HEADER RIBOSOMAL PROTEIN 28-JUN-23 8JVS TITLE CRYSTAL STRUCTURE OF THE CHIMERIC PROTEIN TKOL2_V1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TKOL2_V1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES 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 KEYWDS OB FOLD, RIBOSOMAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.YAGI,S.TAGAMI REVDAT 2 07-AUG-24 8JVS 1 JRNL REVDAT 1 03-JUL-24 8JVS 0 JRNL AUTH S.YAGI,S.TAGAMI JRNL TITL AN ANCESTRAL FOLD REVEALS THE EVOLUTIONARY LINK BETWEEN RNA JRNL TITL 2 POLYMERASE AND RIBOSOMAL PROTEINS. JRNL REF NAT COMMUN V. 15 5938 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39025855 JRNL DOI 10.1038/S41467-024-50013-9 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17449 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1759 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 34.8810 - 3.5260 1.00 1218 134 0.1795 0.1926 REMARK 3 2 3.5260 - 2.7991 1.00 1206 136 0.1954 0.2001 REMARK 3 3 2.7991 - 2.4454 1.00 1212 140 0.2108 0.2637 REMARK 3 4 2.4454 - 2.2218 1.00 1183 136 0.1938 0.2022 REMARK 3 5 2.2218 - 2.0626 1.00 1215 139 0.1957 0.1789 REMARK 3 6 2.0626 - 1.9410 1.00 1200 133 0.2061 0.2152 REMARK 3 7 1.9410 - 1.8438 1.00 1206 132 0.2189 0.1987 REMARK 3 8 1.8438 - 1.7635 1.00 1227 135 0.2395 0.2955 REMARK 3 9 1.7635 - 1.6956 1.00 1193 135 0.2395 0.3046 REMARK 3 10 1.6956 - 1.6371 1.00 1232 130 0.2402 0.2832 REMARK 3 11 1.6371 - 1.5859 1.00 1198 140 0.2408 0.2338 REMARK 3 12 1.5859 - 1.5406 1.00 1201 138 0.2415 0.2672 REMARK 3 13 1.5406 - 1.5001 1.00 1199 131 0.2394 0.3031 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.440 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 : 0.007 388 REMARK 3 ANGLE : 1.130 522 REMARK 3 CHIRALITY : 0.640 64 REMARK 3 PLANARITY : 0.005 66 REMARK 3 DIHEDRAL : 24.398 154 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.2914 6.0300 8.4161 REMARK 3 T TENSOR REMARK 3 T11: 0.2471 T22: 0.1892 REMARK 3 T33: 0.1885 T12: 0.0001 REMARK 3 T13: 0.0227 T23: -0.0470 REMARK 3 L TENSOR REMARK 3 L11: 3.3652 L22: 8.7912 REMARK 3 L33: 4.1036 L12: 1.8186 REMARK 3 L13: -0.1976 L23: -4.8653 REMARK 3 S TENSOR REMARK 3 S11: -0.1243 S12: 0.2104 S13: -0.0270 REMARK 3 S21: -0.2660 S22: -0.0464 S23: -0.2643 REMARK 3 S31: 0.2502 S32: 0.2290 S33: 0.2253 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 25 THROUGH 39 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.4868 5.8317 14.2418 REMARK 3 T TENSOR REMARK 3 T11: 0.2540 T22: 0.1929 REMARK 3 T33: 0.2421 T12: -0.0045 REMARK 3 T13: 0.0109 T23: -0.0424 REMARK 3 L TENSOR REMARK 3 L11: 4.0843 L22: 7.7151 REMARK 3 L33: 5.2964 L12: 3.6923 REMARK 3 L13: -2.2841 L23: -4.7747 REMARK 3 S TENSOR REMARK 3 S11: -0.0204 S12: 0.1015 S13: 0.2558 REMARK 3 S21: 0.3891 S22: 0.1566 S23: 0.3784 REMARK 3 S31: -0.1137 S32: -0.3083 S33: -0.2142 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 40 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.6016 1.7574 11.7240 REMARK 3 T TENSOR REMARK 3 T11: 0.2086 T22: 0.1952 REMARK 3 T33: 0.2309 T12: 0.0416 REMARK 3 T13: 0.0202 T23: -0.0345 REMARK 3 L TENSOR REMARK 3 L11: 4.8298 L22: 3.1489 REMARK 3 L33: 8.0745 L12: 1.9838 REMARK 3 L13: 2.8593 L23: 1.6163 REMARK 3 S TENSOR REMARK 3 S11: -0.0445 S12: 0.2671 S13: -0.2791 REMARK 3 S21: -0.1355 S22: 0.1293 S23: -0.2480 REMARK 3 S31: 0.4533 S32: 0.5198 S33: -0.0526 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 8JVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300038840. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-22 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17462 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 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) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% PEG400, 100MM TRIS PH8.5, 2000MM REMARK 280 LITHIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 34.29950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.25450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.25450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.14975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.25450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.25450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.44925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.25450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.25450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.14975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.25450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.25450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.44925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 34.29950 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: 1900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 34.29950 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 GLY A 1 REMARK 465 PRO A 2 REMARK 465 MET A 3 REMARK 465 PRO A 4 REMARK 465 GLY A 5 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 O HOH A 142 O HOH A 149 2.10 REMARK 500 NZ LYS A 54 O HOH A 101 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 134 O HOH A 144 5445 2.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 8JVS A 1 55 PDB 8JVS 8JVS 1 55 SEQRES 1 A 55 GLY PRO MET PRO GLY LYS LYS VAL VAL ALA ARG VAL GLU SEQRES 2 A 55 GLU ILE LEU HIS ASP PRO GLY ARG THR ALA PRO VAL ALA SEQRES 3 A 55 ARG VAL LYS PHE GLU ASP GLY THR LYS LYS LEU ILE ILE SEQRES 4 A 55 ALA PRO GLU GLY VAL LYS VAL GLY ASP VAL VAL GLU VAL SEQRES 5 A 55 LYS LYS VAL FORMUL 2 HOH *51(H2 O) SHEET 1 AA1 4 LYS A 35 ILE A 39 0 SHEET 2 AA1 4 VAL A 25 PHE A 30 -1 N ALA A 26 O ILE A 38 SHEET 3 AA1 4 VAL A 8 HIS A 17 -1 N GLU A 13 O ARG A 27 SHEET 4 AA1 4 VAL A 49 VAL A 52 -1 O VAL A 50 N ALA A 10 CRYST1 40.509 40.509 68.599 90.00 90.00 90.00 P 41 21 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 0.024686 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024686 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014577 0.00000