HEADER LIGASE 25-JAN-19 6JB6 TITLE CRYSTAL STRUCTURE OF UB-CONJUGATED UBE2K C92K&K97A MUTANT (ISOPEPTIDE TITLE 2 LINKAGE), 2.7 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 K; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: UBE2K, E2 UBIQUITIN-CONJUGATING ENZYME K,HUNTINGTIN- COMPND 9 INTERACTING PROTEIN 2,HIP-2,UBIQUITIN CARRIER PROTEIN,UBIQUITIN- COMPND 10 CONJUGATING ENZYME E2-25 KDA,UBIQUITIN-CONJUGATING ENZYME E2-25K, COMPND 11 UBIQUITIN-PROTEIN LIGASE; COMPND 12 EC: 2.3.2.23; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBB; 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: UBE2K, HIP2, LIG; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.-G.LEE,H.-S.YOUN,Y.LEE,J.Y.AN,K.R.PARK,J.Y.KANG,S.A.MUN,J.PARK, AUTHOR 2 T.PARK,M.W.JIN,J.YANG,S.H.EOM REVDAT 2 27-MAR-24 6JB6 1 REMARK REVDAT 1 20-MAR-19 6JB6 0 JRNL AUTH J.-G.LEE,S.H.EOM JRNL TITL CRYSTAL STRUCTURE OF UB-CONJUGATED UBE2K C92K&K97A MUTANT JRNL TITL 2 (ISOPEPTIDE LINKAGE), 2.7 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.3 REMARK 3 NUMBER OF REFLECTIONS : 7713 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.750 REMARK 3 FREE R VALUE TEST SET COUNT : 752 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 45.8100 - 4.6200 0.99 1616 173 0.2191 0.2302 REMARK 3 2 4.6200 - 3.6600 1.00 1579 171 0.2224 0.2700 REMARK 3 3 3.6600 - 3.2000 0.98 1535 170 0.2685 0.3504 REMARK 3 4 3.2000 - 2.9100 0.82 1288 139 0.2890 0.3306 REMARK 3 5 2.9100 - 2.7000 0.61 943 99 0.2948 0.3338 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) : 0.296 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.89 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 : 0.005 2223 REMARK 3 ANGLE : 0.712 3015 REMARK 3 CHIRALITY : 0.048 348 REMARK 3 PLANARITY : 0.006 389 REMARK 3 DIHEDRAL : 22.078 845 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 6JB6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1300010780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9091 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.670 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, PEG 400, MAGNESIUM CHLORIDE, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 72.89900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 72.89900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.10000 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 APPLY THE FOLLOWING TO CHAINS: B, 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 -4 REMARK 465 ALA A -3 REMARK 465 MET A -2 REMARK 465 GLY A -1 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 C GLY B 76 NZ LYS A 92 1.40 REMARK 500 CA GLY B 76 NZ LYS A 92 1.40 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 ASN B 60 45.68 34.89 REMARK 500 ARG B 74 -72.26 -57.96 REMARK 500 VAL A 32 -70.50 -86.55 REMARK 500 ALA A 97 -107.68 -133.10 REMARK 500 PRO A 160 20.94 -68.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 6JB6 B 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 6JB6 A 1 200 UNP P61086 UBE2K_HUMAN 1 200 SEQADV 6JB6 GLY A -4 UNP P61086 EXPRESSION TAG SEQADV 6JB6 ALA A -3 UNP P61086 EXPRESSION TAG SEQADV 6JB6 MET A -2 UNP P61086 EXPRESSION TAG SEQADV 6JB6 GLY A -1 UNP P61086 EXPRESSION TAG SEQADV 6JB6 SER A 0 UNP P61086 EXPRESSION TAG SEQADV 6JB6 LYS A 92 UNP P61086 CYS 92 ENGINEERED MUTATION SEQADV 6JB6 ALA A 97 UNP P61086 LYS 97 ENGINEERED MUTATION 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 SEQRES 1 A 205 GLY ALA MET GLY SER MET ALA ASN ILE ALA VAL GLN ARG SEQRES 2 A 205 ILE LYS ARG GLU PHE LYS GLU VAL LEU LYS SER GLU GLU SEQRES 3 A 205 THR SER LYS ASN GLN ILE LYS VAL ASP LEU VAL ASP GLU SEQRES 4 A 205 ASN PHE THR GLU LEU ARG GLY GLU ILE ALA GLY PRO PRO SEQRES 5 A 205 ASP THR PRO TYR GLU GLY GLY ARG TYR GLN LEU GLU ILE SEQRES 6 A 205 LYS ILE PRO GLU THR TYR PRO PHE ASN PRO PRO LYS VAL SEQRES 7 A 205 ARG PHE ILE THR LYS ILE TRP HIS PRO ASN ILE SER SER SEQRES 8 A 205 VAL THR GLY ALA ILE LYS LEU ASP ILE LEU ALA ASP GLN SEQRES 9 A 205 TRP ALA ALA ALA MET THR LEU ARG THR VAL LEU LEU SER SEQRES 10 A 205 LEU GLN ALA LEU LEU ALA ALA ALA GLU PRO ASP ASP PRO SEQRES 11 A 205 GLN ASP ALA VAL VAL ALA ASN GLN TYR LYS GLN ASN PRO SEQRES 12 A 205 GLU MET PHE LYS GLN THR ALA ARG LEU TRP ALA HIS VAL SEQRES 13 A 205 TYR ALA GLY ALA PRO VAL SER SER PRO GLU TYR THR LYS SEQRES 14 A 205 LYS ILE GLU ASN LEU CYS ALA MET GLY PHE ASP ARG ASN SEQRES 15 A 205 ALA VAL ILE VAL ALA LEU SER SER LYS SER TRP ASP VAL SEQRES 16 A 205 GLU THR ALA THR GLU LEU LEU LEU SER ASN FORMUL 3 HOH *15(H2 O) HELIX 1 AA1 LEU B 8 GLY B 10 5 3 HELIX 2 AA2 THR B 22 GLY B 35 1 14 HELIX 3 AA3 PRO B 37 ASP B 39 5 3 HELIX 4 AA4 ALA A 2 LYS A 18 1 17 HELIX 5 AA5 SER A 19 LYS A 24 1 6 HELIX 6 AA6 LEU A 93 ALA A 97 5 5 HELIX 7 AA7 THR A 105 ALA A 119 1 15 HELIX 8 AA8 ASP A 127 ASN A 137 1 11 HELIX 9 AA9 ASN A 137 GLY A 154 1 18 HELIX 10 AB1 TYR A 162 ALA A 171 1 10 HELIX 11 AB2 ASP A 175 LYS A 186 1 12 HELIX 12 AB3 ASP A 189 LEU A 198 1 10 SHEET 1 AA1 5 THR B 12 GLU B 16 0 SHEET 2 AA1 5 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 AA1 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 AA1 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA1 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 AA2 4 ILE A 27 LEU A 31 0 SHEET 2 AA2 4 GLU A 38 ALA A 44 -1 O GLU A 42 N LYS A 28 SHEET 3 AA2 4 ARG A 55 LYS A 61 -1 O LEU A 58 N GLY A 41 SHEET 4 AA2 4 LYS A 72 PHE A 75 -1 O ARG A 74 N GLU A 59 CISPEP 1 GLY B 75 GLY B 76 0 0.62 CISPEP 2 TYR A 66 PRO A 67 0 2.43 CRYST1 145.798 38.200 56.180 90.00 93.55 90.00 C 1 2 1 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 0.006859 0.000000 0.000426 0.00000 SCALE2 0.000000 0.026178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017834 0.00000