HEADER LIGASE 21-NOV-23 8R6B TITLE DTX1 WWE DOMAIN IN COMPLEX WITH ADP BOUND TO WWE2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE DTX1; 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: DTX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E3 LIGASE, NUCLEOTIDE, WWE DOMAIN, ADP, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR L.MUENZKER,K.M.ZAK,J.BOETTCHER REVDAT 2 07-AUG-24 8R6B 1 JRNL REVDAT 1 31-JUL-24 8R6B 0 JRNL AUTH L.MUNZKER,S.W.KIMANI,M.M.FOWKES,A.DONG,H.ZHENG,Y.LI, JRNL AUTH 2 M.DASOVICH,K.M.ZAK,A.K.L.LEUNG,J.M.ELKINS,D.KESSLER, JRNL AUTH 3 C.H.ARROWSMITH,L.HALABELIAN,J.BOTTCHER JRNL TITL A LIGAND DISCOVERY TOOLBOX FOR THE WWE DOMAIN FAMILY OF JRNL TITL 2 HUMAN E3 LIGASES. JRNL REF COMMUN BIOL V. 7 901 2024 JRNL REFN ESSN 2399-3642 JRNL PMID 39048679 JRNL DOI 10.1038/S42003-024-06584-W REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 5483 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 247 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 35.1500 - 3.1500 0.99 2874 129 0.2161 0.2174 REMARK 3 2 3.1500 - 2.5000 0.86 2362 118 0.2300 0.3070 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) : 0.258 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.507 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.34 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 : 0.003 1437 REMARK 3 ANGLE : 0.715 1960 REMARK 3 CHIRALITY : 0.047 203 REMARK 3 PLANARITY : 0.006 249 REMARK 3 DIHEDRAL : 16.122 530 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 8R6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1292133661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-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 : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999979 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 FEB 5, 2021 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC 1.1.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5530 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 70.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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 (%): 40.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.0, 25 % V/V PEG MME REMARK 280 350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 278K 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 16.92800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.14550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.68600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.14550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.92800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.68600 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: 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 55 114.99 -160.14 REMARK 500 ASP A 174 -145.98 -83.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8R5N RELATED DB: PDB DBREF 8R6B A 21 184 UNP Q86Y01 DTX1_HUMAN 21 184 SEQADV 8R6B GLY A 20 UNP Q86Y01 EXPRESSION TAG SEQRES 1 A 165 GLY ASN VAL ALA ARG VAL VAL VAL TRP GLU TRP LEU ASN SEQRES 2 A 165 GLU HIS SER ARG TRP ARG PRO TYR THR ALA THR VAL CYS SEQRES 3 A 165 HIS HIS ILE GLU ASN VAL LEU LYS GLU ASP ALA ARG GLY SEQRES 4 A 165 SER VAL VAL LEU GLY GLN VAL ASP ALA GLN LEU VAL PRO SEQRES 5 A 165 TYR ILE ILE ASP LEU GLN SER MET HIS GLN PHE ARG GLN SEQRES 6 A 165 ASP THR GLY THR MET ARG PRO VAL ARG ARG ASN PHE TYR SEQRES 7 A 165 ASP PRO SER SER ALA PRO GLY LYS GLY ILE VAL TRP GLU SEQRES 8 A 165 TRP GLU ASN ASP GLY GLY ALA TRP THR ALA TYR ASP MET SEQRES 9 A 165 ASP ILE CYS ILE THR ILE GLN ASN ALA TYR GLU LYS GLN SEQRES 10 A 165 HIS PRO TRP LEU ASP LEU SER SER LEU GLY PHE CYS TYR SEQRES 11 A 165 LEU ILE TYR PHE ASN SER MET SER GLN MET ASN ARG GLN SEQRES 12 A 165 THR ARG ARG ARG ARG ARG LEU ARG ARG ARG LEU ASP LEU SEQRES 13 A 165 ALA TYR PRO LEU THR VAL GLY SER ILE HET ADP A 201 27 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 HOH *5(H2 O) HELIX 1 AA1 THR A 41 ASP A 55 1 15 HELIX 2 AA2 GLY A 63 VAL A 65 5 3 HELIX 3 AA3 ASP A 66 VAL A 70 5 5 HELIX 4 AA4 SER A 101 GLY A 106 1 6 HELIX 5 AA5 ASP A 122 LYS A 135 1 14 HELIX 6 AA6 SER A 143 GLY A 146 5 4 SHEET 1 AA1 6 TRP A 37 PRO A 39 0 SHEET 2 AA1 6 ASN A 21 LEU A 31 -1 N TRP A 30 O ARG A 38 SHEET 3 AA1 6 MET A 89 TYR A 97 -1 O ASN A 95 N VAL A 27 SHEET 4 AA1 6 HIS A 80 ARG A 83 -1 N GLN A 81 O ARG A 90 SHEET 5 AA1 6 TYR A 72 ASP A 75 -1 N ILE A 73 O PHE A 82 SHEET 6 AA1 6 SER A 59 VAL A 61 -1 N VAL A 60 O ILE A 74 SHEET 1 AA2 3 TRP A 37 PRO A 39 0 SHEET 2 AA2 3 ASN A 21 LEU A 31 -1 N TRP A 30 O ARG A 38 SHEET 3 AA2 3 LEU A 179 SER A 183 -1 O GLY A 182 N VAL A 22 SHEET 1 AA3 6 TRP A 118 ALA A 120 0 SHEET 2 AA3 6 ILE A 107 GLU A 112 -1 N TRP A 111 O THR A 119 SHEET 3 AA3 6 ARG A 166 LEU A 173 -1 O ARG A 172 N VAL A 108 SHEET 4 AA3 6 SER A 157 ASN A 160 -1 N GLN A 158 O ARG A 167 SHEET 5 AA3 6 TYR A 149 TYR A 152 -1 N TYR A 152 O SER A 157 SHEET 6 AA3 6 TRP A 139 ASP A 141 -1 N LEU A 140 O ILE A 151 CRYST1 33.856 67.372 70.291 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 0.029537 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014843 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014227 0.00000