HEADER SIGNALING PROTEIN 05-NOV-15 5ELU TITLE ISOFORM-SPECIFIC INHIBITION OF SUMO-DEPENDENT PROTEIN-PROTEIN TITLE 2 INTERACTIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUMO-AFFIRMER-S2B3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: COMPND 6 MASAATGVRAVPGNENSLEIEELARFAVDEHNKKENALLEFVRVVKAKEQVDLTRFPVTTMYYLTLEAK COMPND 7 DGGKKKLYEAKVWVKGYLLEELKHNFKELQEFKPVGDAAAAHHHHHHHH; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 2; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: SUMO-2,HSMT3,SMT3 HOMOLOG 2,SUMO-3,SENTRIN-2,UBIQUITIN-LIKE COMPND 12 PROTEIN SMT3B,SMT3B; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 GENE: PHYTOCYSTATIN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: SUMO2, SMT3B, SMT3H2; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS UBIQUITIN, SUMOYLATION, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.J.HUGHES,C.TIEDE,N.HALL,A.A.S.TANG,C.H.TRINH,K.ZAJAC,U.MANDAL, AUTHOR 2 G.HOWELL,T.A.EDWARDS,M.J.MCPHERSON,D.C.TOMLINSON,A.WHITEHOUSE REVDAT 5 10-JAN-24 5ELU 1 REMARK REVDAT 4 18-APR-18 5ELU 1 JRNL REVDAT 3 07-FEB-18 5ELU 1 COMPND SOURCE JRNL REVDAT 2 30-AUG-17 5ELU 1 REMARK REVDAT 1 16-NOV-16 5ELU 0 JRNL AUTH D.J.HUGHES,C.TIEDE,N.PENSWICK,A.A.TANG,C.H.TRINH,U.MANDAL, JRNL AUTH 2 K.Z.ZAJAC,T.GAULE,G.HOWELL,T.A.EDWARDS,J.DUAN,E.FEYFANT, JRNL AUTH 3 M.J.MCPHERSON,D.C.TOMLINSON,A.WHITEHOUSE JRNL TITL GENERATION OF SPECIFIC INHIBITORS OF SUMO-1- AND JRNL TITL 2 SUMO-2/3-MEDIATED PROTEIN-PROTEIN INTERACTIONS USING AFFIMER JRNL TITL 3 (ADHIRON) TECHNOLOGY. JRNL REF SCI SIGNAL V. 10 2017 JRNL REFN ESSN 1937-9145 JRNL PMID 29138295 JRNL DOI 10.1126/SCISIGNAL.AAJ2005 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.790 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 16171 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.480 REMARK 3 FREE R VALUE TEST SET COUNT : 725 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 28.3951 - 4.0155 1.00 3119 133 0.1604 0.1730 REMARK 3 2 4.0155 - 3.1886 1.00 3074 168 0.1566 0.1836 REMARK 3 3 3.1886 - 2.7859 1.00 3097 129 0.1824 0.2378 REMARK 3 4 2.7859 - 2.5314 1.00 3096 172 0.1912 0.2565 REMARK 3 5 2.5314 - 2.3500 0.98 3060 123 0.2020 0.2588 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 0.217 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1371 REMARK 3 ANGLE : 1.028 1847 REMARK 3 CHIRALITY : 0.039 203 REMARK 3 PLANARITY : 0.004 239 REMARK 3 DIHEDRAL : 14.072 516 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 5ELU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215130. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8893 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 28.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.11000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.10 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: PDB ENTRIES 1WM3 AND 5ELJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M REMARK 280 SODIUM CHLORIDE AND 2.0 M AMMONIUM SULPHATE, VAPOR DIFFUSION, REMARK 280 SITTING 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 20.98750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.78600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.13200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.78600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.98750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.13200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL 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 MET A 18 REMARK 465 ALA A 19 REMARK 465 SER A 20 REMARK 465 ALA A 21 REMARK 465 ALA A 22 REMARK 465 THR A 23 REMARK 465 GLY A 24 REMARK 465 VAL A 25 REMARK 465 ARG A 26 REMARK 465 ALA A 27 REMARK 465 VAL A 28 REMARK 465 PRO A 29 REMARK 465 GLY A 30 REMARK 465 GLY A 122 REMARK 465 ASP A 123 REMARK 465 ALA A 124 REMARK 465 ALA A 125 REMARK 465 ALA A 126 REMARK 465 ALA A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 465 MET B 13 REMARK 465 ASN B 14 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 LYS A 50 CG CD CE NZ REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 GLU A 95 CG CD OE1 OE2 REMARK 470 ASN B 15 CG OD1 ND2 REMARK 470 ARG B 56 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 89 CG CD OE1 NE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 DBREF 5ELU A 18 135 PDB 5ELU 5ELU 18 135 DBREF 5ELU B 14 89 UNP P61956 SUMO2_HUMAN 14 89 SEQADV 5ELU MET B 13 UNP P61956 INITIATING METHIONINE SEQRES 1 A 118 MET ALA SER ALA ALA THR GLY VAL ARG ALA VAL PRO GLY SEQRES 2 A 118 ASN GLU ASN SER LEU GLU ILE GLU GLU LEU ALA ARG PHE SEQRES 3 A 118 ALA VAL ASP GLU HIS ASN LYS LYS GLU ASN ALA LEU LEU SEQRES 4 A 118 GLU PHE VAL ARG VAL VAL LYS ALA LYS GLU GLN VAL ASP SEQRES 5 A 118 LEU THR ARG PHE PRO VAL THR THR MET TYR TYR LEU THR SEQRES 6 A 118 LEU GLU ALA LYS ASP GLY GLY LYS LYS LYS LEU TYR GLU SEQRES 7 A 118 ALA LYS VAL TRP VAL LYS GLY TYR LEU LEU GLU GLU LEU SEQRES 8 A 118 LYS HIS ASN PHE LYS GLU LEU GLN GLU PHE LYS PRO VAL SEQRES 9 A 118 GLY ASP ALA ALA ALA ALA HIS HIS HIS HIS HIS HIS HIS SEQRES 10 A 118 HIS SEQRES 1 B 77 MET ASN ASN ASP HIS ILE ASN LEU LYS VAL ALA GLY GLN SEQRES 2 B 77 ASP GLY SER VAL VAL GLN PHE LYS ILE LYS ARG HIS THR SEQRES 3 B 77 PRO LEU SER LYS LEU MET LYS ALA TYR CYS GLU ARG GLN SEQRES 4 B 77 GLY LEU SER MET ARG GLN ILE ARG PHE ARG PHE ASP GLY SEQRES 5 B 77 GLN PRO ILE ASN GLU THR ASP THR PRO ALA GLN LEU GLU SEQRES 6 B 77 MET GLU ASP GLU ASP THR ILE ASP VAL PHE GLN GLN HET SO4 A 201 5 HET SO4 B 101 5 HET SO4 B 102 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *102(H2 O) HELIX 1 AA1 SER A 34 ASN A 53 1 20 HELIX 2 AA2 LEU A 104 LEU A 108 5 5 HELIX 3 AA3 LEU B 40 GLY B 52 1 13 SHEET 1 AA1 9 LYS A 113 PRO A 120 0 SHEET 2 AA1 9 LYS A 90 VAL A 100 -1 N GLU A 95 O LYS A 119 SHEET 3 AA1 9 THR A 76 ASP A 87 -1 N ASP A 87 O LYS A 90 SHEET 4 AA1 9 GLU A 57 ASP A 69 -1 N ARG A 60 O GLU A 84 SHEET 5 AA1 9 VAL B 29 LYS B 35 1 O GLN B 31 N GLU A 66 SHEET 6 AA1 9 HIS B 17 GLY B 24 -1 N VAL B 22 O VAL B 30 SHEET 7 AA1 9 THR B 83 GLN B 88 1 O ILE B 84 N LYS B 21 SHEET 8 AA1 9 ILE B 58 PHE B 62 -1 N ARG B 59 O PHE B 87 SHEET 9 AA1 9 GLN B 65 PRO B 66 -1 O GLN B 65 N PHE B 62 CISPEP 1 PHE A 73 PRO A 74 0 -5.68 SITE 1 AC1 2 TYR A 80 LYS A 97 SITE 1 AC2 4 ARG A 72 HIS B 17 LYS B 33 HOH B 231 SITE 1 AC3 2 ASN A 53 ARG B 61 CRYST1 41.975 42.264 113.572 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 0.023824 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008805 0.00000