HEADER TRANSFERASE 12-JUL-23 8TG5 TITLE TRNA 2'-PHOSPHOTRANSFERASE (TPT1) FROM PYROCOCCUS HORIKOSHII IN TITLE 2 COMPLEX WITH BRANCHED 2'-PO4 RNA 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 KEYWDS TRNA 2'-PHOSPHOTRANSFERASE, TPT1, TRNA SPLICING, BRANCHED RNA, 2'-PO4 KEYWDS 2 RNA, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.JACEWICZ,S.DANTULURI,S.SHUMAN REVDAT 3 26-JUN-24 8TG5 1 JRNL REVDAT 2 19-JUN-24 8TG5 1 JRNL REVDAT 1 05-JUN-24 8TG5 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15385 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 766 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 42.6400 - 3.4200 1.00 3080 167 0.1676 0.2136 REMARK 3 2 3.4200 - 2.7100 1.00 2909 157 0.2057 0.2550 REMARK 3 3 2.7100 - 2.3700 1.00 2904 136 0.2246 0.2716 REMARK 3 4 2.3700 - 2.1500 1.00 2867 154 0.2192 0.2896 REMARK 3 5 2.1500 - 2.0000 1.00 2859 152 0.2793 0.3364 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) : 0.277 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.573 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.84 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 1589 REMARK 3 ANGLE : 0.931 2155 REMARK 3 CHIRALITY : 0.060 228 REMARK 3 PLANARITY : 0.009 264 REMARK 3 DIHEDRAL : 12.344 214 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.9740 14.3533 53.1896 REMARK 3 T TENSOR REMARK 3 T11: 0.2018 T22: 0.2722 REMARK 3 T33: 0.2028 T12: -0.0353 REMARK 3 T13: -0.0083 T23: 0.0152 REMARK 3 L TENSOR REMARK 3 L11: 4.9577 L22: 3.7844 REMARK 3 L33: 4.2563 L12: -0.6300 REMARK 3 L13: -0.3738 L23: 0.5775 REMARK 3 S TENSOR REMARK 3 S11: -0.0791 S12: 0.3513 S13: -0.0133 REMARK 3 S21: 0.0151 S22: -0.0505 S23: -0.0639 REMARK 3 S31: -0.0238 S32: 0.3853 S33: 0.1116 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 83 THROUGH 177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0964 0.9019 31.6794 REMARK 3 T TENSOR REMARK 3 T11: 0.3496 T22: 0.2905 REMARK 3 T33: 0.3750 T12: 0.0061 REMARK 3 T13: 0.0337 T23: -0.0737 REMARK 3 L TENSOR REMARK 3 L11: 4.1125 L22: 3.2570 REMARK 3 L33: 6.2002 L12: -0.1427 REMARK 3 L13: 1.6863 L23: 1.4998 REMARK 3 S TENSOR REMARK 3 S11: -0.0219 S12: -0.2098 S13: 0.0795 REMARK 3 S21: -0.2265 S22: -0.1432 S23: 0.0430 REMARK 3 S31: -0.1080 S32: -0.0102 S33: 0.1289 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 8TG5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000275896. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-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 : 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 : 15452 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.30 REMARK 200 R MERGE FOR SHELL (I) : 1.01300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 52.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-BICINE (PH 8.3 OR 8.5), 0.1 REMARK 280 M AMINO 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, AND 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 19.14550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.61950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.67200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.61950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.14550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.67200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 -35.55 -133.17 REMARK 500 SER A 16 56.25 -144.17 REMARK 500 ARG A 83 58.29 -90.73 REMARK 500 LYS A 114 65.52 -108.29 REMARK 500 ARG A 115 -143.57 47.50 REMARK 500 GLN A 116 -114.42 44.93 REMARK 500 HIS A 167 147.75 -173.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 202 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 13 O REMARK 620 2 GLY A 28 O 118.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 203 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 86 OE2 REMARK 620 2 ASP A 87 O 109.5 REMARK 620 3 ILE A 155 O 113.5 70.1 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8TFI RELATED DB: PDB DBREF 8TG5 A 2 177 UNP O57899 KPTA_PYRHO 2 177 SEQADV 8TG5 SER A 1 UNP O57899 EXPRESSION TAG SEQADV 8TG5 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 9S2 A 201 67 HET K A 202 1 HET K A 203 1 HET CL A 204 1 HET CL A 205 1 HET CL A 206 1 HETNAM 9S2 (2S,3R,4R,5S)-2-(6-AMINO-9H-PURIN-9-YL)-4-{[(S)-{[(2R, HETNAM 2 9S2 3S,4R,5S)-5-(6-AMINO-9H-PURIN-9-YL)-3,4- HETNAM 3 9S2 DIHYDROXYOXOLAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}- HETNAM 4 9S2 5-({[(S)-{[(2R,3R,4S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4- HETNAM 5 9S2 HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]OXY}(HYDROXY) HETNAM 6 9S2 PHOSPHORYL]OXY}METHYL)OXOLAN-3-YL DIHYDROGEN PHOSPHATE HETNAM 7 9S2 (NON-PREFERRED NAME) HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION FORMUL 2 9S2 C30 H38 N15 O19 P3 FORMUL 3 K 2(K 1+) FORMUL 5 CL 3(CL 1-) FORMUL 8 HOH *62(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 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 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 LINK O LEU A 13 K K A 202 1555 1555 2.97 LINK O GLY A 28 K K A 202 1555 1555 2.70 LINK OE2 GLU A 86 K K A 203 1555 1555 2.66 LINK O ASP A 87 K K A 203 1555 1555 3.03 LINK O ILE A 155 K K A 203 1555 1555 3.26 CRYST1 38.291 45.344 125.239 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 0.026116 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022054 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007985 0.00000