HEADER SIGNALING PROTEIN 11-JUL-13 4LN2 TITLE THE SECOND SH3 DOMAIN FROM CAP/PONSIN IN COMPLEX WITH PROLINE RICH TITLE 2 PEPTIDE FROM VINCULIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORBIN AND SH3 DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 866-930; COMPND 5 SYNONYM: PONSIN, SH3 DOMAIN PROTEIN 5, SH3P12, C-CBL-ASSOCIATED COMPND 6 PROTEIN, CAP; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROLINE RICH PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 857-867; 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: KIAA0894, KIAA1296, SH3D5, SORBS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: VCL; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SH3 DOMAIN, CELL MIGRATION, FOCAL ADHESION, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.ZHAO,F.LI,J.WU,Y.SHI,Z.ZHANG,Q.GONG REVDAT 4 08-NOV-23 4LN2 1 SEQADV REVDAT 3 10-DEC-14 4LN2 1 JRNL REVDAT 2 04-JUN-14 4LN2 1 REMARK REVDAT 1 28-MAY-14 4LN2 0 JRNL AUTH D.ZHAO,X.WANG,J.PENG,C.WANG,F.LI,Q.SUN,Y.ZHANG,J.ZHANG, JRNL AUTH 2 G.CAI,X.ZUO,J.WU,Y.SHI,Z.ZHANG,Q.GONG JRNL TITL STRUCTURAL INVESTIGATION OF THE INTERACTION BETWEEN THE JRNL TITL 2 TANDEM SH3 DOMAINS OF C-CBL-ASSOCIATED PROTEIN AND VINCULIN JRNL REF J.STRUCT.BIOL. V. 187 194 2014 JRNL REFN ISSN 1047-8477 JRNL PMID 24878663 JRNL DOI 10.1016/J.JSB.2014.05.009 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 36766 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 + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1945 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2543 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 615 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.02000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.023 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.023 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.014 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.551 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 682 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 651 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 931 ; 1.335 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1502 ; 0.696 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 84 ; 6.839 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 34 ;33.568 ;22.941 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 115 ; 9.534 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;17.051 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 96 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 791 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 157 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 330 ; 2.703 ; 0.743 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 329 ; 2.707 ; 0.743 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 416 ; 3.005 ; 1.122 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 407 ; 8.075 ; 1.181 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 352 ; 6.890 ; 0.833 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 346 ; 8.915 ; 0.912 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 508 ;11.106 ; 1.314 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 841 ;13.533 ; 8.434 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 761 ;12.754 ; 7.323 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1333 ; 1.908 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 21 ;26.540 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1414 ;10.879 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4LN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080835. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36766 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 34.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: PHASES REMARK 200 STARTING MODEL: 2O9S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: EVAPORATION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 14.43500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.43000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.92500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.43000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.43500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.92500 REMARK 290 SMTRY3 4 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: 840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 GLN A 863 REMARK 465 HIS A 864 REMARK 465 GLU B 857 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 MET A 865 CG SD CE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LNP RELATED DB: PDB REMARK 900 RELATED ID: 2MOX RELATED DB: PDB DBREF 4LN2 A 866 930 UNP Q9BX66 SRBS1_HUMAN 866 930 DBREF 4LN2 B 857 867 UNP P18206 VINC_HUMAN 857 867 SEQADV 4LN2 GLN A 863 UNP Q9BX66 EXPRESSION TAG SEQADV 4LN2 HIS A 864 UNP Q9BX66 EXPRESSION TAG SEQADV 4LN2 MET A 865 UNP Q9BX66 EXPRESSION TAG SEQRES 1 A 68 GLN HIS MET VAL LEU GLU TYR GLY GLU ALA ILE ALA LYS SEQRES 2 A 68 PHE ASN PHE ASN GLY ASP THR GLN VAL GLU MET SER PHE SEQRES 3 A 68 ARG LYS GLY GLU ARG ILE THR LEU LEU ARG GLN VAL ASP SEQRES 4 A 68 GLU ASN TRP TYR GLU GLY ARG ILE PRO GLY THR SER ARG SEQRES 5 A 68 GLN GLY ILE PHE PRO ILE THR TYR VAL ASP VAL ILE LYS SEQRES 6 A 68 ARG PRO LEU SEQRES 1 B 11 GLU LEU ALA PRO PRO LYS PRO PRO LEU PRO GLU FORMUL 3 HOH *121(H2 O) SHEET 1 A 5 GLN A 915 PRO A 919 0 SHEET 2 A 5 TRP A 904 ARG A 908 -1 N GLY A 907 O GLY A 916 SHEET 3 A 5 ARG A 893 GLN A 899 -1 N THR A 895 O ARG A 908 SHEET 4 A 5 GLY A 870 ALA A 874 -1 N ALA A 872 O ILE A 894 SHEET 5 A 5 VAL A 923 LYS A 927 -1 O ASP A 924 N ILE A 873 CRYST1 28.870 45.850 52.860 90.00 90.00 90.00 P 21 21 21 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 0.034638 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018918 0.00000