HEADER PROTEIN BINDING 23-JUL-26 32TC TITLE CRYSTAL STRUCTURE OF THE HUMAN SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN TITLE 2 SPSB4 BOUND TO FRAGMENT Z104474228 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SSB-4; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: N-TERMINAL SER-MET FROM AFFINITY TAG, RESIDUES 28-233 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SPSB4, SSB4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS E3 LIGASE, SOCS BOX, FRAGMENT, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.T.RANDALL,N.A.COSTELLO,L.KOEKEMOER,F.VON DELFT REVDAT 1 12-AUG-26 32TC 0 JRNL AUTH G.T.RANDALL,N.A.COSTELLO,L.KOEKEMOER,F.VON DELFT JRNL TITL CRYSTALLOGRAPHIC FRAGMENT SCREENING OF A HUMAN E3 LIGASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 26302 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1339 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 31.8100 - 3.3600 1.00 2620 165 0.1542 0.1868 REMARK 3 2 3.3600 - 2.6700 1.00 2539 142 0.1668 0.2297 REMARK 3 3 2.6700 - 2.3300 1.00 2505 144 0.1875 0.2548 REMARK 3 4 2.3300 - 2.1200 1.00 2512 137 0.2094 0.2498 REMARK 3 5 2.1200 - 1.9600 1.00 2519 113 0.1977 0.2358 REMARK 3 6 1.9600 - 1.8500 1.00 2511 120 0.2391 0.2887 REMARK 3 7 1.8500 - 1.7600 1.00 2474 125 0.2615 0.3256 REMARK 3 8 1.7600 - 1.6800 0.99 2494 125 0.3069 0.3649 REMARK 3 9 1.6800 - 1.6100 0.99 2459 133 0.3463 0.4271 REMARK 3 10 1.6100 - 1.5600 0.95 2330 135 0.3626 0.3683 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.265 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.378 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.97 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 1690 REMARK 3 ANGLE : 0.999 2308 REMARK 3 CHIRALITY : 0.060 236 REMARK 3 PLANARITY : 0.010 309 REMARK 3 DIHEDRAL : 8.178 248 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 32TC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-26. REMARK 100 THE DEPOSITION ID IS D_1292159183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-26 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9156 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26521 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 31.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 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 : 0.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: DIMPLE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE PH 5.5, 20% REMARK 280 PEG3000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.22350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.22350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 31.80850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.80850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.22350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.80850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 34.22350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.80850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 42.00000 REMARK 290 SMTRY3 8 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL A 305 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 524 LIES ON A SPECIAL POSITION. 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 SER A 26 REMARK 465 MET A 27 REMARK 465 GLY A 28 REMARK 465 ALA A 29 REMARK 465 GLU A 30 REMARK 465 GLU A 233 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 32RM RELATED DB: PDB REMARK 900 32RM IS THE APO PROTEIN AND SAME CRYSTAL SYSTEM USED IN THIS REMARK 900 FRAGMENT SOAK DBREF 32TC A 28 233 UNP Q96A44 SPSB4_HUMAN 28 233 SEQADV 32TC SER A 26 UNP Q96A44 EXPRESSION TAG SEQADV 32TC MET A 27 UNP Q96A44 EXPRESSION TAG SEQRES 1 A 208 SER MET GLY ALA GLU PRO GLY ARG PRO ALA ARG LEU ASP SEQRES 2 A 208 GLN LEU LEU ASP MET PRO ALA ALA GLY LEU ALA VAL GLN SEQRES 3 A 208 LEU ARG HIS ALA TRP ASN PRO GLU ASP ARG SER LEU ASN SEQRES 4 A 208 VAL PHE VAL LYS ASP ASP ASP ARG LEU THR PHE HIS ARG SEQRES 5 A 208 HIS PRO VAL ALA GLN SER THR ASP GLY ILE ARG GLY LYS SEQRES 6 A 208 VAL GLY HIS ALA ARG GLY LEU HIS ALA TRP GLN ILE ASN SEQRES 7 A 208 TRP PRO ALA ARG GLN ARG GLY THR HIS ALA VAL VAL GLY SEQRES 8 A 208 VAL ALA THR ALA ARG ALA PRO LEU HIS SER VAL GLY TYR SEQRES 9 A 208 THR ALA LEU VAL GLY SER ASP ALA GLU SER TRP GLY TRP SEQRES 10 A 208 ASP LEU GLY ARG SER ARG LEU TYR HIS ASP GLY LYS ASN SEQRES 11 A 208 GLN PRO GLY VAL ALA TYR PRO ALA PHE LEU GLY PRO ASP SEQRES 12 A 208 GLU ALA PHE ALA LEU PRO ASP SER LEU LEU VAL VAL LEU SEQRES 13 A 208 ASP MET ASP GLU GLY THR LEU SER PHE ILE VAL ASP GLY SEQRES 14 A 208 GLN TYR LEU GLY VAL ALA PHE ARG GLY LEU LYS GLY LYS SEQRES 15 A 208 LYS LEU TYR PRO VAL VAL SER ALA VAL TRP GLY HIS CYS SEQRES 16 A 208 GLU VAL THR MET ARG TYR ILE ASN GLY LEU ASP PRO GLU HET FLC A 301 13 HET 60P A 302 9 HET 60P A 303 9 HET 60P A 304 9 HET CL A 305 1 HET SO4 A 306 5 HET SO4 A 307 5 HETNAM FLC CITRATE ANION HETNAM 60P 3-METHYLTHIOPHENE-2-CARBOXYLIC ACID HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 2 FLC C6 H5 O7 3- FORMUL 3 60P 3(C6 H6 O2 S) FORMUL 6 CL CL 1- FORMUL 7 SO4 2(O4 S 2-) FORMUL 9 HOH *140(H2 O) HELIX 1 AA1 PRO A 34 ASP A 42 1 9 HELIX 2 AA2 GLY A 47 HIS A 54 1 8 HELIX 3 AA3 PRO A 105 ARG A 109 5 5 SHEET 1 AA1 3 TRP A 56 ARG A 61 0 SHEET 2 AA1 3 SER A 83 GLY A 89 -1 O ARG A 88 N ASN A 57 SHEET 3 AA1 3 HIS A 125 VAL A 127 -1 O SER A 126 N THR A 84 SHEET 1 AA2 7 TRP A 56 ARG A 61 0 SHEET 2 AA2 7 SER A 83 GLY A 89 -1 O ARG A 88 N ASN A 57 SHEET 3 AA2 7 TYR A 210 ALA A 215 -1 O ALA A 215 N ASP A 85 SHEET 4 AA2 7 VAL A 114 ALA A 118 -1 N ALA A 118 O TYR A 210 SHEET 5 AA2 7 SER A 139 ASP A 143 -1 O TRP A 142 N VAL A 115 SHEET 6 AA2 7 ARG A 148 HIS A 151 -1 O ARG A 148 N ASP A 143 SHEET 7 AA2 7 VAL A 159 ALA A 160 -1 O VAL A 159 N LEU A 149 SHEET 1 AA3 7 VAL A 65 LYS A 68 0 SHEET 2 AA3 7 ASP A 71 ARG A 77 -1 O HIS A 76 N PHE A 66 SHEET 3 AA3 7 GLU A 221 LEU A 230 -1 O MET A 224 N LEU A 73 SHEET 4 AA3 7 LEU A 97 ASN A 103 -1 N ASN A 103 O THR A 223 SHEET 5 AA3 7 SER A 176 ASP A 182 -1 O VAL A 179 N TRP A 100 SHEET 6 AA3 7 THR A 187 VAL A 192 -1 O ILE A 191 N LEU A 178 SHEET 7 AA3 7 GLN A 195 PHE A 201 -1 O ALA A 200 N LEU A 188 CISPEP 1 TYR A 161 PRO A 162 0 -0.66 CRYST1 63.617 84.000 68.447 90.00 90.00 90.00 C 2 2 21 8 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 0.015719 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011905 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014610 0.00000 CONECT 1596 1597 1602 1603 CONECT 1597 1596 1598 CONECT 1598 1597 1599 1600 1608 CONECT 1599 1598 1604 1605 CONECT 1600 1598 1601 CONECT 1601 1600 1606 1607 CONECT 1602 1596 CONECT 1603 1596 CONECT 1604 1599 CONECT 1605 1599 CONECT 1606 1601 CONECT 1607 1601 CONECT 1608 1598 CONECT 1609 1610 1613 CONECT 1610 1609 1611 1615 CONECT 1611 1610 1612 1614 CONECT 1612 1611 1613 CONECT 1613 1609 1612 CONECT 1614 1611 CONECT 1615 1610 1616 1617 CONECT 1616 1615 CONECT 1617 1615 CONECT 1618 1619 1622 CONECT 1619 1618 1620 1624 CONECT 1620 1619 1621 1623 CONECT 1621 1620 1622 CONECT 1622 1618 1621 CONECT 1623 1620 CONECT 1624 1619 1625 1626 CONECT 1625 1624 CONECT 1626 1624 CONECT 1627 1628 1631 CONECT 1628 1627 1629 1633 CONECT 1629 1628 1630 1632 CONECT 1630 1629 1631 CONECT 1631 1627 1630 CONECT 1632 1629 CONECT 1633 1628 1634 1635 CONECT 1634 1633 CONECT 1635 1633 CONECT 1637 1638 1639 1640 1641 CONECT 1638 1637 CONECT 1639 1637 CONECT 1640 1637 CONECT 1641 1637 CONECT 1642 1643 1644 1645 1646 CONECT 1643 1642 CONECT 1644 1642 CONECT 1645 1642 CONECT 1646 1642 MASTER 239 0 7 3 17 0 0 6 1756 1 50 16 END