HEADER SIGNALING PROTEIN 11-JUL-13 4LNP
TITLE THE FIRST 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: PROTEIN-PROTEIN BINDING DOMAIN, UNP RESIDUES 794-854;
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: VINCULIN;
COMPND 10 CHAIN: B;
COMPND 11 FRAGMENT: PROLINE RICH PEPTIDE, UNP RESIDUES 870-879;
COMPND 12 SYNONYM: METAVINCULIN, MV;
COMPND 13 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, PROLINE RICH PEPTIDE, FOCAL ADHESION,
KEYWDS 2 SIGNALING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR D.ZHAO,F.LI,J.WU,Y.SHI,Z.ZHANG,Q.GONG
REVDAT 4 20-MAR-24 4LNP 1 REMARK
REVDAT 3 10-DEC-14 4LNP 1 JRNL
REVDAT 2 04-JUN-14 4LNP 1 REMARK
REVDAT 1 28-MAY-14 4LNP 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. 1.41 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) : 1.41
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.06
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 3 NUMBER OF REFLECTIONS : 13539
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) : 0.137
REMARK 3 FREE R VALUE : 0.194
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 711
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) : 1.41
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.45
REMARK 3 REFLECTION IN BIN (WORKING SET) : 892
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.50
REMARK 3 BIN R VALUE (WORKING SET) : 0.2000
REMARK 3 BIN FREE R VALUE SET COUNT : 40
REMARK 3 BIN FREE R VALUE : 0.2980
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 587
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 83
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.04
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.06000
REMARK 3 B22 (A**2) : -0.17000
REMARK 3 B33 (A**2) : 0.11000
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): 0.063
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.064
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.613
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 661 ; 0.023 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 640 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 907 ; 2.394 ; 2.002
REMARK 3 BOND ANGLES OTHERS (DEGREES): 1493 ; 1.049 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 81 ; 6.891 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 35 ;33.164 ;23.143
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 114 ;14.617 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;13.520 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 90 ; 0.160 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 738 ; 0.012 ; 0.022
REMARK 3 GENERAL PLANES OTHERS (A): 149 ; 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): 298 ; 1.841 ; 0.986
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 296 ; 1.818 ; 0.979
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 372 ; 2.146 ; 1.476
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 373 ; 2.154 ; 1.480
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 363 ; 6.500 ; 1.297
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 359 ; 6.421 ; 1.282
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 528 ; 7.513 ; 1.830
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 743 ; 5.156 ; 9.728
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 706 ; 4.849 ; 8.972
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1301 ; 4.763 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 18 ;41.807 ; 5.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1340 ;18.399 ; 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 4LNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUL-13.
REMARK 100 THE DEPOSITION ID IS D_1000080858.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 77
REMARK 200 PH : 8.0
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 : 13539
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410
REMARK 200 RESOLUTION RANGE LOW (A) : 38.060
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.95
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0, EVAPORATION, TEMPERATURE 293K
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 12.24000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.47000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.92500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.47000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.24000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.92500
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: 930 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 5160 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 VAL B 870 CG1 CG2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ASP A 803 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4LN2 RELATED DB: PDB
REMARK 900 RELATED ID: 2MOX RELATED DB: PDB
DBREF 4LNP A 794 854 UNP Q9BX66 SRBS1_HUMAN 794 854
DBREF 4LNP B 870 879 UNP P18206 VINC_HUMAN 870 879
SEQRES 1 A 61 GLU MET ARG PRO ALA ARG ALA LYS PHE ASP PHE LYS ALA
SEQRES 2 A 61 GLN THR LEU LYS GLU LEU PRO LEU GLN LYS GLY ASP ILE
SEQRES 3 A 61 VAL TYR ILE TYR LYS GLN ILE ASP GLN ASN TRP TYR GLU
SEQRES 4 A 61 GLY GLU HIS HIS GLY ARG VAL GLY ILE PHE PRO ARG THR
SEQRES 5 A 61 TYR ILE GLU LEU LEU PRO PRO ALA GLU
SEQRES 1 B 10 VAL PRO PRO PRO ARG PRO PRO PRO PRO GLU
FORMUL 3 HOH *83(H2 O)
SHEET 1 A 5 ARG A 838 PRO A 843 0
SHEET 2 A 5 TRP A 830 HIS A 835 -1 N TYR A 831 O PHE A 842
SHEET 3 A 5 ILE A 819 GLN A 825 -1 N LYS A 824 O GLU A 832
SHEET 4 A 5 ARG A 796 ALA A 800 -1 N ARG A 796 O ILE A 822
SHEET 5 A 5 ILE A 847 LEU A 849 -1 O GLU A 848 N ARG A 799
CRYST1 24.480 49.850 58.940 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 0.040850 0.000000 0.000000 0.00000
SCALE2 0.000000 0.020060 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016966 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
