HEADER PEPTIDE BINDING PROTEIN 18-MAY-22 7XTY TITLE CRYSTAL STRUCTURE OF THE SECOND PDZ DOMAIN FROM HUMAN PTPN13 IN TITLE 2 COMPLEX WITH APC PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 13; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: FAS-ASSOCIATED PROTEIN-TYROSINE PHOSPHATASE 1,FAP-1,PTP-BAS, COMPND 5 PROTEIN-TYROSINE PHOSPHATASE 1E,PTP-E1,HPTPE1,PROTEIN-TYROSINE COMPND 6 PHOSPHATASE PTPL1; COMPND 7 EC: 3.1.3.48; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: APC-PEPTIDE; COMPND 11 CHAIN: C, D; COMPND 12 SYNONYM: PROTEIN APC,DELETED IN POLYPOSIS 2.5; COMPND 13 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: PTPN13, PNP1, PTP1E, PTPL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28AS; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS PROTEIN-PROTEIN COMPLEX, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.Q.JING,X.N.SUN,W.H.MA,W.J.ZHOU,D.L.WU REVDAT 2 29-NOV-23 7XTY 1 REMARK REVDAT 1 17-MAY-23 7XTY 0 JRNL AUTH L.Q.JING,X.N.SUN,W.H.MA,W.J.ZHOU,D.L.WU JRNL TITL TARGETING PTPN13 WITH 11 AMINO ACID PEPTIDES OF C-TERMINAL JRNL TITL 2 APC PREVENTS IMMUNE EVASION OF COLORECTAL CANCER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 12144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1215 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 3.4652 - 3.0275 1.00 1230 136 0.1836 0.2751 REMARK 3 2 3.0275 - 2.7509 1.00 1237 138 0.1972 0.2424 REMARK 3 3 2.7509 - 2.5538 1.00 1237 137 0.2068 0.2242 REMARK 3 4 2.5538 - 2.4032 1.00 1225 137 0.2163 0.2678 REMARK 3 5 2.4032 - 2.2829 0.98 1194 133 0.1965 0.2627 REMARK 3 6 2.2829 - 2.1836 0.94 1165 129 0.2079 0.2672 REMARK 3 7 2.1836 - 2.1000 0.88 1079 120 0.2190 0.2407 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.28 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 7XTY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : SIEMENS-NICOLET REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12152 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.17300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.37400 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: 3LNY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRIC ACID (PH 3.5), 3M NACL, PH REMARK 280 6.8, VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 48.73100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.20350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.73100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.20350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 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: 900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 LYS A 1362 REMARK 465 PRO A 1363 REMARK 465 GLN A 1453 REMARK 465 SER A 1454 REMARK 465 PRO A 1455 REMARK 465 THR A 1456 REMARK 465 GLN B 1453 REMARK 465 SER B 1454 REMARK 465 PRO B 1455 REMARK 465 THR B 1456 REMARK 465 ARG C 2833 REMARK 465 HIS C 2834 REMARK 465 SER C 2835 REMARK 465 ARG D 2833 REMARK 465 HIS D 2834 REMARK 465 SER D 2835 REMARK 465 GLY D 2836 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A1371 CA - CB - CG ANGL. DEV. = 16.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A1375 48.08 39.46 REMARK 500 ARG A1391 -133.70 48.65 REMARK 500 ASN A1422 -124.38 46.92 REMARK 500 GLN A1443 -134.36 55.82 REMARK 500 HIS B1392 -1.66 61.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XTY A 1362 1456 UNP Q12923 PTN13_HUMAN 1362 1456 DBREF 7XTY B 1362 1456 UNP Q12923 PTN13_HUMAN 1362 1456 DBREF 7XTY C 2833 2843 UNP P25054 APC_HUMAN 2833 2843 DBREF 7XTY D 2833 2843 UNP P25054 APC_HUMAN 2833 2843 SEQRES 1 A 95 LYS PRO GLY ASP ILE PHE GLU VAL GLU LEU ALA LYS ASN SEQRES 2 A 95 ASP ASN SER LEU GLY ILE SER VAL THR GLY GLY VAL ASN SEQRES 3 A 95 THR SER VAL ARG HIS GLY GLY ILE TYR VAL LYS ALA VAL SEQRES 4 A 95 ILE PRO GLN GLY ALA ALA GLU SER ASP GLY ARG ILE HIS SEQRES 5 A 95 LYS GLY ASP ARG VAL LEU ALA VAL ASN GLY VAL SER LEU SEQRES 6 A 95 GLU GLY ALA THR HIS LYS GLN ALA VAL GLU THR LEU ARG SEQRES 7 A 95 ASN THR GLY GLN VAL VAL HIS LEU LEU LEU GLU LYS GLY SEQRES 8 A 95 GLN SER PRO THR SEQRES 1 B 95 LYS PRO GLY ASP ILE PHE GLU VAL GLU LEU ALA LYS ASN SEQRES 2 B 95 ASP ASN SER LEU GLY ILE SER VAL THR GLY GLY VAL ASN SEQRES 3 B 95 THR SER VAL ARG HIS GLY GLY ILE TYR VAL LYS ALA VAL SEQRES 4 B 95 ILE PRO GLN GLY ALA ALA GLU SER ASP GLY ARG ILE HIS SEQRES 5 B 95 LYS GLY ASP ARG VAL LEU ALA VAL ASN GLY VAL SER LEU SEQRES 6 B 95 GLU GLY ALA THR HIS LYS GLN ALA VAL GLU THR LEU ARG SEQRES 7 B 95 ASN THR GLY GLN VAL VAL HIS LEU LEU LEU GLU LYS GLY SEQRES 8 B 95 GLN SER PRO THR SEQRES 1 C 11 ARG HIS SER GLY SER TYR LEU VAL THR SER VAL SEQRES 1 D 11 ARG HIS SER GLY SER TYR LEU VAL THR SER VAL FORMUL 5 HOH *131(H2 O) HELIX 1 AA1 ILE A 1401 SER A 1408 1 8 HELIX 2 AA2 THR A 1430 ASN A 1440 1 11 HELIX 3 AA3 VAL B 1390 GLY B 1393 5 4 HELIX 4 AA4 GLY B 1404 GLY B 1410 1 7 HELIX 5 AA5 THR B 1430 THR B 1441 1 12 SHEET 1 AA1 4 ILE A1366 ALA A1372 0 SHEET 2 AA1 4 VAL A1444 GLU A1450 -1 O LEU A1449 N PHE A1367 SHEET 3 AA1 4 ARG A1417 VAL A1421 -1 N LEU A1419 O LEU A1448 SHEET 4 AA1 4 VAL A1424 SER A1425 -1 O VAL A1424 N VAL A1421 SHEET 1 AA2 3 ILE A1395 VAL A1400 0 SHEET 2 AA2 3 ILE A1380 GLY A1384 -1 N SER A1381 O LYS A1398 SHEET 3 AA2 3 THR C2841 VAL C2843 -1 O VAL C2843 N ILE A1380 SHEET 1 AA3 4 ILE B1366 ALA B1372 0 SHEET 2 AA3 4 VAL B1444 GLU B1450 -1 O LEU B1447 N VAL B1369 SHEET 3 AA3 4 ARG B1417 VAL B1421 -1 N LEU B1419 O LEU B1448 SHEET 4 AA3 4 VAL B1424 SER B1425 -1 O VAL B1424 N VAL B1421 SHEET 1 AA4 3 ILE B1395 VAL B1400 0 SHEET 2 AA4 3 ILE B1380 GLY B1384 -1 N SER B1381 O LYS B1398 SHEET 3 AA4 3 THR D2841 VAL D2843 -1 O THR D2841 N VAL B1382 CRYST1 97.462 32.407 69.917 90.00 108.86 90.00 C 1 2 1 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 0.010260 0.000000 0.003504 0.00000 SCALE2 0.000000 0.030858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015114 0.00000