HEADER PEPTIDE BINDING PROTEIN 29-JUL-21 7RNV TITLE SH2 DOMAIN OF GUANINE NUCLEOTIDE EXCHANGE FACTOR VAV2 IN COMPLEX WITH TITLE 2 AN ACTIN PEPTIDE WITH PHOSPHORYLATED TYROSINE 53 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANINE NUCLEOTIDE EXCHANGE FACTOR VAV2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH2 DOMAIN (UNP RESIDUES 665-774); COMPND 5 SYNONYM: VAV-2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ACTIN, ALPHA SKELETAL MUSCLE; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 52-60; COMPND 11 SYNONYM: ALPHA-ACTIN-1; COMPND 12 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: VAV2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS PHOSPHORYLATED TYROSINE BINDING PROTEIN, ACTIN PEPTIDE, PEPTIDE KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.DAI,J.R.HORTON,X.CHENG REVDAT 4 16-OCT-24 7RNV 1 REMARK REVDAT 3 15-NOV-23 7RNV 1 REMARK REVDAT 2 18-OCT-23 7RNV 1 REMARK REVDAT 1 11-AUG-21 7RNV 0 JRNL AUTH A.AMELIE,S.DAI,X.SHEN,J.R.HORTON,X.ZHANG,X.CHENG JRNL TITL THE FUNCTIONAL ANALYSIS OF A MAJOR TYROSINE PHOSPHORYLATION JRNL TITL 2 SITE ON ACTIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 7686 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.890 REMARK 3 FREE R VALUE TEST SET COUNT : 760 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 26.8000 - 3.6700 1.00 1511 172 0.1861 0.2207 REMARK 3 2 3.6700 - 2.9200 1.00 1445 154 0.2194 0.2878 REMARK 3 3 2.9200 - 2.5500 0.99 1415 154 0.2779 0.3205 REMARK 3 4 2.5500 - 2.3200 0.98 1398 150 0.2926 0.3101 REMARK 3 5 2.3200 - 2.1500 0.82 1157 130 0.3761 0.4250 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.341 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.816 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.47 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 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 : 0.002 940 REMARK 3 ANGLE : 0.465 1273 REMARK 3 CHIRALITY : 0.043 135 REMARK 3 PLANARITY : 0.002 161 REMARK 3 DIHEDRAL : 22.169 341 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 7RNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000258640. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-003 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7715 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 26.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 2IUI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M REMARK 280 TRIS HYDROCHLORIDE, PH 8.5, 30% PEG4000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z 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 REMARK 290 7555 -X+1/2,Y+1/2,-Z 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 0.00000 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 0.00000 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 30.74600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.71600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.74600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.71600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.74600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.71600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.74600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.71600 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 915 LIES ON A SPECIAL POSITION. 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 660 REMARK 465 PRO A 661 REMARK 465 LEU A 662 REMARK 465 GLY A 663 REMARK 465 SER A 664 REMARK 465 ARG A 770 REMARK 465 GLU A 771 REMARK 465 ARG A 772 REMARK 465 SER A 773 REMARK 465 ALA A 774 REMARK 465 GLY A 775 REMARK 465 ILE A 776 REMARK 465 LEU A 777 REMARK 465 LYS B 50 REMARK 465 ASP B 51 REMARK 465 GLU B 57 REMARK 465 ALA B 58 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 665 CG CD OE1 OE2 REMARK 470 LYS A 688 CG CD CE NZ REMARK 470 LYS A 753 CG CD CE NZ REMARK 470 LYS A 757 CG CD CE NZ 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 ASN A 714 -106.43 53.11 REMARK 500 ASN A 714 -106.33 53.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RNV A 665 774 UNP P52735 VAV2_HUMAN 665 774 DBREF 7RNV B 50 58 UNP P68133 ACTS_HUMAN 52 60 SEQADV 7RNV GLY A 660 UNP P52735 EXPRESSION TAG SEQADV 7RNV PRO A 661 UNP P52735 EXPRESSION TAG SEQADV 7RNV LEU A 662 UNP P52735 EXPRESSION TAG SEQADV 7RNV GLY A 663 UNP P52735 EXPRESSION TAG SEQADV 7RNV SER A 664 UNP P52735 EXPRESSION TAG SEQADV 7RNV GLY A 775 UNP P52735 EXPRESSION TAG SEQADV 7RNV ILE A 776 UNP P52735 EXPRESSION TAG SEQADV 7RNV LEU A 777 UNP P52735 EXPRESSION TAG SEQRES 1 A 118 GLY PRO LEU GLY SER GLU ILE ASP TYR THR ALA TYR PRO SEQRES 2 A 118 TRP PHE ALA GLY ASN MET GLU ARG GLN GLN THR ASP ASN SEQRES 3 A 118 LEU LEU LYS SER HIS ALA SER GLY THR TYR LEU ILE ARG SEQRES 4 A 118 GLU ARG PRO ALA GLU ALA GLU ARG PHE ALA ILE SER ILE SEQRES 5 A 118 LYS PHE ASN ASP GLU VAL LYS HIS ILE LYS VAL VAL GLU SEQRES 6 A 118 LYS ASP ASN TRP ILE HIS ILE THR GLU ALA LYS LYS PHE SEQRES 7 A 118 ASP SER LEU LEU GLU LEU VAL GLU TYR TYR GLN CYS HIS SEQRES 8 A 118 SER LEU LYS GLU SER PHE LYS GLN LEU ASP THR THR LEU SEQRES 9 A 118 LYS TYR PRO TYR LYS SER ARG GLU ARG SER ALA GLY ILE SEQRES 10 A 118 LEU SEQRES 1 B 9 LYS ASP SER PTR VAL GLY ASP GLU ALA MODRES 7RNV PTR B 53 TYR MODIFIED RESIDUE HET PTR B 53 16 HET EDO A 801 4 HET EDO A 802 4 HETNAM PTR O-PHOSPHOTYROSINE HETNAM EDO 1,2-ETHANEDIOL HETSYN PTR PHOSPHONOTYROSINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PTR C9 H12 N O6 P FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *37(H2 O) HELIX 1 AA1 ASP A 667 TYR A 671 5 5 HELIX 2 AA2 GLU A 679 LYS A 688 1 10 HELIX 3 AA3 SER A 739 HIS A 750 1 12 HELIX 4 AA4 SER A 751 SER A 755 5 5 SHEET 1 AA1 4 PHE A 674 ASN A 677 0 SHEET 2 AA1 4 THR A 694 GLU A 699 1 O ILE A 697 N ALA A 675 SHEET 3 AA1 4 PHE A 707 PHE A 713 -1 O LYS A 712 N THR A 694 SHEET 4 AA1 4 GLU A 716 LYS A 721 -1 O ILE A 720 N ILE A 709 SHEET 1 AA2 3 PHE A 674 ASN A 677 0 SHEET 2 AA2 3 THR A 694 GLU A 699 1 O ILE A 697 N ALA A 675 SHEET 3 AA2 3 TYR A 765 PRO A 766 1 O TYR A 765 N TYR A 695 SHEET 1 AA3 3 VAL A 723 LYS A 725 0 SHEET 2 AA3 3 TRP A 728 THR A 732 -1 O HIS A 730 N VAL A 723 SHEET 3 AA3 3 LYS A 735 PHE A 737 -1 O PHE A 737 N ILE A 729 SSBOND 1 CYS A 749 CYS A 749 1555 4556 2.04 LINK C SER B 52 N PTR B 53 1555 1555 1.33 LINK C PTR B 53 N VAL B 54 1555 1555 1.33 CRYST1 61.492 109.432 41.867 90.00 90.00 90.00 C 2 2 2 8 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 0.016262 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009138 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023885 0.00000