HEADER NUCLEAR PROTEIN/PROTEIN BINDING 14-NOV-19 6UYQ TITLE CRYSTAL STRUCTURE OF K45-ACETYLATED SUMO1 IN COMPLEX WITH PML-SIM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SUMO-1,GAP-MODIFYING PROTEIN 1,GMP1,SMT3 HOMOLOG 3,SENTRIN, COMPND 5 UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1,UBIQUITIN-LIKE PROTEIN SMT3C, COMPND 6 SMT3C,UBIQUITIN-LIKE PROTEIN UBL1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PROTEIN PML; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: PROMYELOCYTIC LEUKEMIA PROTEIN,RING FINGER PROTEIN 71, COMPND 13 TRIPARTITE MOTIF-CONTAINING PROTEIN 19; COMPND 14 ENGINEERED: YES; COMPND 15 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: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-CL.43; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX2T; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: PML, MYL, PP8675, RNF71, TRIM19; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PGEX2T KEYWDS SUMO1, PML, SUMO INTERACTION MOTIF, PHOSPHOSIM, NUCLEAR PROTEIN- KEYWDS 2 PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.M.WAHBA,C.GAGNON,X.H.MASCLE,M.LUSSIER-PRICE,L.CAPPADOCIA, AUTHOR 2 K.SAKAGUCHI,J.G.OMICHINSKI REVDAT 5 15-NOV-23 6UYQ 1 ATOM REVDAT 4 11-OCT-23 6UYQ 1 REMARK REVDAT 3 19-FEB-20 6UYQ 1 JRNL REVDAT 2 08-JAN-20 6UYQ 1 JRNL REVDAT 1 27-NOV-19 6UYQ 0 JRNL AUTH X.H.MASCLE,C.GAGNON,H.M.WAHBA,M.LUSSIER-PRICE,L.CAPPADOCIA, JRNL AUTH 2 K.SAKAGUCHI,J.G.OMICHINSKI JRNL TITL ACETYLATION OF SUMO1 ALTERS INTERACTIONS WITH THE SIMS OF JRNL TITL 2 PML AND DAXX IN A PROTEIN-SPECIFIC MANNER. JRNL REF STRUCTURE V. 28 157 2020 JRNL REFN ISSN 0969-2126 JRNL PMID 31879127 JRNL DOI 10.1016/J.STR.2019.11.019 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14-3260_1496 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 18492 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1850 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 37.8230 - 3.5278 1.00 1417 158 0.1660 0.1806 REMARK 3 2 3.5278 - 2.8004 1.00 1351 151 0.1602 0.1448 REMARK 3 3 2.8004 - 2.4465 1.00 1317 145 0.1419 0.1548 REMARK 3 4 2.4465 - 2.2228 0.99 1309 146 0.1292 0.1632 REMARK 3 5 2.2228 - 2.0635 0.99 1298 144 0.1266 0.1780 REMARK 3 6 2.0635 - 1.9418 0.99 1298 144 0.1291 0.1775 REMARK 3 7 1.9418 - 1.8446 0.99 1278 142 0.1260 0.1528 REMARK 3 8 1.8446 - 1.7643 0.98 1264 141 0.1275 0.1795 REMARK 3 9 1.7643 - 1.6964 0.98 1272 141 0.1422 0.1982 REMARK 3 10 1.6964 - 1.6378 0.98 1267 141 0.1601 0.2164 REMARK 3 11 1.6378 - 1.5866 0.98 1266 141 0.1772 0.2219 REMARK 3 12 1.5866 - 1.5413 0.97 1246 138 0.2050 0.2490 REMARK 3 13 1.5413 - 1.5010 0.81 1059 118 0.2642 0.2948 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.75 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6UYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000244125. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-AUG-16 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 : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18492 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.501 REMARK 200 RESOLUTION RANGE LOW (A) : 37.823 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 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: 4WJO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM CACODYLATE PH6.5, 16% REMARK 280 PEG3350, 10MM CALCIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 19.11750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.76050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.53950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.76050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.11750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.53950 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: 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 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 15 REMARK 465 SER A 16 REMARK 465 LYS A 17 REMARK 465 GLU A 18 REMARK 465 GLN A 94 REMARK 465 THR A 95 REMARK 465 GLY A 96 REMARK 465 GLY A 97 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 GLY B 3 REMARK 465 ALA B 4 REMARK 465 GLY B 5 REMARK 465 GLU B 6 REMARK 465 SER B 16 REMARK 465 SER B 17 REMARK 465 GLU B 18 REMARK 465 ASP B 19 REMARK 465 SER B 20 REMARK 465 ASP B 21 REMARK 465 ALA B 22 REMARK 465 GLU B 23 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 O HOH A 117 O HOH A 172 1.84 REMARK 500 O HOH A 101 O HOH A 108 1.87 REMARK 500 N ALA B 7 O HOH B 101 1.94 REMARK 500 OG SER A 31 O HOH A 101 1.98 REMARK 500 O HOH A 137 O HOH A 176 2.01 REMARK 500 O HOH A 168 O HOH A 186 2.04 REMARK 500 O HOH A 130 O HOH A 191 2.07 REMARK 500 O HOH A 106 O HOH B 105 2.13 REMARK 500 O HOH A 117 O HOH A 178 2.17 REMARK 500 N GLY A 19 O HOH A 102 2.18 REMARK 500 O HOH A 154 O HOH A 193 2.18 REMARK 500 O HOH A 115 O HOH A 189 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 117 O HOH A 165 4445 1.84 REMARK 500 O HOH A 156 O HOH A 200 4445 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WJQ RELATED DB: PDB REMARK 900 RELATED ID: 4WJP RELATED DB: PDB REMARK 900 RELATED ID: 4WJO RELATED DB: PDB REMARK 900 RELATED ID: 4WJN RELATED DB: PDB DBREF 6UYQ A 17 97 UNP P63165 SUMO1_HUMAN 17 97 DBREF 6UYQ B 2 29 UNP P29590 PML_HUMAN 547 574 SEQADV 6UYQ GLY A 15 UNP P63165 EXPRESSION TAG SEQADV 6UYQ SER A 16 UNP P63165 EXPRESSION TAG SEQADV 6UYQ ALA A 52 UNP P63165 CYS 52 ENGINEERED MUTATION SEQADV 6UYQ GLY B 1 UNP P29590 EXPRESSION TAG SEQADV 6UYQ TYR B 29 UNP P29590 GLU 574 ENGINEERED MUTATION SEQRES 1 A 83 GLY SER LYS GLU GLY GLU TYR ILE LYS LEU LYS VAL ILE SEQRES 2 A 83 GLY GLN ASP SER SER GLU ILE HIS PHE LYS VAL LYS MET SEQRES 3 A 83 THR THR HIS LEU ALY LYS LEU LYS GLU SER TYR ALA GLN SEQRES 4 A 83 ARG GLN GLY VAL PRO MET ASN SER LEU ARG PHE LEU PHE SEQRES 5 A 83 GLU GLY GLN ARG ILE ALA ASP ASN HIS THR PRO LYS GLU SEQRES 6 A 83 LEU GLY MET GLU GLU GLU ASP VAL ILE GLU VAL TYR GLN SEQRES 7 A 83 GLU GLN THR GLY GLY SEQRES 1 B 29 GLY SER GLY ALA GLY GLU ALA GLU GLU ARG VAL VAL VAL SEQRES 2 B 29 ILE SER SER SER GLU ASP SER ASP ALA GLU ASN SER SER SEQRES 3 B 29 SER ARG TYR MODRES 6UYQ ALY A 45 LYS MODIFIED RESIDUE HET ALY A 45 26 HETNAM ALY N(6)-ACETYLLYSINE FORMUL 1 ALY C8 H16 N2 O3 FORMUL 3 HOH *132(H2 O) HELIX 1 AA1 LEU A 44 GLY A 56 1 13 HELIX 2 AA2 PRO A 58 ASN A 60 5 3 HELIX 3 AA3 THR A 76 GLY A 81 1 6 SHEET 1 AA1 6 GLN A 69 ARG A 70 0 SHEET 2 AA1 6 LEU A 62 PHE A 66 -1 N PHE A 66 O GLN A 69 SHEET 3 AA1 6 VAL A 87 GLN A 92 -1 O GLU A 89 N LEU A 65 SHEET 4 AA1 6 ILE A 22 ILE A 27 1 N LYS A 25 O ILE A 88 SHEET 5 AA1 6 GLU A 33 VAL A 38 -1 O PHE A 36 N LEU A 24 SHEET 6 AA1 6 VAL B 11 VAL B 13 1 O VAL B 12 N LYS A 37 LINK C LEU A 44 N ALY A 45 1555 1555 1.33 LINK C ALY A 45 N LYS A 46 1555 1555 1.33 CRYST1 38.235 47.079 63.521 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 0.026154 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021241 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015743 0.00000