PDB Short entry for 4JEG HEADER SIGNALING PROTEIN/PROTEIN BINDING 26-FEB-13 4JEG TITLE CRYSTAL STRUCTURE OF MONOBODY CS1/SHP2 C-SH2 DOMAIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-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 CS1; 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 5 12-MAR-14 4JEG 1 AUTHOR REVDAT 4 20-NOV-13 4JEG 1 REMARK REVDAT 3 25-SEP-13 4JEG 1 JRNL REVDAT 2 11-SEP-13 4JEG 1 JRNL REVDAT 1 28-AUG-13 4JEG 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. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10352 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 498 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 19.3477 - 3.6433 1.00 2551 121 0.1683 0.1863 REMARK 3 2 3.6433 - 2.8949 1.00 2442 130 0.1772 0.2068 REMARK 3 3 2.8949 - 2.5299 1.00 2441 132 0.2158 0.3047 REMARK 3 4 2.5299 - 2.3000 0.99 2420 115 0.2370 0.3141 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 : 0.40 REMARK 3 B_SOL : 40.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22390 REMARK 3 B22 (A**2) : -0.22390 REMARK 3 B33 (A**2) : 0.44790 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 : 0.004 1682 REMARK 3 ANGLE : 0.885 2284 REMARK 3 CHIRALITY : 0.062 249 REMARK 3 PLANARITY : 0.004 287 REMARK 3 DIHEDRAL : 14.989 605 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 4JEG 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 RCSB077942. 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 : 6.5 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 : 10358 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 19.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.42300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400 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 (%): 47.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M BIS-TRIS, 0.2M REMARK 280 SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 10.59333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.18667 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 15.89000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.48333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 5.29667 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: 2110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 97 REMARK 465 LEU A 98 REMARK 465 LYS A 99 REMARK 465 TYR A 100 REMARK 465 PRO A 101 REMARK 465 GLY A 158 REMARK 465 GLU A 159 REMARK 465 SER A 160 REMARK 465 ASN A 161 REMARK 465 LYS A 220 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 LEU A 117 112.72 -162.74 REMARK 500 LYS A 129 -13.59 -143.21 REMARK 500 VAL A 181 41.52 -109.08 REMARK 500 LYS A 213 -94.61 -127.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JE4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MONOBODY NSA1/SHP2 N-SH2 DOMAIN COMPLEX DBREF 4JEG A 97 217 UNP Q06124 PTN11_HUMAN 97 217 DBREF 4JEG B 1 94 PDB 4JEG 4JEG 1 94 SEQADV 4JEG LYS A 218 UNP Q06124 EXPRESSION TAG SEQADV 4JEG GLU A 219 UNP Q06124 EXPRESSION TAG SEQADV 4JEG LYS A 220 UNP Q06124 EXPRESSION TAG SEQRES 1 A 124 GLU LEU LYS TYR PRO LEU ASN CYS ALA ASP PRO THR SER SEQRES 2 A 124 GLU ARG TRP PHE HIS GLY HIS LEU SER GLY LYS GLU ALA SEQRES 3 A 124 GLU LYS LEU LEU THR GLU LYS GLY LYS HIS GLY SER PHE SEQRES 4 A 124 LEU VAL ARG GLU SER GLN SER HIS PRO GLY ASP PHE VAL SEQRES 5 A 124 LEU SER VAL ARG THR GLY ASP ASP LYS GLY GLU SER ASN SEQRES 6 A 124 ASP GLY LYS SER LYS VAL THR HIS VAL MET ILE ARG CYS SEQRES 7 A 124 GLN GLU LEU LYS TYR ASP VAL GLY GLY GLY GLU ARG PHE SEQRES 8 A 124 ASP SER LEU THR ASP LEU VAL GLU HIS TYR LYS LYS ASN SEQRES 9 A 124 PRO MET VAL GLU THR LEU GLY THR VAL LEU GLN LEU LYS SEQRES 10 A 124 GLN PRO LEU ASN LYS 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 TYR TRP PRO TYR TYR 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 SER TYR SEQRES 7 B 94 ASP SER TYR TYR TYR TYR GLY SER PRO ILE SER ILE ASN SEQRES 8 B 94 TYR ARG THR FORMUL 3 HOH *80(H2 O) HELIX 1 1 SER A 118 LYS A 129 1 12 HELIX 2 2 SER A 189 ASN A 200 1 12 SHEET 1 A 4 PHE A 135 GLU A 139 0 SHEET 2 A 4 PHE A 147 GLY A 154 -1 O SER A 150 N LEU A 136 SHEET 3 A 4 LYS A 166 GLN A 175 -1 O THR A 168 N VAL A 151 SHEET 4 A 4 LYS A 178 ASP A 180 -1 O ASP A 180 N ARG A 173 SHEET 1 B 7 PHE A 135 GLU A 139 0 SHEET 2 B 7 PHE A 147 GLY A 154 -1 O SER A 150 N LEU A 136 SHEET 3 B 7 LYS A 166 GLN A 175 -1 O THR A 168 N VAL A 151 SHEET 4 B 7 TYR B 45 PRO B 52 -1 O TRP B 46 N HIS A 169 SHEET 5 B 7 TYR B 31 GLU B 38 -1 N TYR B 32 O VAL B 51 SHEET 6 B 7 ASP B 68 GLY B 76 -1 O TYR B 74 N VAL B 33 SHEET 7 B 7 ILE B 88 ARG B 93 -1 O ILE B 90 N ILE B 71 SHEET 1 C 2 VAL A 203 THR A 205 0 SHEET 2 C 2 THR A 208 LEU A 210 -1 O LEU A 210 N VAL A 203 SHEET 1 D 3 GLU B 9 THR B 14 0 SHEET 2 D 3 SER B 17 SER B 21 -1 O LEU B 19 N VAL B 11 SHEET 3 D 3 THR B 57 SER B 61 -1 O ILE B 60 N LEU B 18 SSBOND 1 CYS A 104 CYS A 174 1555 1555 2.03 CISPEP 1 VAL B 4 PRO B 5 0 2.58 CISPEP 2 TRP B 42 PRO B 43 0 3.69 CRYST1 111.700 111.700 31.780 90.00 90.00 120.00 P 61 6 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 0.008953 0.005169 0.000000 0.00000 SCALE2 0.000000 0.010338 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031466 0.00000