HEADER TRANSFERASE 26-FEB-16 5IFR TITLE STRUCTURE OF THE STABLE UBE2D3-UBDHA CONJUGATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME D3,E2 COMPND 5 UBIQUITIN-CONJUGATING ENZYME D3,UBIQUITIN CARRIER PROTEIN D3, COMPND 6 UBIQUITIN-CONJUGATING ENZYME E2(17)KB 3,UBIQUITIN-CONJUGATING ENZYME COMPND 7 E2-17 KDA 3,UBIQUITIN-PROTEIN LIGASE D3; COMPND 8 EC: 2.3.2.23,2.3.2.24; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: POLYUBIQUITIN-B; COMPND 12 CHAIN: B; COMPND 13 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: UBE2D3, UBC5C, UBCH5C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBB; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN CONJUGATE, DEHYDROALANINE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.N.PRUNEDA,M.P.C.MULDER,K.WITTING,H.OVAA,D.KOMANDER REVDAT 7 10-JAN-24 5IFR 1 REMARK REVDAT 6 10-JUL-19 5IFR 1 REMARK REVDAT 5 20-FEB-19 5IFR 1 REMARK LINK REVDAT 4 13-SEP-17 5IFR 1 REMARK REVDAT 3 29-JUN-16 5IFR 1 JRNL REVDAT 2 01-JUN-16 5IFR 1 JRNL REVDAT 1 11-MAY-16 5IFR 0 JRNL AUTH M.P.MULDER,K.WITTING,I.BERLIN,J.N.PRUNEDA,K.P.WU,J.G.CHANG, JRNL AUTH 2 R.MERKX,J.BIALAS,M.GROETTRUP,A.C.VERTEGAAL,B.A.SCHULMAN, JRNL AUTH 3 D.KOMANDER,J.NEEFJES,F.EL OUALID,H.OVAA JRNL TITL A CASCADING ACTIVITY-BASED PROBE SEQUENTIALLY TARGETS JRNL TITL 2 E1-E2-E3 UBIQUITIN ENZYMES. JRNL REF NAT.CHEM.BIOL. V. 12 523 2016 JRNL REFN ESSN 1552-4469 JRNL PMID 27182664 JRNL DOI 10.1038/NCHEMBIO.2084 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 11589 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 595 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 52.6929 - 3.4921 0.98 2794 148 0.1477 0.1899 REMARK 3 2 3.4921 - 2.7718 0.98 2725 141 0.2185 0.2690 REMARK 3 3 2.7718 - 2.4214 0.99 2761 151 0.2557 0.3249 REMARK 3 4 2.4214 - 2.2000 0.99 2714 155 0.2717 0.3330 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.600 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 : 0.002 1819 REMARK 3 ANGLE : 0.580 2475 REMARK 3 CHIRALITY : 0.024 279 REMARK 3 PLANARITY : 0.003 322 REMARK 3 DIHEDRAL : 10.392 683 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 -2 THROUGH 147) REMARK 3 ORIGIN FOR THE GROUP (A): -15.5783 -26.4573 27.2069 REMARK 3 T TENSOR REMARK 3 T11: 0.2009 T22: 0.2158 REMARK 3 T33: 0.2274 T12: -0.0424 REMARK 3 T13: -0.0497 T23: -0.0123 REMARK 3 L TENSOR REMARK 3 L11: 5.0055 L22: 4.1858 REMARK 3 L33: 4.7162 L12: -1.9268 REMARK 3 L13: -2.6390 L23: 0.8928 REMARK 3 S TENSOR REMARK 3 S11: -0.0949 S12: -0.2552 S13: -0.2944 REMARK 3 S21: 0.0727 S22: -0.1797 S23: -0.0270 REMARK 3 S31: 0.0516 S32: -0.1871 S33: 0.2353 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 76) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9620 -14.2079 5.9481 REMARK 3 T TENSOR REMARK 3 T11: 0.5476 T22: 0.3698 REMARK 3 T33: 0.3632 T12: 0.0211 REMARK 3 T13: 0.0692 T23: -0.0716 REMARK 3 L TENSOR REMARK 3 L11: 4.5655 L22: 4.1316 REMARK 3 L33: 5.1401 L12: 1.2893 REMARK 3 L13: 0.2607 L23: -0.7773 REMARK 3 S TENSOR REMARK 3 S11: 0.1412 S12: 0.2372 S13: -0.0839 REMARK 3 S21: -0.1694 S22: 0.0300 S23: -0.1551 REMARK 3 S31: -0.0391 S32: 0.3632 S33: -0.1787 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 5IFR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-AUG-14 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 : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11594 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 52.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.76000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 3UGB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM TRIPOTASSIUM CITRATE, 20% PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 26.13550 REMARK 290 SMTRY3 2 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: 860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 122 CD OE1 OE2 REMARK 470 LYS A 144 CG CD CE NZ REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 GLU B 64 CG CD OE1 OE2 REMARK 470 ARG B 74 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 85 CB ALA B 76 1.76 REMARK 500 REMARK 500 REMARK: NULL 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 42 47.62 -94.13 REMARK 500 ARG A 90 -101.12 -145.57 REMARK 500 GLN B 62 -166.37 -109.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 DBREF 5IFR A 2 147 UNP P61077 UB2D3_HUMAN 2 147 DBREF 5IFR B 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 5IFR GLY A -3 UNP P61077 EXPRESSION TAG SEQADV 5IFR PRO A -2 UNP P61077 EXPRESSION TAG SEQADV 5IFR LEU A -1 UNP P61077 EXPRESSION TAG SEQADV 5IFR GLY A 0 UNP P61077 EXPRESSION TAG SEQADV 5IFR SER A 1 UNP P61077 EXPRESSION TAG SEQADV 5IFR ALA B 76 UNP P0CG47 GLY 76 CONFLICT SEQRES 1 A 151 GLY PRO LEU GLY SER ALA LEU LYS ARG ILE ASN LYS GLU SEQRES 2 A 151 LEU SER ASP LEU ALA ARG ASP PRO PRO ALA GLN CYS SER SEQRES 3 A 151 ALA GLY PRO VAL GLY ASP ASP MET PHE HIS TRP GLN ALA SEQRES 4 A 151 THR ILE MET GLY PRO ASN ASP SER PRO TYR GLN GLY GLY SEQRES 5 A 151 VAL PHE PHE LEU THR ILE HIS PHE PRO THR ASP TYR PRO SEQRES 6 A 151 PHE LYS PRO PRO LYS VAL ALA PHE THR THR ARG ILE TYR SEQRES 7 A 151 HIS PRO ASN ILE ASN SER ASN GLY SER ILE CYS LEU ASP SEQRES 8 A 151 ILE LEU ARG SER GLN TRP SER PRO ALA LEU THR ILE SER SEQRES 9 A 151 LYS VAL LEU LEU SER ILE CYS SER LEU LEU CYS ASP PRO SEQRES 10 A 151 ASN PRO ASP ASP PRO LEU VAL PRO GLU ILE ALA ARG ILE SEQRES 11 A 151 TYR LYS THR ASP ARG ASP LYS TYR ASN ARG ILE SER ARG SEQRES 12 A 151 GLU TRP THR GLN LYS TYR ALA MET SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY ALA HET GOL A 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *77(H2 O) HELIX 1 AA1 GLY A -3 ASP A 16 1 20 HELIX 2 AA2 LEU A 86 ARG A 90 5 5 HELIX 3 AA3 THR A 98 ASP A 112 1 15 HELIX 4 AA4 VAL A 120 ASP A 130 1 11 HELIX 5 AA5 ASP A 130 ALA A 146 1 17 HELIX 6 AA6 THR B 22 GLY B 35 1 14 HELIX 7 AA7 PRO B 37 ASP B 39 5 3 SHEET 1 AA1 4 CYS A 21 PRO A 25 0 SHEET 2 AA1 4 HIS A 32 MET A 38 -1 O GLN A 34 N GLY A 24 SHEET 3 AA1 4 VAL A 49 HIS A 55 -1 O ILE A 54 N TRP A 33 SHEET 4 AA1 4 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55 SHEET 1 AA2 5 THR B 12 GLU B 16 0 SHEET 2 AA2 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 AA2 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 AA2 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 AA2 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 CISPEP 1 TYR A 60 PRO A 61 0 3.80 SITE 1 AC1 2 ARG A 136 HOH A 312 CRYST1 42.125 52.271 53.624 90.00 100.78 90.00 P 1 21 1 2 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 0.023739 0.000000 0.004519 0.00000 SCALE2 0.000000 0.019131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018983 0.00000