HEADER LIGASE 30-NOV-22 8BTX TITLE STRUCTURE OF HUMAN ARCHEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ARCHEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ZBTB8OS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS ARCHEASE, HUMAN, LIGASE, TRNA SPLICING EXPDTA X-RAY DIFFRACTION AUTHOR J.KOPP,J.L.GERBER,J.PESCHEK REVDAT 2 17-APR-24 8BTX 1 JRNL REVDAT 1 13-DEC-23 8BTX 0 JRNL AUTH J.L.GERBER,S.I.MORALES GUZMAN,L.WORF,P.HUBBE,J.KOPP, JRNL AUTH 2 J.PESCHEK JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO ACTIVATION OF THE JRNL TITL 2 HUMAN RNA LIGASE RTCB BY ARCHEASE. JRNL REF NAT COMMUN V. 15 2378 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38493148 JRNL DOI 10.1038/S41467-024-46568-2 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18925 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) : 0.194 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 942 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 39.9900 - 3.5200 1.00 2757 132 0.1588 0.1743 REMARK 3 2 3.5200 - 2.7900 1.00 2586 137 0.2175 0.2489 REMARK 3 3 2.7900 - 2.4400 1.00 2564 140 0.2506 0.3054 REMARK 3 4 2.4400 - 2.2200 1.00 2524 131 0.2290 0.2690 REMARK 3 5 2.2200 - 2.0600 1.00 2539 133 0.2418 0.2637 REMARK 3 6 2.0600 - 1.9400 1.00 2522 125 0.2826 0.3683 REMARK 3 7 1.9400 - 1.8400 1.00 2491 144 0.3083 0.3275 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.419 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.33 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 1351 REMARK 3 ANGLE : 0.841 1839 REMARK 3 CHIRALITY : 0.053 198 REMARK 3 PLANARITY : 0.008 240 REMARK 3 DIHEDRAL : 13.102 498 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 22 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2055 28.4577 29.7070 REMARK 3 T TENSOR REMARK 3 T11: 0.8369 T22: 0.6748 REMARK 3 T33: 0.7843 T12: 0.1519 REMARK 3 T13: 0.0046 T23: 0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.2350 L22: 1.1901 REMARK 3 L33: 1.7938 L12: -0.2040 REMARK 3 L13: 0.5829 L23: -1.0979 REMARK 3 S TENSOR REMARK 3 S11: -0.1659 S12: 0.5749 S13: -0.0198 REMARK 3 S21: -0.4176 S22: 0.2512 S23: -0.0331 REMARK 3 S31: -1.1978 S32: 0.2411 S33: 0.0073 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 36 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.7768 12.2945 37.5016 REMARK 3 T TENSOR REMARK 3 T11: 0.4687 T22: 0.4498 REMARK 3 T33: 0.4747 T12: -0.0130 REMARK 3 T13: 0.0491 T23: -0.1052 REMARK 3 L TENSOR REMARK 3 L11: 2.6304 L22: 3.2119 REMARK 3 L33: 2.0102 L12: -1.3249 REMARK 3 L13: -0.2759 L23: -0.3489 REMARK 3 S TENSOR REMARK 3 S11: 0.2027 S12: 0.0803 S13: -0.1195 REMARK 3 S21: 0.0997 S22: -0.1224 S23: 0.2399 REMARK 3 S31: -0.1623 S32: -0.0234 S33: -0.0702 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 8BTX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292120353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-21 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9737 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20210205 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 1.12.10 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18949 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 79.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 27.50 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 25.10 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: PHASER 2.8.3 REMARK 200 STARTING MODEL: 5YZ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 1966 UM IN 25 MM HEPES PH REMARK 280 7.5, 100MM NACL, 5 % GLYCEROL, 1MM TCEP RESERVOIR: 0.2 M REMARK 280 AMMONIUM CHLORIDE, 20% W/V PEG 3350 DROP COMPOSITION: 200 NL REMARK 280 RESERVOIR + 200 NL PROTEIN, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z+1/2 REMARK 290 4555 Y,-X,Z+1/2 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.58200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.58200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 32.58200 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 32.58200 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 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 -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 SER A 5 REMARK 465 ARG A 6 REMARK 465 VAL A 7 REMARK 465 SER A 8 REMARK 465 ASN A 9 REMARK 465 PRO A 10 REMARK 465 ALA A 11 REMARK 465 VAL A 12 REMARK 465 MET A 13 REMARK 465 ALA A 14 REMARK 465 GLN A 15 REMARK 465 GLU A 16 REMARK 465 GLU A 17 REMARK 465 GLU A 18 REMARK 465 ASP A 19 REMARK 465 VAL A 20 REMARK 465 ARG A 21 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 115 -102.43 66.18 REMARK 500 GLU A 168 -130.05 -111.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8BTT RELATED DB: PDB DBREF 8BTX A 1 179 UNP A8K0B5 A8K0B5_HUMAN 1 179 SEQADV 8BTX GLY A -3 UNP A8K0B5 EXPRESSION TAG SEQADV 8BTX SER A -2 UNP A8K0B5 EXPRESSION TAG SEQADV 8BTX HIS A -1 UNP A8K0B5 EXPRESSION TAG SEQADV 8BTX MET A 0 UNP A8K0B5 EXPRESSION TAG SEQRES 1 A 183 GLY SER HIS MET MET LYS GLY GLY SER ARG VAL SER ASN SEQRES 2 A 183 PRO ALA VAL MET ALA GLN GLU GLU GLU ASP VAL ARG ASP SEQRES 3 A 183 TYR ASN LEU THR GLU GLU GLN LYS ALA ILE LYS ALA LYS SEQRES 4 A 183 TYR PRO PRO VAL ASN ARG LYS TYR GLU TYR LEU ASP HIS SEQRES 5 A 183 THR ALA ASP VAL GLN LEU HIS ALA TRP GLY ASP THR LEU SEQRES 6 A 183 GLU GLU ALA PHE GLU GLN CYS ALA MET ALA MET PHE GLY SEQRES 7 A 183 TYR MET THR ASP THR GLY THR VAL GLU PRO LEU GLN THR SEQRES 8 A 183 VAL GLU VAL GLU THR GLN GLY ASP ASP LEU GLN SER LEU SEQRES 9 A 183 LEU PHE HIS PHE LEU ASP GLU TRP LEU TYR LYS PHE SER SEQRES 10 A 183 ALA ASP GLU PHE PHE ILE PRO ARG GLU VAL LYS VAL LEU SEQRES 11 A 183 SER ILE ASP GLN ARG ASN PHE LYS LEU ARG SER ILE GLY SEQRES 12 A 183 TRP GLY GLU GLU PHE SER LEU SER LYS HIS PRO GLN GLY SEQRES 13 A 183 THR GLU VAL LYS ALA ILE THR TYR SER ALA MET GLN VAL SEQRES 14 A 183 TYR ASN GLU GLU ASN PRO GLU VAL PHE VAL ILE ILE ASP SEQRES 15 A 183 ILE FORMUL 2 HOH *43(H2 O) HELIX 1 AA1 THR A 26 TYR A 36 1 11 HELIX 2 AA2 THR A 60 THR A 77 1 18 HELIX 3 AA3 ASP A 78 VAL A 82 5 5 HELIX 4 AA4 ASP A 96 ALA A 114 1 19 SHEET 1 AA1 4 TYR A 43 ASP A 47 0 SHEET 2 AA1 4 ASP A 51 TRP A 57 -1 O GLN A 53 N LEU A 46 SHEET 3 AA1 4 GLU A 172 ASP A 178 -1 O VAL A 175 N LEU A 54 SHEET 4 AA1 4 ALA A 157 ILE A 158 -1 N ALA A 157 O ASP A 178 SHEET 1 AA2 4 TYR A 43 ASP A 47 0 SHEET 2 AA2 4 ASP A 51 TRP A 57 -1 O GLN A 53 N LEU A 46 SHEET 3 AA2 4 GLU A 172 ASP A 178 -1 O VAL A 175 N LEU A 54 SHEET 4 AA2 4 GLN A 164 TYR A 166 -1 N TYR A 166 O GLU A 172 SHEET 1 AA3 3 GLN A 86 GLN A 93 0 SHEET 2 AA3 3 LYS A 134 GLU A 143 -1 O GLY A 141 N GLN A 86 SHEET 3 AA3 3 PHE A 118 ASP A 129 -1 N ASP A 129 O LYS A 134 CRYST1 79.981 79.981 65.164 90.00 90.00 90.00 P 42 2 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 0.012503 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015346 0.00000