PDB Short entry for 4JE4 HEADER SIGNALING PROTEIN/PROTEIN BINDING 26-FEB-13 4JE4 TITLE CRYSTAL STRUCTURE OF MONOBODY NSA1/SHP2 N-SH2 DOMAIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL SH2 DOMAIN; COMPND 5 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE 1D, PTP-1D, PROTEIN-TYROSINE COMPND 6 PHOSPHATASE 2C, PTP-2C, SH-PTP2, SHP-2, SHP2, SH-PTP3; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: MONOBODY NSA1; COMPND 10 CHAIN: B; COMPND 11 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: PTP2C, PTPN11, SHPTP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHBT; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PHFT2 KEYWDS ENGINEERED BINDING PROTEIN, SHP2 SH2-MONOBODY COMPLEX, PHOSPHATASE, KEYWDS 2 PHOSPHOTYROSINE BINDING, PHOSPHORYLATION, SIGNALING PROTEIN-PROTEIN KEYWDS 3 BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.SHA,S.KOIDE REVDAT 4 12-MAR-14 4JE4 1 AUTHOR REVDAT 3 25-SEP-13 4JE4 1 JRNL REVDAT 2 11-SEP-13 4JE4 1 JRNL REVDAT 1 28-AUG-13 4JE4 0 JRNL AUTH F.SHA,E.B.GENCER,S.GEORGEON,A.KOIDE,N.YASUI,S.KOIDE, JRNL AUTH 2 O.HANTSCHEL JRNL TITL DISSECTION OF THE BCR-ABL SIGNALING NETWORK USING HIGHLY JRNL TITL 2 SPECIFIC MONOBODY INHIBITORS TO THE SHP2 SH2 DOMAINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 14924 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23980151 JRNL DOI 10.1073/PNAS.1303640110 REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.8 REMARK 3 NUMBER OF REFLECTIONS : 6926 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.530 REMARK 3 FREE R VALUE TEST SET COUNT : 314 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 34.5529 - 2.9054 0.94 3827 198 0.1986 0.2459 REMARK 3 2 2.9054 - 2.3100 0.71 2785 116 0.2178 0.2815 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 31.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.00580 REMARK 3 B22 (A**2) : -0.97180 REMARK 3 B33 (A**2) : 0.97760 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.003 1573 REMARK 3 ANGLE : 0.768 2145 REMARK 3 CHIRALITY : 0.051 234 REMARK 3 PLANARITY : 0.004 272 REMARK 3 DIHEDRAL : 12.294 558 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 4JE4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-13. REMARK 100 THE RCSB ID CODE IS RCSB077930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979180 REMARK 200 MONOCHROMATOR : SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8427 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.310 REMARK 200 RESOLUTION RANGE LOW (A) : 34.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.27700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.1M TRIS-HCL, 0.2M REMARK 280 MAGNESIUM CHLORIDE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 15.29050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.22050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.54900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.22050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.29050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.54900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 1 REMARK 465 THR A 2 REMARK 465 GLU A 105 REMARK 465 LYS A 106 REMARK 465 VAL B 1 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 ARG A 4 -77.41 72.16 REMARK 500 SER B 85 -149.40 -163.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JEG RELATED DB: PDB DBREF 4JE4 A 1 103 UNP Q06124 PTN11_HUMAN 1 103 DBREF 4JE4 B 1 94 PDB 4JE4 4JE4 1 94 SEQADV 4JE4 LYS A 104 UNP Q06124 EXPRESSION TAG SEQADV 4JE4 GLU A 105 UNP Q06124 EXPRESSION TAG SEQADV 4JE4 LYS A 106 UNP Q06124 EXPRESSION TAG SEQRES 1 A 106 MET THR SER ARG ARG TRP PHE HIS PRO ASN ILE THR GLY SEQRES 2 A 106 VAL GLU ALA GLU ASN LEU LEU LEU THR ARG GLY VAL ASP SEQRES 3 A 106 GLY SER PHE LEU ALA ARG PRO SER LYS SER ASN PRO GLY SEQRES 4 A 106 ASP PHE THR LEU SER VAL ARG ARG ASN GLY ALA VAL THR SEQRES 5 A 106 HIS ILE LYS ILE GLN ASN THR GLY ASP TYR TYR ASP LEU SEQRES 6 A 106 TYR GLY GLY GLU LYS PHE ALA THR LEU ALA GLU LEU VAL SEQRES 7 A 106 GLN TYR TYR MET GLU HIS HIS GLY GLN LEU LYS GLU LYS SEQRES 8 A 106 ASN GLY ASP VAL ILE GLU LEU LYS TYR PRO LEU ASN LYS SEQRES 9 A 106 GLU LYS SEQRES 1 B 94 VAL SER SER VAL PRO THR LYS LEU GLU VAL VAL ALA ALA SEQRES 2 B 94 THR PRO THR SER LEU LEU ILE SER TRP ASP ALA PRO ALA SEQRES 3 B 94 VAL THR VAL ASP TYR TYR VAL ILE THR TYR GLY GLU THR SEQRES 4 B 94 GLY SER GLY GLY TYR ALA TRP GLN GLU PHE GLU VAL PRO SEQRES 5 B 94 GLY SER LYS SER THR ALA THR ILE SER GLY LEU LYS PRO SEQRES 6 B 94 GLY VAL ASP TYR THR ILE THR VAL TYR ALA GLY TYR TYR SEQRES 7 B 94 GLY TYR PRO THR TYR TYR SER SER PRO ILE SER ILE ASN SEQRES 8 B 94 TYR ARG THR FORMUL 3 HOH *85(H2 O) HELIX 1 1 THR A 12 GLY A 24 1 13 HELIX 2 2 THR A 73 HIS A 84 1 12 SHEET 1 A 5 TYR A 63 ASP A 64 0 SHEET 2 A 5 ALA A 50 ASN A 58 -1 N GLN A 57 O ASP A 64 SHEET 3 A 5 PHE A 41 ARG A 47 -1 N ARG A 47 O ALA A 50 SHEET 4 A 5 SER A 28 PRO A 33 -1 N ARG A 32 O THR A 42 SHEET 5 A 5 TYR A 100 PRO A 101 1 O TYR A 100 N PHE A 29 SHEET 1 B 6 TYR A 63 ASP A 64 0 SHEET 2 B 6 ALA A 50 ASN A 58 -1 N GLN A 57 O ASP A 64 SHEET 3 B 6 TYR B 83 ARG B 93 -1 O TYR B 84 N HIS A 53 SHEET 4 B 6 ASP B 68 TYR B 77 -1 N TYR B 77 O TYR B 83 SHEET 5 B 6 TYR B 31 GLU B 38 -1 N THR B 35 O THR B 72 SHEET 6 B 6 GLN B 47 PRO B 52 -1 O VAL B 51 N TYR B 32 SHEET 1 C 3 THR B 6 ALA B 13 0 SHEET 2 C 3 LEU B 18 ASP B 23 -1 O SER B 21 N GLU B 9 SHEET 3 C 3 THR B 57 ILE B 60 -1 O ILE B 60 N LEU B 18 CISPEP 1 PRO A 38 GLY A 39 0 -5.86 CISPEP 2 TYR B 80 PRO B 81 0 1.61 CRYST1 30.581 69.098 84.441 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 0.032700 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011843 0.00000