED DB: PDB DBREF 8G1H A 1 258 PDB 8G1H 8G1H 1 258 SEQRES 1 A 258 MET ARG VAL ALA LEU THR ILE ALA GLY SER ASP SER GLY SEQRES 2 A 258 GLY GLY ALA GLY VAL GLN ALA ASP LEU LYS THR PHE SER SEQRES 3 A 258 ARG PHE GLY VAL TYR GLY MET SER ALA LEU THR LEU VAL SEQRES 4 A 258 THR ALA GLN ASN THR LEU GLY VAL GLN ARG VAL HIS LEU SEQRES 5 A 258 LEU PRO PRO GLU LEU VAL TYR ALA GLN ILE GLN ALA VAL SEQRES 6 A 258 ALA GLU ASP LEU PRO ILE HIS ALA ALA LYS THR GLY ALA SEQRES 7 A 258 LEU GLY ASN ALA ALA ILE VAL GLU ALA VAL ALA GLU ALA SEQRES 8 A 258 VAL ARG ARG PHE GLY ILE ARG PRO LEU VAL VAL ASP PRO SEQRES 9 A 258 VAL MET VAL ALA LYS SER GLY ASP PRO LEU LEU ALA PRO SEQRES 10 A 258 GLU ALA VAL ALA ALA LEU LYS GLU ARG LEU PHE PRO LEU SEQRES 11 A 258 ALA THR LEU ILE THR PRO ASN ARG LEU GLU ALA GLU ALA SEQRES 12 A 258 LEU LEU GLY ARG PRO ILE ARG THR LEU GLU GLU ALA GLU SEQRES 13 A 258 GLU ALA ALA LYS ALA LEU LEU ALA LEU GLY PRO LYS ALA SEQRES 14 A 258 VAL LEU LEU LYS GLY GLY HIS LEU GLU GLY GLU GLU ALA SEQRES 15 A 258 VAL ASP LEU LEU ALA THR GLY GLU GLY ILE ARG ARG PHE SEQRES 16 A 258 SER ALA PRO ARG VAL GLN THR ARG ASN THR HIS GLY THR SEQRES 17 A 258 GLY CSO THR LEU SER ALA ALA ILE ALA ALA LEU LEU ALA SEQRES 18 A 258 LEU GLY ARG PRO LEU GLU GLU ALA VAL ALA GLU ALA LYS SEQRES 19 A 258 ALA TYR LEU THR ARG ALA LEU GLU THR ALA PRO SER LEU SEQRES 20 A 258 GLY HIS GLY HIS GLY PRO LEU ASN HIS PHE ALA HET CSO A 210 7 HET EDO A 301 4 HET PO4 A 302 5 HET PO4 A 303 5 HET EDO A 304 4 HETNAM CSO S-HYDROXYCYSTEINE HETNAM EDO 1,2-ETHANEDIOL HETNAM PO4 PHOSPHATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 EDO 2(C2 H6 O2) FORMUL 3 PO4 2(O4 P 3-) FORMUL 6 HOH *27(H2 O) HELIX 1 AA1 ALA A 16 PHE A 28 1 13 HELIX 2 AA2 PRO A 54 GLU A 67 1 14 HELIX 3 AA3 ASN A 81 GLY A 96 1 16 HELIX 4 AA4 ALA A 116 ARG A 126 1 11 HELIX 5 AA5 LEU A 127 ALA A 131 5 5 HELIX 6 AA6 ASN A 137 GLY A 146 1 10 HELIX 7 AA7 THR A 151 LEU A 163 1 13 HELIX 8 AA8 ALA A 164 GLY A 166 5 3 HELIX 9 AA9 GLY A 207 LEU A 222 1 16 HELIX 10 AB1 PRO A 225 THR A 243 1 19 SHEET 1 AA1 6 GLY A 46 LEU A 52 0 SHEET 2 AA1 6 TYR A 31 ASN A 43 -1 N VAL A 39 O HIS A 51 SHEET 3 AA1 6 VAL A 3 ASP A 11 1 N THR A 6 O ALA A 35 SHEET 4 AA1 6 ALA A 73 THR A 76 1 O LYS A 75 N LEU A 5 SHEET 5 AA1 6 LEU A 100 VAL A 102 1 O VAL A 101 N ALA A 74 SHEET 6 AA1 6 LEU A 133 ILE A 134 1 O LEU A 133 N VAL A 102 SHEET 1 AA2 3 VAL A 170 GLU A 178 0 SHEET 2 AA2 3 GLU A 181 ALA A 187 -1 O LEU A 185 N LEU A 172 SHEET 3 AA2 3 ILE A 192 PRO A 198 -1 O ALA A 197 N ALA A 182 LINK C GLY A 209 N CSO A 210 1555 1555 1.33 LINK C CSO A 210 N THR A 211 1555 1555 1.33 CISPEP 1 ARG A 98 PRO A 99 0 -20.51 CRYST1 59.410 59.410 254.936 90.00 90.00 120.00 P 61 2 2 12 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 0.016832 0.009718 0.000000 0.00000 SCALE2 0.000000 0.019436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003923 0.00000