HEADER LIGASE 25-JAN-19 6JB7 TITLE CRYSTAL STRUCTURE OF UB-CONJUGATED UBE2K C92K&K97A MUTANT (ISOPEPTIDE TITLE 2 LINKAGE), 2.1 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 6JB7 1 REMARK REVDAT 1 20-MAR-19 6JB7 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), 2.1 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19642 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.580 REMARK 3 FREE R VALUE TEST SET COUNT : 1881 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 31.0200 - 4.9300 0.99 1439 155 0.1677 0.1760 REMARK 3 2 4.9300 - 3.9200 1.00 1385 142 0.1694 0.2072 REMARK 3 3 3.9200 - 3.4200 1.00 1370 146 0.2032 0.2444 REMARK 3 4 3.4200 - 3.1100 1.00 1391 143 0.2362 0.2857 REMARK 3 5 3.1100 - 2.8900 1.00 1362 149 0.2334 0.2922 REMARK 3 6 2.8900 - 2.7200 1.00 1360 144 0.2425 0.2623 REMARK 3 7 2.7200 - 2.5800 1.00 1383 148 0.2423 0.2628 REMARK 3 8 2.5800 - 2.4700 1.00 1373 142 0.2437 0.2996 REMARK 3 9 2.4700 - 2.3700 1.00 1334 140 0.2427 0.2841 REMARK 3 10 2.3700 - 2.2900 1.00 1374 147 0.2463 0.2537 REMARK 3 11 2.2900 - 2.2200 0.99 1318 141 0.2740 0.3254 REMARK 3 12 2.2200 - 2.1600 0.99 1349 142 0.2401 0.3408 REMARK 3 13 2.1600 - 2.1000 0.96 1323 142 0.2374 0.2605 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) : 0.239 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.203 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.33 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 2217 REMARK 3 ANGLE : 0.620 3007 REMARK 3 CHIRALITY : 0.044 347 REMARK 3 PLANARITY : 0.004 388 REMARK 3 DIHEDRAL : 20.529 843 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 6JB7 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_1300010750. 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 : 21798 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 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 (%): 54.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 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 73.04400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.06200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.04400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.06200 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 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 1.48 REMARK 500 O GLY B 76 NZ LYS A 92 2.10 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 GLN B 62 -167.12 -117.29 REMARK 500 ARG B 72 129.16 -178.38 REMARK 500 LEU B 73 -89.37 -134.27 REMARK 500 ASP A 33 -137.88 -89.44 REMARK 500 ALA A 97 -114.93 -129.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 6JB7 B 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 6JB7 A 1 200 UNP P61086 UBE2K_HUMAN 1 200 SEQADV 6JB7 LYS A 92 UNP P61086 CYS 92 ENGINEERED MUTATION SEQADV 6JB7 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 200 MET ALA ASN ILE ALA VAL GLN ARG ILE LYS ARG GLU PHE SEQRES 2 A 200 LYS GLU VAL LEU LYS SER GLU GLU THR SER LYS ASN GLN SEQRES 3 A 200 ILE LYS VAL ASP LEU VAL ASP GLU ASN PHE THR GLU LEU SEQRES 4 A 200 ARG GLY GLU ILE ALA GLY PRO PRO ASP THR PRO TYR GLU SEQRES 5 A 200 GLY GLY ARG TYR GLN LEU GLU ILE LYS ILE PRO GLU THR SEQRES 6 A 200 TYR PRO PHE ASN PRO PRO LYS VAL ARG PHE ILE THR LYS SEQRES 7 A 200 ILE TRP HIS PRO ASN ILE SER SER VAL THR GLY ALA ILE SEQRES 8 A 200 LYS LEU ASP ILE LEU ALA ASP GLN TRP ALA ALA ALA MET SEQRES 9 A 200 THR LEU ARG THR VAL LEU LEU SER LEU GLN ALA LEU LEU SEQRES 10 A 200 ALA ALA ALA GLU PRO ASP ASP PRO GLN ASP ALA VAL VAL SEQRES 11 A 200 ALA ASN GLN TYR LYS GLN ASN PRO GLU MET PHE LYS GLN SEQRES 12 A 200 THR ALA ARG LEU TRP ALA HIS VAL TYR ALA GLY ALA PRO SEQRES 13 A 200 VAL SER SER PRO GLU TYR THR LYS LYS ILE GLU ASN LEU SEQRES 14 A 200 CYS ALA MET GLY PHE ASP ARG ASN ALA VAL ILE VAL ALA SEQRES 15 A 200 LEU SER SER LYS SER TRP ASP VAL GLU THR ALA THR GLU SEQRES 16 A 200 LEU LEU LEU SER ASN FORMUL 3 HOH *52(H2 O) HELIX 1 AA1 THR B 22 GLY B 35 1 14 HELIX 2 AA2 PRO B 37 ASP B 39 5 3 HELIX 3 AA3 LEU B 56 ASN B 60 5 5 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 SER A 159 ALA A 171 1 13 HELIX 11 AB2 ASP A 175 LYS A 186 1 12 HELIX 12 AB3 ASP A 189 ASN A 200 1 12 SHEET 1 AA1 5 ILE B 13 GLU B 16 0 SHEET 2 AA1 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 AA1 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 AA1 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 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 ARG A 40 N ASP A 30 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 LYS A 72 N LYS A 61 CISPEP 1 TYR A 66 PRO A 67 0 7.97 CRYST1 146.088 38.124 60.266 90.00 90.90 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 0.006845 0.000000 0.000107 0.00000 SCALE2 0.000000 0.026230 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016595 0.00000