HEADER STRUCTURAL PROTEIN 19-MAR-20 7BOL TITLE UBIQUITIN-CONJUGATING ENZYME, UBE2D2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-CONJUGATING ENZYME UBE2D2; COMPND 5 EC: 2.3.2.23,2.3.2.24; COMPND 6 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: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN-CONJUGATING ENZYME, UBE2D2, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.O.LEE,K.S.RYU,S.-W.CHI REVDAT 3 29-NOV-23 7BOL 1 REMARK REVDAT 2 20-APR-22 7BOL 1 JRNL REVDAT 1 24-MAR-21 7BOL 0 JRNL AUTH M.S.LEE,S.O.LEE,J.CHOI,M.RYU,M.K.LEE,J.H.KIM,E.HWANG, JRNL AUTH 2 C.K.LEE,S.W.CHI,K.S.RYU JRNL TITL MUL1-RING RECRUITS THE SUBSTRATE, P53-TAD AS A COMPLEX WITH JRNL TITL 2 UBE2D2-UB CONJUGATE. JRNL REF FEBS J. 2022 JRNL REFN ISSN 1742-464X JRNL PMID 35048531 JRNL DOI 10.1111/FEBS.16360 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 14967 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) : 0.193 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 721 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 26.4760 - 3.0716 1.00 3074 147 0.1763 0.1871 REMARK 3 2 3.0716 - 2.4385 0.99 2893 143 0.1937 0.2135 REMARK 3 3 2.4385 - 2.1304 0.98 2883 137 0.1819 0.2100 REMARK 3 4 2.1304 - 1.9357 0.97 2783 157 0.2056 0.2776 REMARK 3 5 1.9357 - 1.7970 0.91 2613 137 0.2609 0.3002 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.39 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 : 0.007 1220 REMARK 3 ANGLE : 0.919 1664 REMARK 3 CHIRALITY : 0.054 179 REMARK 3 PLANARITY : 0.006 217 REMARK 3 DIHEDRAL : 19.073 743 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 7BOL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016217. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14967 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.797 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 : 6.100 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2ESK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M AMMONIUM SULFATE 0.1 M SODIUM REMARK 280 CITRATE PH 5.6 1.0 M LITHIUM SULFATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K 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 24.18700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.63500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.09250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.63500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.18700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.09250 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 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 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 HD22 ASN A 114 O HOH A 201 1.32 REMARK 500 ND2 ASN A 114 O HOH A 201 1.97 REMARK 500 O HOH A 302 O HOH A 303 2.05 REMARK 500 O HOH A 206 O HOH A 248 2.11 REMARK 500 O HOH A 299 O HOH A 322 2.13 REMARK 500 OH TYR A 134 O HOH A 202 2.15 REMARK 500 O HOH A 202 O HOH A 278 2.17 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 ALA A 19 94.74 -66.01 REMARK 500 ASP A 42 -13.58 76.48 REMARK 500 ARG A 90 -103.06 -131.81 REMARK 500 ASP A 130 77.93 -152.92 REMARK 500 REMARK 500 REMARK: NULL DBREF 7BOL A 1 147 UNP P62837 UB2D2_HUMAN 1 147 SEQADV 7BOL SER A 0 UNP P62837 EXPRESSION TAG SEQRES 1 A 148 SER MET ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP SEQRES 2 A 148 LEU ALA ARG ASP PRO PRO ALA GLN CYS SER ALA GLY PRO SEQRES 3 A 148 VAL GLY ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET SEQRES 4 A 148 GLY PRO ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE SEQRES 5 A 148 LEU THR ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO SEQRES 6 A 148 PRO LYS VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN SEQRES 7 A 148 ILE ASN SER ASN GLY SER ILE CYS LEU ASP ILE LEU ARG SEQRES 8 A 148 SER GLN TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU SEQRES 9 A 148 LEU SER ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP SEQRES 10 A 148 ASP PRO LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR SEQRES 11 A 148 ASP ARG GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR SEQRES 12 A 148 GLN LYS TYR ALA MET FORMUL 2 HOH *124(H2 O) HELIX 1 AA1 SER A 0 ASP A 16 1 17 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 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 PHE A 50 N ILE A 37 SHEET 4 AA1 4 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55 CISPEP 1 TYR A 60 PRO A 61 0 5.85 CRYST1 48.374 52.185 63.270 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 0.020672 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019163 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015805 0.00000