HEADER TRANSFERASE 07-NOV-16 5TUT TITLE UBCH5A-UB ISOPEPTIDE CONJUGATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBCH5A, (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME D1, COMPND 5 E2 UBIQUITIN-CONJUGATING ENZYME D1, STIMULATOR OF FE TRANSPORT, SFT, COMPND 6 UBC4/5 HOMOLOG, UBCH5, UBIQUITIN CARRIER PROTEIN D1, UBIQUITIN- COMPND 7 CONJUGATING ENZYME E2(17)KB 1, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA COMPND 8 1, UBIQUITIN-PROTEIN LIGASE D1; COMPND 9 EC: 2.3.2.23, 2.3.2.24; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES; COMPND 12 MOL_ID: 2; COMPND 13 MOLECULE: UBIQUITIN; COMPND 14 CHAIN: B; COMPND 15 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: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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 BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS E2 CONJUGATING ENZYME, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.G.SANCHEZ,J.M.WAGNER,O.PORNILLOS REVDAT 3 04-OCT-23 5TUT 1 REMARK REVDAT 2 01-JAN-20 5TUT 1 REMARK REVDAT 1 08-NOV-17 5TUT 0 JRNL AUTH J.G.SANCHEZ,J.M.WAGNER,O.PORNILLOS JRNL TITL UBCH5A-UB ISOPEPTIDE CONJUGATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 6708 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 684 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 32.1159 - 4.4502 1.00 1259 160 0.1626 0.1782 REMARK 3 2 4.4502 - 3.5337 1.00 1235 144 0.1655 0.2090 REMARK 3 3 3.5337 - 3.0874 1.00 1265 114 0.2287 0.3026 REMARK 3 4 3.0874 - 2.8053 0.99 1197 143 0.2623 0.3456 REMARK 3 5 2.8053 - 2.6044 0.85 1068 123 0.2700 0.3123 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.92 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 : 0.003 1838 REMARK 3 ANGLE : 0.596 2494 REMARK 3 CHIRALITY : 0.042 276 REMARK 3 PLANARITY : 0.004 323 REMARK 3 DIHEDRAL : 9.994 1124 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): 5.4821 -0.3689 25.0272 REMARK 3 T TENSOR REMARK 3 T11: 0.2160 T22: 0.1962 REMARK 3 T33: 0.2273 T12: 0.0036 REMARK 3 T13: -0.0264 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 0.5260 L22: 0.4967 REMARK 3 L33: 0.3861 L12: -0.1372 REMARK 3 L13: 0.0500 L23: 0.3890 REMARK 3 S TENSOR REMARK 3 S11: -0.0376 S12: 0.0307 S13: -0.0207 REMARK 3 S21: 0.0492 S22: 0.0176 S23: 0.0466 REMARK 3 S31: -0.0293 S32: -0.0244 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 76) REMARK 3 ORIGIN FOR THE GROUP (A): -17.7144 11.2935 45.9221 REMARK 3 T TENSOR REMARK 3 T11: 0.3143 T22: 0.3541 REMARK 3 T33: 0.2870 T12: -0.0234 REMARK 3 T13: 0.0489 T23: -0.0282 REMARK 3 L TENSOR REMARK 3 L11: 0.1846 L22: 0.0166 REMARK 3 L33: 0.3890 L12: 0.0079 REMARK 3 L13: 0.0584 L23: 0.0011 REMARK 3 S TENSOR REMARK 3 S11: -0.2868 S12: -0.0215 S13: -0.1559 REMARK 3 S21: 0.0513 S22: 0.0189 S23: 0.0397 REMARK 3 S31: 0.1658 S32: -0.2158 S33: -0.0002 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 5TUT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1000224839. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-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 : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6719 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRIES 2C4P & 1UBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HAMPTON PEG/ION F10, VAPOR DIFFUSION, REMARK 280 SITTING DROP 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 25.70500 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: 770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 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 NZ LYS A 85 C GLY B 76 1.32 REMARK 500 OD2 ASP A 12 NH2 ARG A 15 2.15 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 -5.00 75.05 REMARK 500 ARG A 90 -90.06 -157.78 REMARK 500 ASP A 112 80.64 -153.81 REMARK 500 ASN A 114 79.56 -119.71 REMARK 500 REMARK 500 REMARK: NULL DBREF 5TUT A 1 147 UNP P51668 UB2D1_HUMAN 1 147 DBREF 5TUT B 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 5TUT GLY A -2 UNP P51668 EXPRESSION TAG SEQADV 5TUT SER A -1 UNP P51668 EXPRESSION TAG SEQADV 5TUT HIS A 0 UNP P51668 EXPRESSION TAG SEQADV 5TUT LYS A 85 UNP P51668 CYS 85 ENGINEERED MUTATION SEQRES 1 A 150 GLY SER HIS MET ALA LEU LYS ARG ILE GLN LYS GLU LEU SEQRES 2 A 150 SER ASP LEU GLN ARG ASP PRO PRO ALA HIS CYS SER ALA SEQRES 3 A 150 GLY PRO VAL GLY ASP ASP LEU PHE HIS TRP GLN ALA THR SEQRES 4 A 150 ILE MET GLY PRO PRO ASP SER ALA TYR GLN GLY GLY VAL SEQRES 5 A 150 PHE PHE LEU THR VAL HIS PHE PRO THR ASP TYR PRO PHE SEQRES 6 A 150 LYS PRO PRO LYS ILE ALA PHE THR THR LYS ILE TYR HIS SEQRES 7 A 150 PRO ASN ILE ASN SER ASN GLY SER ILE LYS LEU ASP ILE SEQRES 8 A 150 LEU ARG SER GLN TRP SER PRO ALA LEU THR VAL SER LYS SEQRES 9 A 150 VAL LEU LEU SER ILE CYS SER LEU LEU CYS ASP PRO ASN SEQRES 10 A 150 PRO ASP ASP PRO LEU VAL PRO ASP ILE ALA GLN ILE TYR SEQRES 11 A 150 LYS SER ASP LYS GLU LYS TYR ASN ARG HIS ALA ARG GLU SEQRES 12 A 150 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 GLY HELIX 1 AA1 GLY A -2 ASP A 16 1 19 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 HELIX 8 AA8 LEU B 56 ASN B 60 5 5 SHEET 1 AA1 4 SER A 22 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 VAL 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 LYS B 6 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 4.36 CRYST1 41.949 51.410 53.157 90.00 101.39 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 0.023838 0.000000 0.004800 0.00000 SCALE2 0.000000 0.019451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019190 0.00000