HEADER NUCLEAR PROTEIN/PROTEIN BINDING 14-NOV-19 6UYV TITLE CRYSTAL STRUCTURE OF K46-ACETYLATED SUMO1 IN COMPLEX WITH TITLE 2 PHOSPHORYLATED 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 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: PML, MYL, PP8675, RNF71, TRIM19; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 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 6UYV 1 ATOM REVDAT 4 11-OCT-23 6UYV 1 REMARK REVDAT 3 19-FEB-20 6UYV 1 JRNL REVDAT 2 08-JAN-20 6UYV 1 JRNL REVDAT 1 27-NOV-19 6UYV 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23071 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.670 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 29.6260 - 3.3754 1.00 1625 154 0.1769 0.1848 REMARK 3 2 3.3754 - 2.6797 1.00 1556 148 0.1670 0.1813 REMARK 3 3 2.6797 - 2.3411 1.00 1519 144 0.1486 0.1693 REMARK 3 4 2.3411 - 2.1271 1.00 1510 144 0.1317 0.1339 REMARK 3 5 2.1271 - 1.9747 1.00 1526 145 0.1263 0.1638 REMARK 3 6 1.9747 - 1.8583 1.00 1496 141 0.1267 0.1559 REMARK 3 7 1.8583 - 1.7653 1.00 1488 141 0.1379 0.1673 REMARK 3 8 1.7653 - 1.6884 0.99 1467 140 0.1369 0.1855 REMARK 3 9 1.6884 - 1.6234 1.00 1501 142 0.1430 0.1918 REMARK 3 10 1.6234 - 1.5674 1.00 1488 142 0.1466 0.2106 REMARK 3 11 1.5674 - 1.5184 1.00 1470 140 0.1644 0.1933 REMARK 3 12 1.5184 - 1.4750 1.00 1491 140 0.1830 0.2291 REMARK 3 13 1.4750 - 1.4362 1.00 1482 141 0.2198 0.2949 REMARK 3 14 1.4362 - 1.4011 0.98 1452 138 0.2714 0.2700 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) : 15.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.69 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 6UYV 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_1000244131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-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 : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97680 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 : 23072 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.401 REMARK 200 RESOLUTION RANGE LOW (A) : 29.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 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: 4WJN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 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 19.10250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.81200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.45950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.81200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.10250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.45950 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 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 SEP B 16 REMARK 465 SEP B 17 REMARK 465 GLU B 18 REMARK 465 ASP B 19 REMARK 465 SEP B 20 REMARK 465 ASP B 21 REMARK 465 ALA B 22 REMARK 465 GLU B 23 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU B 6 CB CG CD OE1 OE2 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 OE2 GLU B 9 O HOH B 101 1.87 REMARK 500 OG SER A 31 O HOH A 101 1.93 REMARK 500 O HOH A 101 O HOH A 110 1.95 REMARK 500 O HOH A 143 O HOH A 174 1.97 REMARK 500 O HOH A 169 O HOH A 181 2.12 REMARK 500 O HOH A 136 O HOH A 162 2.12 REMARK 500 O HOH A 103 O HOH A 143 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 183 O HOH B 117 2555 1.94 REMARK 500 O HOH A 168 O HOH A 179 3554 2.07 REMARK 500 O HOH A 102 O HOH A 191 4555 2.09 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 6UYV A 17 97 UNP P63165 SUMO1_HUMAN 17 97 DBREF 6UYV B 2 29 UNP P29590 PML_HUMAN 547 574 SEQADV 6UYV GLY A 15 UNP P63165 EXPRESSION TAG SEQADV 6UYV SER A 16 UNP P63165 EXPRESSION TAG SEQADV 6UYV ALA A 52 UNP P63165 CYS 52 ENGINEERED MUTATION SEQADV 6UYV GLY B 1 UNP P29590 EXPRESSION TAG SEQADV 6UYV 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 LYS ALY 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 SEP SEP SEP GLU ASP SEP ASP ALA GLU ASN SER SER SEQRES 3 B 29 SER ARG TYR MODRES 6UYV ALY A 46 LYS MODIFIED RESIDUE MODRES 6UYV SEP B 15 SER MODIFIED RESIDUE HET ALY A 46 26 HET SEP B 15 14 HETNAM ALY N(6)-ACETYLLYSINE HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 ALY C8 H16 N2 O3 FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 HOH *113(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 ILE A 27 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 LYS A 45 N ALY A 46 1555 1555 1.32 LINK C ALY A 46 N LEU A 47 1555 1555 1.33 LINK C ILE B 14 N SEP B 15 1555 1555 1.32 CRYST1 38.205 46.919 63.624 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 0.026175 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021313 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015717 0.00000