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