HEADER SIGNALING PROTEIN/SIGNALING PROTEIN 08-AUG-00 1GCQ TITLE CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL SH3 DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: VAV PROTO-ONCOGENE; COMPND 8 CHAIN: C; COMPND 9 FRAGMENT: N-TERMINAL SH3 DOMAIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-2T; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 CELL_LINE: HEMATOPOIETIC CELLS; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS SH3 DOMAIN, PROTEIN-PROTEIN COMPLEX, GRB2, VAV, SIGNALING PROTEIN- KEYWDS 2 SIGNALING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.NISHIDA,K.NAGATA,Y.HACHIMORI,K.OGURA,F.INAGAKI REVDAT 4 27-DEC-23 1GCQ 1 REMARK SEQADV REVDAT 3 24-FEB-09 1GCQ 1 VERSN REVDAT 2 28-JAN-03 1GCQ 1 REMARK REVDAT 1 08-AUG-01 1GCQ 0 JRNL AUTH M.NISHIDA,K.NAGATA,Y.HACHIMORI,M.HORIUCHI,K.OGURA, JRNL AUTH 2 V.MANDIYAN,J.SCHLESSINGER,F.INAGAKI JRNL TITL NOVEL RECOGNITION MODE BETWEEN VAV AND GRB2 SH3 DOMAINS. JRNL REF EMBO J. V. 20 2995 2001 JRNL REFN ISSN 0261-4189 JRNL PMID 11406576 JRNL DOI 10.1093/EMBOJ/20.12.2995 REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 27162 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1358 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1481 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.10 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 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.395 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.270 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.500 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 1GCQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-AUG-00. REMARK 100 THE DEPOSITION ID IS D_1000005036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0375 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28649 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 39.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -10000. REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.19900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-METHYL-2,4-PENTANEDIOL, IMIDAZOLE, REMARK 280 MAGNESIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.2K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 41.68500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.68500 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.02500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.41000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.02500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.41000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.68500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.02500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.41000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 41.68500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.02500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.41000 REMARK 290 SMTRY3 8 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 GLY A 157 REMARK 465 ASN A 214 REMARK 465 ARG A 215 REMARK 465 ASN A 216 REMARK 465 VAL A 217 REMARK 465 GLY B 157 REMARK 465 SER B 158 REMARK 465 ASN B 216 REMARK 465 VAL B 217 REMARK 465 HIS C 660 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 SER C 592 -166.06 -164.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 218 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GCP RELATED DB: PDB REMARK 900 1GCP CONTAINS VAV SH3 DOMAINS. DBREF 1GCQ A 159 217 UNP P62993 GRB2_HUMAN 159 217 DBREF 1GCQ B 159 217 UNP P62993 GRB2_HUMAN 159 217 DBREF 1GCQ C 595 660 UNP P27870 VAV_MOUSE 595 660 SEQADV 1GCQ GLY A 157 UNP P62993 CLONING ARTIFACT SEQADV 1GCQ SER A 158 UNP P62993 CLONING ARTIFACT SEQADV 1GCQ GLY B 157 UNP P62993 CLONING ARTIFACT SEQADV 1GCQ SER B 158 UNP P62993 CLONING ARTIFACT SEQADV 1GCQ GLY C 591 UNP P27870 CLONING ARTIFACT SEQADV 1GCQ SER C 592 UNP P27870 CLONING ARTIFACT SEQADV 1GCQ HIS C 593 UNP P27870 CLONING ARTIFACT SEQADV 1GCQ MET C 594 UNP P27870 CLONING ARTIFACT SEQRES 1 A 61 GLY SER THR TYR VAL GLN ALA LEU PHE ASP PHE ASP PRO SEQRES 2 A 61 GLN GLU ASP GLY GLU LEU GLY PHE ARG ARG GLY ASP PHE SEQRES 3 A 61 ILE HIS VAL MET ASP ASN SER ASP PRO ASN TRP TRP LYS SEQRES 4 A 61 GLY ALA CYS HIS GLY GLN THR GLY MET PHE PRO ARG ASN SEQRES 5 A 61 TYR VAL THR PRO VAL ASN ARG ASN VAL SEQRES 1 B 61 GLY SER THR TYR VAL GLN ALA LEU PHE ASP PHE ASP PRO SEQRES 2 B 61 GLN GLU ASP GLY GLU LEU GLY PHE ARG ARG GLY ASP PHE SEQRES 3 B 61 ILE HIS VAL MET ASP ASN SER ASP PRO ASN TRP TRP LYS SEQRES 4 B 61 GLY ALA CYS HIS GLY GLN THR GLY MET PHE PRO ARG ASN SEQRES 5 B 61 TYR VAL THR PRO VAL ASN ARG ASN VAL SEQRES 1 C 70 GLY SER HIS MET PRO LYS MET GLU VAL PHE GLN GLU TYR SEQRES 2 C 70 TYR GLY ILE PRO PRO PRO PRO GLY ALA PHE GLY PRO PHE SEQRES 3 C 70 LEU ARG LEU ASN PRO GLY ASP ILE VAL GLU LEU THR LYS SEQRES 4 C 70 ALA GLU ALA GLU HIS ASN TRP TRP GLU GLY ARG ASN THR SEQRES 5 C 70 ALA THR ASN GLU VAL GLY TRP PHE PRO CYS ASN ARG VAL SEQRES 6 C 70 HIS PRO TYR VAL HIS HET MRD A 218 8 HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL FORMUL 4 MRD C6 H14 O2 FORMUL 5 HOH *189(H2 O) HELIX 1 1 PRO C 609 PHE C 613 5 5 SHEET 1 A 5 GLN A 201 PRO A 206 0 SHEET 2 A 5 TRP A 193 CYS A 198 -1 O TRP A 194 N PHE A 205 SHEET 3 A 5 PHE A 182 ASP A 187 -1 N HIS A 184 O ALA A 197 SHEET 4 A 5 THR A 159 ALA A 163 -1 O THR A 159 N VAL A 185 SHEET 5 A 5 VAL A 210 VAL A 213 -1 O THR A 211 N GLN A 162 SHEET 1 B 5 GLN B 201 PRO B 206 0 SHEET 2 B 5 TRP B 193 CYS B 198 -1 N TRP B 194 O PHE B 205 SHEET 3 B 5 PHE B 182 ASP B 187 -1 N HIS B 184 O ALA B 197 SHEET 4 B 5 TYR B 160 ALA B 163 -1 O VAL B 161 N ILE B 183 SHEET 5 B 5 VAL B 210 PRO B 212 -1 O THR B 211 N GLN B 162 SHEET 1 C 5 VAL C 647 PRO C 651 0 SHEET 2 C 5 TRP C 636 ASN C 641 -1 N TRP C 637 O PHE C 650 SHEET 3 C 5 ILE C 624 LYS C 629 -1 N GLU C 626 O ARG C 640 SHEET 4 C 5 LYS C 596 VAL C 599 -1 N MET C 597 O VAL C 625 SHEET 5 C 5 VAL C 655 PRO C 657 -1 O HIS C 656 N GLU C 598 CISPEP 1 ILE C 606 PRO C 607 0 -1.13 SITE 1 AC1 7 ALA A 197 CYS A 198 HIS A 199 GLY A 200 SITE 2 AC1 7 HOH A 227 HOH C 56 ILE C 624 CRYST1 48.050 126.820 83.370 90.00 90.00 90.00 C 2 2 21 16 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 0.020810 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011990 0.00000