HEADER TRANSFERASE 01-AUG-16 5GP7 TITLE STRUCTURAL BASIS FOR THE BINDING BETWEEN TANKYRASE-1 AND USP25 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TANKYRASE-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 799-957; COMPND 5 EC: 2.4.2.30; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 25; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 1046-1055; COMPND 11 SYNONYM: USP25; COMPND 12 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: TNKS; 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: USP25; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TANKYRASE, USP25, ANKYRIN REPEATS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,D.XU,T.FU,L.PAN REVDAT 3 08-NOV-23 5GP7 1 REMARK REVDAT 2 27-SEP-17 5GP7 1 REMARK REVDAT 1 12-JUL-17 5GP7 0 JRNL AUTH D.XU,J.LIU,T.FU,B.SHAN,L.QIAN,L.PAN,J.YUAN JRNL TITL USP25 REGULATES WNT SIGNALING BY CONTROLLING THE STABILITY JRNL TITL 2 OF TANKYRASES JRNL REF GENES DEV. V. 31 1024 2017 JRNL REFN ISSN 1549-5477 JRNL PMID 28619731 JRNL DOI 10.1101/GAD.300889.117 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 25690 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 (%) : 7.790 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 39.3161 - 3.6203 1.00 1750 148 0.1626 0.1901 REMARK 3 2 3.6203 - 2.8738 1.00 1725 146 0.1609 0.2002 REMARK 3 3 2.8738 - 2.5106 1.00 1708 143 0.1658 0.2016 REMARK 3 4 2.5106 - 2.2811 1.00 1728 146 0.1641 0.1894 REMARK 3 5 2.2811 - 2.1176 1.00 1699 144 0.1672 0.2013 REMARK 3 6 2.1176 - 1.9928 1.00 1713 145 0.1618 0.2030 REMARK 3 7 1.9928 - 1.8930 1.00 1716 144 0.1780 0.2106 REMARK 3 8 1.8930 - 1.8106 0.99 1692 144 0.1849 0.2519 REMARK 3 9 1.8106 - 1.7409 1.00 1695 142 0.1844 0.2130 REMARK 3 10 1.7409 - 1.6808 1.00 1710 145 0.1898 0.2495 REMARK 3 11 1.6808 - 1.6282 1.00 1688 142 0.1958 0.2360 REMARK 3 12 1.6282 - 1.5817 0.99 1704 145 0.1938 0.2176 REMARK 3 13 1.5817 - 1.5401 0.95 1599 135 0.2023 0.2388 REMARK 3 14 1.5401 - 1.5025 0.91 1563 131 0.2207 0.2527 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) : 20.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 1346 REMARK 3 ANGLE : 0.956 1836 REMARK 3 CHIRALITY : 0.058 212 REMARK 3 PLANARITY : 0.007 245 REMARK 3 DIHEDRAL : 9.453 836 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 5GP7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1300001218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97776 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9300 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) : 1.53 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: HKL-3000 REMARK 200 STARTING MODEL: 3TWU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES/SODIUM HYDROXIDE, 200 MM REMARK 280 SODIUM CHLORIDE, 20% (W/V) PEG 6000, PH 7.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.62100 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 GLU A 958 REMARK 465 ASN A 959 REMARK 465 LEU A 960 REMARK 465 TYR A 961 REMARK 465 PHE A 962 REMARK 465 GLN A 963 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 GLN A 834 OE1 NE2 REMARK 470 SER B1046 OG REMARK 470 LEU B1047 CG CD1 CD2 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 1238 O HOH A 1254 2.11 REMARK 500 O HOH A 1195 O HOH A 1259 2.18 REMARK 500 O HOH A 1288 O HOH A 1306 2.18 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 1124 O HOH A 1137 1554 2.09 REMARK 500 O HOH A 1284 O HOH A 1303 1554 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1002 DBREF 5GP7 A 799 957 UNP O95271 TNKS1_HUMAN 799 957 DBREF 5GP7 B 1046 1055 UNP Q9UHP3 UBP25_HUMAN 1046 1055 SEQADV 5GP7 GLY A 795 UNP O95271 EXPRESSION TAG SEQADV 5GP7 PRO A 796 UNP O95271 EXPRESSION TAG SEQADV 5GP7 GLY A 797 UNP O95271 EXPRESSION TAG SEQADV 5GP7 SER A 798 UNP O95271 EXPRESSION TAG SEQADV 5GP7 GLU A 958 UNP O95271 EXPRESSION TAG SEQADV 5GP7 ASN A 959 UNP O95271 EXPRESSION TAG SEQADV 5GP7 LEU A 960 UNP O95271 EXPRESSION TAG SEQADV 5GP7 TYR A 961 UNP O95271 EXPRESSION TAG SEQADV 5GP7 PHE A 962 UNP O95271 EXPRESSION TAG SEQADV 5GP7 GLN A 963 UNP O95271 EXPRESSION TAG SEQRES 1 A 169 GLY PRO GLY SER ASP LEU LEU ARG GLY ASP ALA ALA LEU SEQRES 2 A 169 LEU ASP ALA ALA LYS LYS GLY CYS LEU ALA ARG VAL GLN SEQRES 3 A 169 LYS LEU CYS THR PRO GLU ASN ILE ASN CYS ARG ASP THR SEQRES 4 A 169 GLN GLY ARG ASN SER THR PRO LEU HIS LEU ALA ALA GLY SEQRES 5 A 169 TYR ASN ASN LEU GLU VAL ALA GLU TYR LEU LEU GLU HIS SEQRES 6 A 169 GLY ALA ASP VAL ASN ALA GLN ASP LYS GLY GLY LEU ILE SEQRES 7 A 169 PRO LEU HIS ASN ALA ALA SER TYR GLY HIS VAL ASP ILE SEQRES 8 A 169 ALA ALA LEU LEU ILE LYS TYR ASN THR CYS VAL ASN ALA SEQRES 9 A 169 THR ASP LYS TRP ALA PHE THR PRO LEU HIS GLU ALA ALA SEQRES 10 A 169 GLN LYS GLY ARG THR GLN LEU CYS ALA LEU LEU LEU ALA SEQRES 11 A 169 HIS GLY ALA ASP PRO THR MET LYS ASN GLN GLU GLY GLN SEQRES 12 A 169 THR PRO LEU ASP LEU ALA THR ALA ASP ASP ILE ARG ALA SEQRES 13 A 169 LEU LEU ILE ASP ALA MET PRO GLU ASN LEU TYR PHE GLN SEQRES 1 B 10 SER LEU SER ARG THR PRO ALA ASP GLY ARG HET GOL A1001 6 HET GOL A1002 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *245(H2 O) HELIX 1 AA1 GLY A 795 GLY A 814 1 20 HELIX 2 AA2 CYS A 815 CYS A 823 1 9 HELIX 3 AA3 THR A 839 TYR A 847 1 9 HELIX 4 AA4 ASN A 849 HIS A 859 1 11 HELIX 5 AA5 ILE A 872 GLY A 881 1 10 HELIX 6 AA6 HIS A 882 TYR A 892 1 11 HELIX 7 AA7 THR A 905 GLY A 914 1 10 HELIX 8 AA8 ARG A 915 HIS A 925 1 11 HELIX 9 AA9 THR A 938 ALA A 943 1 6 HELIX 10 AB1 ALA A 945 MET A 956 1 12 SITE 1 AC1 5 ASP A 832 GLN A 834 GLY A 835 HOH A1244 SITE 2 AC1 5 HOH B1109 SITE 1 AC2 3 PRO A 825 HOH A1113 HOH A1239 CRYST1 35.506 59.242 39.995 90.00 100.68 90.00 P 1 21 1 2 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 0.028164 0.000000 0.005309 0.00000 SCALE2 0.000000 0.016880 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025444 0.00000