PDB Short entry for 6R75 HEADER LIGASE 28-MAR-19 6R75 TITLE CRYSTAL STRUCTURE OF HUMAN UBE2T E54R MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 T; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL PROLIFERATION-INDUCING GENE 50 PROTEIN,E2 UBIQUITIN- COMPND 5 CONJUGATING ENZYME T,UBIQUITIN CARRIER PROTEIN T,UBIQUITIN-PROTEIN COMPND 6 LIGASE T; COMPND 7 EC: 2.3.2.23; COMPND 8 ENGINEERED: YES; COMPND 9 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: UBE2T, HSPC150, PIG50; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA REPAIR, E2, UBIQUITINATION, ALLOSTERY, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR V.K.CHAUGULE,M.L.RENNIE,H.WALDEN,C.ARKINSON,O.KAMARAINEN,R.TOTH REVDAT 4 24-JAN-24 6R75 1 REMARK REVDAT 3 04-MAR-20 6R75 1 JRNL REVDAT 2 22-JAN-20 6R75 1 JRNL REVDAT 1 16-OCT-19 6R75 0 JRNL AUTH V.K.CHAUGULE,C.ARKINSON,M.L.RENNIE,O.KAMARAINEN,R.TOTH, JRNL AUTH 2 H.WALDEN JRNL TITL ALLOSTERIC MECHANISM FOR SITE-SPECIFIC UBIQUITINATION OF JRNL TITL 2 FANCD2. JRNL REF NAT.CHEM.BIOL. V. 16 291 2020 JRNL REFN ESSN 1552-4469 JRNL PMID 31873223 JRNL DOI 10.1038/S41589-019-0426-Z REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 9330 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 451 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.84000 REMARK 3 B22 (A**2) : -1.08000 REMARK 3 B33 (A**2) : -1.76000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.272 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.211 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.137 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.057 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6R75 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101499. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-17 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 : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.966 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9878 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.10000 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: 1YH2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.5, 20% V/V REMARK 280 GLYCEROL ETHOXYLATE, 3% V/V POLY(ETHYLENE IMINE), VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 23.06500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.10000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.09500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.10000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.06500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.09500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 LYS A 154 REMARK 465 GLN A 155 REMARK 465 LYS A 156 REMARK 465 ALA A 157 REMARK 465 ASP A 158 REMARK 465 GLU A 159 REMARK 465 GLU A 160 REMARK 465 GLU A 161 REMARK 465 MET A 162 REMARK 465 LEU A 163 REMARK 465 ASP A 164 REMARK 465 ASN A 165 REMARK 465 LEU A 166 REMARK 465 PRO A 167 REMARK 465 GLU A 168 REMARK 465 ALA A 169 REMARK 465 GLY A 170 REMARK 465 ASP A 171 REMARK 465 SER A 172 REMARK 465 ARG A 173 REMARK 465 VAL A 174 REMARK 465 HIS A 175 REMARK 465 ASN A 176 REMARK 465 SER A 177 REMARK 465 THR A 178 REMARK 465 GLN A 179 REMARK 465 LYS A 180 REMARK 465 ARG A 181 REMARK 465 LYS A 182 REMARK 465 ALA A 183 REMARK 465 SER A 184 REMARK 465 GLN A 185 REMARK 465 LEU A 186 REMARK 465 VAL A 187 REMARK 465 GLY A 188 REMARK 465 ILE A 189 REMARK 465 GLU A 190 REMARK 465 LYS A 191 REMARK 465 LYS A 192 REMARK 465 PHE A 193 REMARK 465 HIS A 194 REMARK 465 PRO A 195 REMARK 465 ASP A 196 REMARK 465 VAL A 197 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 LYS A 48 -5.33 74.11 REMARK 500 ASN A 119 72.99 -111.63 REMARK 500 ASP A 122 68.38 -108.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 6R75 A 1 197 UNP Q9NPD8 UBE2T_HUMAN 1 197 SEQADV 6R75 GLY A -3 UNP Q9NPD8 EXPRESSION TAG SEQADV 6R75 PRO A -2 UNP Q9NPD8 EXPRESSION TAG SEQADV 6R75 GLY A -1 UNP Q9NPD8 EXPRESSION TAG SEQADV 6R75 SER A 0 UNP Q9NPD8 EXPRESSION TAG SEQADV 6R75 ARG A 54 UNP Q9NPD8 GLU 54 ENGINEERED MUTATION SEQRES 1 A 201 GLY PRO GLY SER MET GLN ARG ALA SER ARG LEU LYS ARG SEQRES 2 A 201 GLU LEU HIS MET LEU ALA THR GLU PRO PRO PRO GLY ILE SEQRES 3 A 201 THR CYS TRP GLN ASP LYS ASP GLN MET ASP ASP LEU ARG SEQRES 4 A 201 ALA GLN ILE LEU GLY GLY ALA ASN THR PRO TYR GLU LYS SEQRES 5 A 201 GLY VAL PHE LYS LEU ARG VAL ILE ILE PRO GLU ARG TYR SEQRES 6 A 201 PRO PHE GLU PRO PRO GLN ILE ARG PHE LEU THR PRO ILE SEQRES 7 A 201 TYR HIS PRO ASN ILE ASP SER ALA GLY ARG ILE CYS LEU SEQRES 8 A 201 ASP VAL LEU LYS LEU PRO PRO LYS GLY ALA TRP ARG PRO SEQRES 9 A 201 SER LEU ASN ILE ALA THR VAL LEU THR SER ILE GLN LEU SEQRES 10 A 201 LEU MET SER GLU PRO ASN PRO ASP ASP PRO LEU MET ALA SEQRES 11 A 201 ASP ILE SER SER GLU PHE LYS TYR ASN LYS PRO ALA PHE SEQRES 12 A 201 LEU LYS ASN ALA ARG GLN TRP THR GLU LYS HIS ALA ARG SEQRES 13 A 201 GLN LYS GLN LYS ALA ASP GLU GLU GLU MET LEU ASP ASN SEQRES 14 A 201 LEU PRO GLU ALA GLY ASP SER ARG VAL HIS ASN SER THR SEQRES 15 A 201 GLN LYS ARG LYS ALA SER GLN LEU VAL GLY ILE GLU LYS SEQRES 16 A 201 LYS PHE HIS PRO ASP VAL FORMUL 2 HOH *57(H2 O) HELIX 1 AA1 GLY A -3 GLU A 17 1 21 HELIX 2 AA2 LEU A 87 LYS A 91 5 5 HELIX 3 AA3 ASN A 103 GLU A 117 1 15 HELIX 4 AA4 MET A 125 ASN A 135 1 11 HELIX 5 AA5 ASN A 135 ALA A 151 1 17 SHEET 1 AA1 4 ILE A 22 TRP A 25 0 SHEET 2 AA1 4 ASP A 33 LEU A 39 -1 O GLN A 37 N THR A 23 SHEET 3 AA1 4 VAL A 50 ILE A 56 -1 O VAL A 55 N LEU A 34 SHEET 4 AA1 4 GLN A 67 PHE A 70 -1 O GLN A 67 N ILE A 56 CISPEP 1 TYR A 61 PRO A 62 0 -1.06 CISPEP 2 PRO A 93 PRO A 94 0 3.78 CRYST1 46.130 46.190 74.200 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 0.021678 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013477 0.00000