HEADER TRANSFERASE 12-JUL-23 8TFY TITLE TRNA 2'-PHOSPHOTRANSFERASE (TPT1) FROM PYROCOCCUS HORIKOSHII IN TITLE 2 COMPLEX WITH NADP 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 GENE: KPTA, PH0160; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: CODON PLUS; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B-HIS10SMT3 KEYWDS TRNA 2'-PHOSPHOTRANSFERASE, TPT1, TRNA SPLICING, NADP, NAD, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.JACEWICZ,S.DANTULURI,S.SHUMAN REVDAT 1 08-NOV-23 8TFY 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. 1.54 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 32431 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1603 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 29.2000 - 3.4200 1.00 3021 162 0.1714 0.1790 REMARK 3 2 3.4200 - 2.7200 1.00 2876 159 0.1804 0.1872 REMARK 3 3 2.7200 - 2.3700 1.00 2866 133 0.1773 0.1879 REMARK 3 4 2.3700 - 2.1600 1.00 2810 150 0.1688 0.2229 REMARK 3 5 2.1600 - 2.0000 1.00 2821 149 0.1525 0.1843 REMARK 3 6 2.0000 - 1.8800 1.00 2800 139 0.1516 0.1783 REMARK 3 7 1.8800 - 1.7900 0.99 2750 143 0.1583 0.2347 REMARK 3 8 1.7900 - 1.7100 0.98 2759 145 0.1634 0.2083 REMARK 3 9 1.7100 - 1.6500 0.98 2736 140 0.1580 0.1941 REMARK 3 10 1.6500 - 1.5900 0.98 2701 141 0.1698 0.2300 REMARK 3 11 1.5900 - 1.5400 0.97 2688 142 0.2140 0.2697 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) : 0.142 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.271 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.53 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 1543 REMARK 3 ANGLE : 0.968 2085 REMARK 3 CHIRALITY : 0.063 223 REMARK 3 PLANARITY : 0.011 260 REMARK 3 DIHEDRAL : 8.836 232 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 8TFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000275867. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-23 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 : NSLS-II REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33140 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 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 : 9.300 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 42.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 1.00500 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: 8TFI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1-0.3 M TRIS-BICINE (PH 8.3 OR 8.5), REMARK 280 0.1 M AMINO ACID ADDITIVES MIXTURE (0.02 M EACH OF DL-GLUTAMIC REMARK 280 ACID MONOHYDRATE, DL-ALANINE, GLYCINE, DL-LYSINE MONOHYDRATE AND REMARK 280 DL-SERINE), 16-29.6% ETHYLENE GLYCOL, AND 8-14.8% PEG-8000, REMARK 280 VAPOR 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 19.33550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.40400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.26550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.40400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.33550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.26550 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 303 O HOH A 382 2.01 REMARK 500 O HOH A 392 O HOH A 395 2.15 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 SER A 16 59.72 -142.16 REMARK 500 ARG A 83 50.65 -90.04 REMARK 500 ARG A 115 18.03 54.26 REMARK 500 GLN A 116 -114.22 -79.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAP A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8TFI RELATED DB: PDB REMARK 900 LIGAND-FREE TPT1 PROTEIN FROM P.HORIKOSHII DBREF 8TFY A 2 177 UNP O57899 KPTA_PYRHO 2 177 SEQADV 8TFY SER A 1 UNP O57899 EXPRESSION TAG SEQADV 8TFY 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 NAP A 201 31 HET CL A 202 1 HET CL A 203 1 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM CL CHLORIDE ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *103(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 ARG A 40 1 9 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 PRO A 112 GLN A 116 5 5 HELIX 7 AA7 ASN A 123 MET A 132 1 10 HELIX 8 AA8 ARG A 133 GLY A 135 5 3 HELIX 9 AA9 ALA A 145 LYS A 151 1 7 HELIX 10 AB1 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 ILE A 143 N LEU A 93 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 CRYST1 38.671 44.531 124.808 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 0.025859 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022456 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008012 0.00000