HEADER LIGASE 01-JUN-23 8T0S TITLE CRYSTAL STRUCTURE OF UBE2G2 ADDUCT WITH PHENETHYL ISOTHIOCYANATE TITLE 2 (PEITC) AT THE CYS48 POSITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 G2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: E2 UBIQUITIN-CONJUGATING ENZYME G2,UBIQUITIN CARRIER PROTEIN COMPND 5 G2,UBIQUITIN-PROTEIN LIGASE G2; COMPND 6 EC: 2.3.2.23; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: HUMAN UBE2G2(C75S/C89S) PROTEIN WAS TREATED WITH COMPND 10 PHENYLETHYL ISOTHIOCYANATE WHEN THE CYS48 SIDE CHAIN FORMED A COMPND 11 COVALENT BOND WITH THE LIGAND, RESULTING IN THE 6M6 AS A NON-STANDARD COMPND 12 AMINO ACID RESIDUE.; COMPND 13 MOL_ID: 2; COMPND 14 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE AMFR; COMPND 15 CHAIN: B; COMPND 16 SYNONYM: AUTOCRINE MOTILITY FACTOR RECEPTOR,AMF RECEPTOR,RING FINGER COMPND 17 PROTEIN 45,GP78; COMPND 18 EC: 2.3.2.36; COMPND 19 ENGINEERED: YES; COMPND 20 OTHER_DETAILS: THE G2BR DOMAIN CONTAINS RESIDUES 574-600 FROM HUMAN COMPND 21 E3 ENZYME GP78 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBE2G2, UBC7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS HUMAN E2 ENZYME UBE2G2, UBE2G2 ADDUCT, PHENETHYL ISOTHIOCYANATE, KEYWDS 2 PEITC, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR C.WANG,G.X.SHAW,G.SHI,X.JI REVDAT 1 05-JUN-24 8T0S 0 JRNL AUTH C.WANG,G.X.SHAW,G.SHI,X.JI JRNL TITL CRYSTAL STRUCTURE OF UBE2G2 ADDUCT WITH PHENETHYL JRNL TITL 2 ISOTHIOCYANATE (PEITC) AT THE CYS48 POSITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 14602 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.850 REMARK 3 FREE R VALUE TEST SET COUNT : 1000 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 27.7000 - 3.7300 0.99 2053 151 0.1601 0.1827 REMARK 3 2 3.7300 - 2.9600 1.00 1958 144 0.1688 0.2230 REMARK 3 3 2.9600 - 2.5900 1.00 1940 143 0.1848 0.1859 REMARK 3 4 2.5900 - 2.3500 1.00 1927 141 0.1981 0.2568 REMARK 3 5 2.3500 - 2.1800 1.00 1902 140 0.1895 0.2622 REMARK 3 6 2.1800 - 2.0500 1.00 1923 142 0.2048 0.2238 REMARK 3 7 2.0500 - 1.9500 0.99 1899 139 0.2283 0.3054 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.100 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 : 0.007 1721 REMARK 3 ANGLE : 0.910 2339 REMARK 3 CHIRALITY : 0.055 239 REMARK 3 PLANARITY : 0.007 317 REMARK 3 DIHEDRAL : 15.966 683 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 8T0S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000274960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14738 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.88000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG MME 5000, NACL, ETC., PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 23.94700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.95050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.67250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.95050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.94700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.67250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 ALA A 2 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 147 64.04 -152.74 REMARK 500 REMARK 500 REMARK: NULL DBREF 8T0S A 1 165 UNP P60604 UB2G2_HUMAN 1 165 DBREF 8T0S B 574 600 UNP Q9UKV5 AMFR_HUMAN 574 600 SEQADV 8T0S SER A 75 UNP P60604 CYS 75 ENGINEERED MUTATION SEQADV 8T0S SER A 89 UNP P60604 CYS 89 ENGINEERED MUTATION SEQRES 1 A 165 MET ALA GLY THR ALA LEU LYS ARG LEU MET ALA GLU TYR SEQRES 2 A 165 LYS GLN LEU THR LEU ASN PRO PRO GLU GLY ILE VAL ALA SEQRES 3 A 165 GLY PRO MET ASN GLU GLU ASN PHE PHE GLU TRP GLU ALA SEQRES 4 A 165 LEU ILE MET GLY PRO GLU ASP THR 6M6 PHE GLU PHE GLY SEQRES 5 A 165 VAL PHE PRO ALA ILE LEU SER PHE PRO LEU ASP TYR PRO SEQRES 6 A 165 LEU SER PRO PRO LYS MET ARG PHE THR SER GLU MET PHE SEQRES 7 A 165 HIS PRO ASN ILE TYR PRO ASP GLY ARG VAL SER ILE SER SEQRES 8 A 165 ILE LEU HIS ALA PRO GLY ASP ASP PRO MET GLY TYR GLU SEQRES 9 A 165 SER SER ALA GLU ARG TRP SER PRO VAL GLN SER VAL GLU SEQRES 10 A 165 LYS ILE LEU LEU SER VAL VAL SER MET LEU ALA GLU PRO SEQRES 11 A 165 ASN ASP GLU SER GLY ALA ASN VAL ASP ALA SER LYS MET SEQRES 12 A 165 TRP ARG ASP ASP ARG GLU GLN PHE TYR LYS ILE ALA LYS SEQRES 13 A 165 GLN ILE VAL GLN LYS SER LEU GLY LEU SEQRES 1 B 27 SER ALA ASP GLU ARG GLN ARG MET LEU VAL GLN ARG LYS SEQRES 2 B 27 ASP GLU LEU LEU GLN GLN ALA ARG LYS ARG PHE LEU ASN SEQRES 3 B 27 LYS MODRES 8T0S 6M6 A 48 CYS MODIFIED RESIDUE HET 6M6 A 48 17 HET EDO A 201 4 HETNAM 6M6 S-[(2-PHENYLETHYL)CARBAMOTHIOYL]-L-CYSTEINE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 6M6 C12 H16 N2 O2 S2 FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *167(H2 O) HELIX 1 AA1 GLY A 3 ASN A 19 1 17 HELIX 2 AA2 ILE A 90 HIS A 94 5 5 HELIX 3 AA3 SER A 115 GLU A 129 1 15 HELIX 4 AA4 ASN A 137 ASP A 147 1 11 HELIX 5 AA5 ASP A 147 LEU A 163 1 17 HELIX 6 AA6 ALA B 575 LYS B 600 1 26 SHEET 1 AA1 4 ILE A 24 PRO A 28 0 SHEET 2 AA1 4 GLU A 36 MET A 42 -1 O LEU A 40 N VAL A 25 SHEET 3 AA1 4 VAL A 53 SER A 59 -1 O PHE A 54 N ILE A 41 SHEET 4 AA1 4 LYS A 70 PHE A 73 -1 O ARG A 72 N ILE A 57 LINK C THR A 47 N 6M6 A 48 1555 1555 1.34 LINK C 6M6 A 48 N PHE A 49 1555 1555 1.33 CISPEP 1 TYR A 64 PRO A 65 0 9.64 CRYST1 47.894 59.345 67.901 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 0.020879 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014727 0.00000