HEADER TRANSFERASE 11-JUL-23 8TFI TITLE TRNA 2'-PHOSPHOTRANSFERASE (TPT1) FROM PYROCOCCUS HORIKOSHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE RNA 2'-PHOSPHOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII OT3; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 ATCC: 700860D; SOURCE 5 GENE: KPTA, PH0160; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B-HIS10SMT3 KEYWDS TRNA 2'-PHOSPHOTRANSFERASE, TPT1, TRNA SPLICING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.JACEWICZ,S.DANTULURI,S.SHUMAN REVDAT 2 16-OCT-24 8TFI 1 REMARK REVDAT 1 08-NOV-23 8TFI 0 JRNL AUTH A.JACEWICZ,S.DANTULURI,S.SHUMAN JRNL TITL STRUCTURAL BASIS FOR TPT1-CATALYZED 2'-PO 4 TRANSFER FROM JRNL TITL 2 RNA AND NADP(H) TO NAD. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 99120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37883434 JRNL DOI 10.1073/PNAS.2312999120 REMARK 2 REMARK 2 RESOLUTION. 1.97 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15885 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 765 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 42.1700 - 3.3700 1.00 3184 163 0.1724 0.1967 REMARK 3 2 3.3700 - 2.6700 1.00 3039 135 0.2185 0.2757 REMARK 3 3 2.6700 - 2.3400 1.00 3008 151 0.1994 0.2438 REMARK 3 4 2.3400 - 2.1200 1.00 2938 156 0.2151 0.2654 REMARK 3 5 2.1200 - 1.9700 1.00 2951 160 0.2509 0.2937 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) : 0.213 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.89 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 : 0.009 1499 REMARK 3 ANGLE : 0.951 2015 REMARK 3 CHIRALITY : 0.064 214 REMARK 3 PLANARITY : 0.011 256 REMARK 3 DIHEDRAL : 5.787 206 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8660 14.1097 52.7502 REMARK 3 T TENSOR REMARK 3 T11: 0.2418 T22: 0.3250 REMARK 3 T33: 0.2064 T12: -0.0416 REMARK 3 T13: -0.0277 T23: 0.0256 REMARK 3 L TENSOR REMARK 3 L11: 6.1012 L22: 3.9415 REMARK 3 L33: 7.2174 L12: -0.5162 REMARK 3 L13: -2.0122 L23: 0.3965 REMARK 3 S TENSOR REMARK 3 S11: -0.0108 S12: 0.2278 S13: 0.0165 REMARK 3 S21: -0.0063 S22: -0.0234 S23: -0.0554 REMARK 3 S31: -0.1207 S32: 0.1828 S33: 0.0313 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 83 THROUGH 108 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.6759 0.5427 30.3235 REMARK 3 T TENSOR REMARK 3 T11: 0.3511 T22: 0.3683 REMARK 3 T33: 0.3157 T12: -0.0012 REMARK 3 T13: 0.0773 T23: -0.0228 REMARK 3 L TENSOR REMARK 3 L11: 6.8235 L22: 5.1498 REMARK 3 L33: 7.6464 L12: 1.4057 REMARK 3 L13: 5.6901 L23: 2.9091 REMARK 3 S TENSOR REMARK 3 S11: -0.1938 S12: -0.3065 S13: 0.2128 REMARK 3 S21: -0.3219 S22: 0.0808 S23: -0.0548 REMARK 3 S31: -0.0772 S32: -0.0947 S33: 0.0698 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 109 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5921 6.3289 33.2524 REMARK 3 T TENSOR REMARK 3 T11: 0.5889 T22: 0.5869 REMARK 3 T33: 0.5991 T12: -0.0517 REMARK 3 T13: -0.0216 T23: -0.0373 REMARK 3 L TENSOR REMARK 3 L11: 1.3536 L22: 6.4324 REMARK 3 L33: 1.2436 L12: -2.1281 REMARK 3 L13: 0.3094 L23: 1.2944 REMARK 3 S TENSOR REMARK 3 S11: 0.0026 S12: -0.2253 S13: 0.8829 REMARK 3 S21: 0.8485 S22: -0.1375 S23: -0.5620 REMARK 3 S31: -1.2085 S32: 0.4121 S33: -0.0295 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.5037 -0.9985 32.0557 REMARK 3 T TENSOR REMARK 3 T11: 0.3882 T22: 0.3760 REMARK 3 T33: 0.2533 T12: -0.0122 REMARK 3 T13: 0.0356 T23: -0.0431 REMARK 3 L TENSOR REMARK 3 L11: 8.2639 L22: 4.9209 REMARK 3 L33: 7.1499 L12: 1.0523 REMARK 3 L13: 6.3049 L23: 0.3131 REMARK 3 S TENSOR REMARK 3 S11: 0.0642 S12: -0.0937 S13: 0.0659 REMARK 3 S21: -0.0195 S22: -0.0779 S23: -0.0081 REMARK 3 S31: 0.2108 S32: -0.1000 S33: 0.0523 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 8TFI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000275858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 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 : 15955 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 44.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.83900 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 (%): 52.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1-0.3 M TRIS-BICINE, 0.1 M AMINO REMARK 280 ACID ADDITIVES MIXTURE (0.02 M EACH OF DL-GLUTAMIC ACID REMARK 280 MONOHYDRATE, DL-ALANINE, GLYCINE, DL-LYSINE MONOHYDRATE AND DL- REMARK 280 SERINE), 16-29.6% ETHYLENE GLYCOL, 8-14.8% PEG-8000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 19.23200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.36800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.40350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.36800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.23200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.40350 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 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 327 O HOH A 337 2.00 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 HIS A 15 -39.76 -131.27 REMARK 500 SER A 16 55.75 -140.62 REMARK 500 ARG A 83 49.46 -95.26 REMARK 500 LYS A 114 -17.10 57.39 REMARK 500 GLN A 116 -5.51 80.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 8TFI A 2 177 UNP O57899 KPTA_PYRHO 2 177 SEQADV 8TFI SER A 1 UNP O57899 EXPRESSION TAG SEQADV 8TFI MET A 132 UNP O57899 ARG 132 VARIANT SEQRES 1 A 177 SER ARG PHE LYS VAL SER LYS LEU MET ALA TYR ILE LEU SEQRES 2 A 177 ARG HIS SER PRO TRP GLU PHE GLY LEU GLU PRO ASP GLU SEQRES 3 A 177 GLU GLY PHE VAL SER ILE GLU GLU LEU VAL ASN ALA VAL SEQRES 4 A 177 ARG LYS VAL TYR PRO TRP VAL THR GLU GLU TYR ILE ARG SEQRES 5 A 177 GLU ILE VAL GLU ARG ASP GLU LYS GLY ARG TYR GLU ILE SEQRES 6 A 177 ARG GLY ASN LYS ILE ARG ALA ARG TYR GLY HIS SER TYR SEQRES 7 A 177 PRO VAL ILE LEU ARG HIS GLU GLU ASP LYS GLU SER LYS SEQRES 8 A 177 VAL LEU TYR HIS GLY THR VAL ARG ARG ASN LEU LYS GLY SEQRES 9 A 177 ILE MET ARG GLU GLY ILE LYS PRO MET LYS ARG GLN TYR SEQRES 10 A 177 VAL HIS LEU SER ILE ASN TYR GLU ASP ALA TYR ASN THR SEQRES 11 A 177 GLY MET ARG HIS GLY GLU ASP VAL VAL VAL LEU ILE ILE SEQRES 12 A 177 ASP ALA GLU CYS LEU ARG ASN LYS GLY TYR LYS ILE LEU SEQRES 13 A 177 LYS ALA GLY LYS LYS VAL ARG ILE VAL LYS HIS VAL PRO SEQRES 14 A 177 VAL ASP CYS ILE SER GLY ILE LEU HET CL A 201 1 HET CL A 202 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 2(CL 1-) FORMUL 4 HOH *74(H2 O) HELIX 1 AA1 SER A 1 HIS A 15 1 15 HELIX 2 AA2 PRO A 17 GLY A 21 5 5 HELIX 3 AA3 ILE A 32 LYS A 41 1 10 HELIX 4 AA4 THR A 47 ASP A 58 1 12 HELIX 5 AA5 ASN A 101 GLY A 109 1 9 HELIX 6 AA6 ASN A 123 MET A 132 1 10 HELIX 7 AA7 ARG A 133 GLY A 135 5 3 HELIX 8 AA8 ALA A 145 LYS A 151 1 7 HELIX 9 AA9 PRO A 169 ASP A 171 5 3 SHEET 1 AA1 3 VAL A 30 SER A 31 0 SHEET 2 AA1 3 LYS A 69 ALA A 72 -1 O ILE A 70 N VAL A 30 SHEET 3 AA1 3 TYR A 63 ARG A 66 -1 N ARG A 66 O LYS A 69 SHEET 1 AA2 3 VAL A 92 VAL A 98 0 SHEET 2 AA2 3 VAL A 138 ASP A 144 -1 O LEU A 141 N HIS A 95 SHEET 3 AA2 3 ILE A 173 ILE A 176 -1 O GLY A 175 N ILE A 142 SHEET 1 AA3 3 VAL A 118 SER A 121 0 SHEET 2 AA3 3 VAL A 162 VAL A 165 -1 O VAL A 165 N VAL A 118 SHEET 3 AA3 3 LEU A 156 LYS A 157 -1 N LEU A 156 O ILE A 164 SSBOND 1 CYS A 147 CYS A 172 1555 1555 2.05 CRYST1 38.464 44.807 124.736 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 0.025998 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022318 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008017 0.00000