HEADER RNA BINDING PROTEIN 22-JAN-26 9TZG TITLE X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN (RESIDUES 366-485) OF S. TITLE 2 POMBE THREONYLCARBAMOYLADENOSINE DEHYDRATASE AT 1.55 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA THREONYLCARBAMOYLADENOSINE DEHYDRATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: T(6)A37 DEHYDRATASE; COMPND 5 EC: 6.1.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 GENE: TCD1, SPAC1A6.10, SPAC30D11.15C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS THREONYLCARBAMOYLADENOSINE DEHYDRATASE, T6A, CT6A, TRNA, KEYWDS 2 MODIFICATIONS, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.HIRSCHMANN,E.M.HUBER REVDAT 1 01-APR-26 9TZG 0 JRNL AUTH J.HIRSCHMANN,R.SONNTAG,M.HEISS,E.WEGRZYN,W.HEINEMEYER, JRNL AUTH 2 T.CARELL,E.M.HUBER JRNL TITL X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN (RESIDUES 366-485) JRNL TITL 2 OF S. POMBE THREONYLCARBAMOYLADENOSINE DEHYDRATASE AT 1.55 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.2_5419: ???) 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 17609 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 : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 879 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 42.8900 - 2.8200 0.97 2973 157 0.1784 0.1785 REMARK 3 2 2.8200 - 2.2400 0.95 2783 146 0.2008 0.2544 REMARK 3 3 2.2400 - 1.9500 0.96 2797 147 0.1899 0.2401 REMARK 3 4 1.9500 - 1.7700 0.95 2722 143 0.2355 0.3087 REMARK 3 5 1.7700 - 1.6500 0.96 2736 143 0.2975 0.3367 REMARK 3 6 1.6500 - 1.5500 0.96 2719 143 0.3685 0.3933 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.530 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 : 0.011 1003 REMARK 3 ANGLE : 1.019 1361 REMARK 3 CHIRALITY : 0.069 148 REMARK 3 PLANARITY : 0.012 176 REMARK 3 DIHEDRAL : 19.399 380 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 12.3539 10.7806 21.7727 REMARK 3 T TENSOR REMARK 3 T11: 0.2017 T22: 0.2104 REMARK 3 T33: 0.2110 T12: 0.0063 REMARK 3 T13: 0.0035 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 3.0790 L22: 2.8251 REMARK 3 L33: 1.4479 L12: 0.5629 REMARK 3 L13: -0.5315 L23: -0.2335 REMARK 3 S TENSOR REMARK 3 S11: -0.0082 S12: 0.0454 S13: 0.1272 REMARK 3 S21: -0.0180 S22: -0.0347 S23: -0.0546 REMARK 3 S31: -0.0151 S32: -0.0635 S33: 0.0285 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 9TZG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1292153780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17625 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 43.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL, 0.1 M CITRATE PH 5.5, 1 M REMARK 280 (NH4)2HPO4, FINAL PH 7.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K 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 16.24000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.09000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.58500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.09000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.24000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.58500 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 TOTAL BURIED SURFACE AREA: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 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 364 REMARK 465 SER A 365 REMARK 465 LEU A 484 REMARK 465 TYR A 485 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 ASP A 433 -166.68 -121.35 REMARK 500 ASN A 436 50.28 -102.97 REMARK 500 VAL A 452 -60.34 -109.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9HMO RELATED DB: PDB REMARK 900 SIMILAR STRUCTURE, BUT MORE CONSERVATIVELY EVALUATED DBREF 9TZG A 366 485 UNP O13861 TCD_SCHPO 349 468 SEQADV 9TZG GLY A 364 UNP O13861 EXPRESSION TAG SEQADV 9TZG SER A 365 UNP O13861 EXPRESSION TAG SEQRES 1 A 122 GLY SER MET THR ARG PRO ARG LEU TYR GLU GLU ALA VAL SEQRES 2 A 122 LYS ARG LEU HIS ALA GLU ALA ARG LYS ALA GLY VAL ASN SEQRES 3 A 122 LEU ASP LYS THR PHE ASN ALA SER GLU MET SER TYR ILE SEQRES 4 A 122 ILE GLU GLU VAL TYR VAL GLY ARG SER ALA LEU PRO PRO SEQRES 5 A 122 HIS GLU SER GLN LYS VAL THR VAL VAL ARG TRP ASN PRO SEQRES 6 A 122 GLN LEU PRO PHE ASP HIS THR ASN LEU VAL ALA MET THR SEQRES 7 A 122 ARG ASN GLU ALA ARG TYR HIS GLU ASP ASN VAL LEU ALA SEQRES 8 A 122 LYS ASN VAL ASP PRO SER THR VAL TYR GLY LYS ASP VAL SEQRES 9 A 122 ILE GLU VAL VAL HIS SER PHE LEU ARG ARG LEU ARG MET SEQRES 10 A 122 TRP GLU MET LEU TYR HET PO4 A 501 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *49(H2 O) HELIX 1 AA1 ARG A 368 GLY A 387 1 20 HELIX 2 AA2 ASN A 395 GLU A 405 1 11 HELIX 3 AA3 ARG A 442 VAL A 452 1 11 HELIX 4 AA4 ASP A 458 VAL A 462 5 5 HELIX 5 AA5 GLY A 464 GLU A 482 1 19 SHEET 1 AA1 2 VAL A 421 ARG A 425 0 SHEET 2 AA1 2 LEU A 437 THR A 441 -1 O MET A 440 N THR A 422 CISPEP 1 PRO A 414 PRO A 415 0 7.83 CRYST1 32.480 55.170 68.180 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 0.030788 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014667 0.00000 CONECT 978 979 980 981 982 CONECT 979 978 CONECT 980 978 CONECT 981 978 CONECT 982 978 MASTER 248 0 1 5 2 0 0 6 1024 1 5 10 END