HEADER SIGNALING PROTEIN 25-JAN-03 1NRV TITLE CRYSTAL STRUCTURE OF THE SH2 DOMAIN OF GRB10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 10; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SH2 DOMAIN; COMPND 5 SYNONYM: GRB10 ADAPTER PROTEIN; COMPND 6 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: GRB10 OR GRBIR OR KIAA0207; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS DIMER, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.G.STEIN,S.R.HUBBARD REVDAT 4 16-AUG-23 1NRV 1 REMARK REVDAT 3 24-FEB-09 1NRV 1 VERSN REVDAT 2 13-JAN-04 1NRV 1 JRNL REVDAT 1 15-APR-03 1NRV 0 JRNL AUTH E.G.STEIN,R.GHIRLANDO,S.R.HUBBARD JRNL TITL STRUCTURAL BASIS FOR DIMERIZATION OF THE GRB10 SRC HOMOLOGY JRNL TITL 2 2 DOMAIN. IMPLICATIONS FOR LIGAND SPECIFICITY. JRNL REF J.BIOL.CHEM. V. 278 13257 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12551896 JRNL DOI 10.1074/JBC.M212026200 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 23841 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1210 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 167 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1664 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.65000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -1.76000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.79000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.250 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.900 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.240 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.340 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26168 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 2.840 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37000 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1A81 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 8000, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 24.52000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS THE DIMER IN THE ASYMMETRIC UNIT. 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 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 490 REMARK 465 ASP A 491 REMARK 465 ASP A 492 REMARK 465 GLY A 493 REMARK 465 GLN A 494 REMARK 465 GLU B 490 REMARK 465 ASP B 491 REMARK 465 ASP B 492 REMARK 465 GLY B 493 REMARK 465 GLN B 494 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 439 29.91 -77.45 REMARK 500 LYS A 528 -63.42 -100.59 REMARK 500 GLN B 479 16.38 58.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 1NRV A 429 533 UNP Q13322 GRB10_HUMAN 487 591 DBREF 1NRV B 429 533 UNP Q13322 GRB10_HUMAN 487 591 SEQRES 1 A 105 ILE HIS ARG THR GLN HIS TRP PHE HIS GLY ARG ILE SER SEQRES 2 A 105 ARG GLU GLU SER HIS ARG ILE ILE LYS GLN GLN GLY LEU SEQRES 3 A 105 VAL ASP GLY LEU PHE LEU LEU ARG ASP SER GLN SER ASN SEQRES 4 A 105 PRO LYS ALA PHE VAL LEU THR LEU CYS HIS HIS GLN LYS SEQRES 5 A 105 ILE LYS ASN PHE GLN ILE LEU PRO CYS GLU ASP ASP GLY SEQRES 6 A 105 GLN THR PHE PHE SER LEU ASP ASP GLY ASN THR LYS PHE SEQRES 7 A 105 SER ASP LEU ILE GLN LEU VAL ASP PHE TYR GLN LEU ASN SEQRES 8 A 105 LYS GLY VAL LEU PRO CYS LYS LEU LYS HIS HIS CYS ILE SEQRES 9 A 105 ARG SEQRES 1 B 105 ILE HIS ARG THR GLN HIS TRP PHE HIS GLY ARG ILE SER SEQRES 2 B 105 ARG GLU GLU SER HIS ARG ILE ILE LYS GLN GLN GLY LEU SEQRES 3 B 105 VAL ASP GLY LEU PHE LEU LEU ARG ASP SER GLN SER ASN SEQRES 4 B 105 PRO LYS ALA PHE VAL LEU THR LEU CYS HIS HIS GLN LYS SEQRES 5 B 105 ILE LYS ASN PHE GLN ILE LEU PRO CYS GLU ASP ASP GLY SEQRES 6 B 105 GLN THR PHE PHE SER LEU ASP ASP GLY ASN THR LYS PHE SEQRES 7 B 105 SER ASP LEU ILE GLN LEU VAL ASP PHE TYR GLN LEU ASN SEQRES 8 B 105 LYS GLY VAL LEU PRO CYS LYS LEU LYS HIS HIS CYS ILE SEQRES 9 B 105 ARG FORMUL 3 HOH *179(H2 O) HELIX 1 1 SER A 441 GLN A 452 1 12 HELIX 2 2 ASP A 508 GLN A 517 1 10 HELIX 3 3 SER B 441 GLN B 452 1 12 HELIX 4 4 ASP B 508 GLN B 517 1 10 SHEET 1 A 5 PHE A 497 SER A 498 0 SHEET 2 A 5 LYS A 480 PRO A 488 -1 N LEU A 487 O SER A 498 SHEET 3 A 5 PHE A 471 HIS A 477 -1 N LEU A 475 O LYS A 482 SHEET 4 A 5 LEU A 458 ASP A 463 -1 N LEU A 460 O THR A 474 SHEET 5 A 5 HIS A 529 HIS A 530 1 O HIS A 529 N PHE A 459 SHEET 1 B 5 PHE B 497 SER B 498 0 SHEET 2 B 5 LYS B 480 PRO B 488 -1 N LEU B 487 O SER B 498 SHEET 3 B 5 PHE B 471 HIS B 477 -1 N LEU B 475 O LYS B 482 SHEET 4 B 5 LEU B 458 ASP B 463 -1 N ARG B 462 O VAL B 472 SHEET 5 B 5 HIS B 529 HIS B 530 1 O HIS B 529 N PHE B 459 CRYST1 28.820 49.040 79.610 90.00 96.62 90.00 P 1 21 1 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 0.034698 0.000000 0.004027 0.00000 SCALE2 0.000000 0.020392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012646 0.00000 MASTER 238 0 0 4 10 0 0 6 1843 2 0 18 END