PDB Short entry for 2O9S HEADER SIGNALING PROTEIN 14-DEC-06 2O9S TITLE THE SECOND SH3 DOMAIN FROM PONSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PONSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SRC HOMOLOGY 3 (SH3) DOMAIN; COMPND 5 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: SORBS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET151 KEYWDS SH3 DOMAIN, PONSIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.PINOTSIS,M.WILMANNS REVDAT 4 25-OCT-23 2O9S 1 REMARK SEQADV LINK REVDAT 3 18-OCT-17 2O9S 1 REMARK REVDAT 2 24-FEB-09 2O9S 1 VERSN REVDAT 1 30-OCT-07 2O9S 0 JRNL AUTH K.GEHMLICH,N.PINOTSIS,K.HAYESS,P.F.VAN DER VEN,H.MILTING, JRNL AUTH 2 A.EL BANAYOSY,M.WILMANNS,E.EHLER JRNL TITL PAXILLIN AND PONSIN INTERACT IN NASCENT COSTAMERES OF MUSCLE JRNL TITL 2 CELLS JRNL REF J.MOL.BIOL. V. 369 665 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17462669 JRNL DOI 10.1016/J.JMB.2007.03.050 REMARK 2 REMARK 2 RESOLUTION. 0.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.105 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.104 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.121 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 2.800 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1575 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 60392 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.100 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.099 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.114 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 2.800 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1465 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 52506 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 544 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 677.30 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 539.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 44 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7073 REMARK 3 NUMBER OF RESTRAINTS : 9649 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.035 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.092 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.107 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.122 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.039 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.058 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2O9S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000040866. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8131 REMARK 200 MONOCHROMATOR : GE SINGLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56189 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.830 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.21900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2O2W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M KSCN, 0.1M TRIS/HCL, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 12.37150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.56200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.28100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.56200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.37150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.28100 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 835 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 835 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 843 NH1 - CZ - NH2 ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG A 843 NE - CZ - NH1 ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG A 862 CD - NE - CZ ANGL. DEV. = 11.2 DEGREES REMARK 500 ARG A 862 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 862 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 844 127.39 -37.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A2001 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 833 O REMARK 620 2 ASP A 835 OD1 91.9 REMARK 620 3 HOH A3611 O 111.5 77.1 REMARK 620 4 HOH A3682 O 78.0 60.2 136.9 REMARK 620 5 HOH A3690 O 109.9 29.1 91.8 47.4 REMARK 620 6 HOH A3698 O 161.6 69.7 64.4 93.3 54.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN A 3601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN A 3602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O2W RELATED DB: PDB REMARK 900 POWDER DIFFRACTION MODEL REMARK 900 RELATED ID: 2O9V RELATED DB: PDB DBREF 2O9S A 824 884 UNP A0AED4 A0AED4_HUMAN 824 884 SEQADV 2O9S GLY A 818 UNP A0AED4 EXPRESSION TAG SEQADV 2O9S ILE A 819 UNP A0AED4 EXPRESSION TAG SEQADV 2O9S ASP A 820 UNP A0AED4 EXPRESSION TAG SEQADV 2O9S PRO A 821 UNP A0AED4 EXPRESSION TAG SEQADV 2O9S PHE A 822 UNP A0AED4 EXPRESSION TAG SEQADV 2O9S THR A 823 UNP A0AED4 EXPRESSION TAG SEQRES 1 A 67 GLY ILE ASP PRO PHE THR GLY GLU ALA ILE ALA LYS PHE SEQRES 2 A 67 ASN PHE ASN GLY ASP THR GLN VAL GLU MET SER PHE ARG SEQRES 3 A 67 LYS GLY GLU ARG ILE THR LEU LEU ARG GLN VAL ASP GLU SEQRES 4 A 67 ASN TRP TYR GLU GLY ARG ILE PRO GLY THR SER ARG GLN SEQRES 5 A 67 GLY ILE PHE PRO ILE THR TYR VAL ASP VAL ILE LYS ARG SEQRES 6 A 67 PRO LEU HET NA A2001 1 HET CL A2002 1 HET SCN A3601 3 HET SCN A3602 3 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM SCN THIOCYANATE ION FORMUL 2 NA NA 1+ FORMUL 3 CL CL 1- FORMUL 4 SCN 2(C N S 1-) FORMUL 6 HOH *138(H2 O) SHEET 1 A 5 GLN A 869 PRO A 873 0 SHEET 2 A 5 TRP A 858 ARG A 862 -1 N TYR A 859 O PHE A 872 SHEET 3 A 5 ARG A 847 GLN A 853 -1 N ARG A 852 O GLU A 860 SHEET 4 A 5 GLY A 824 ALA A 828 -1 N GLY A 824 O LEU A 850 SHEET 5 A 5 VAL A 877 LYS A 881 -1 O ASP A 878 N ILE A 827 LINK O ASN A 833 NA NA A2001 1555 1555 2.65 LINK OD1AASP A 835 NA NA A2001 1555 1555 2.81 LINK NA NA A2001 O HOH A3611 1555 1555 2.87 LINK NA NA A2001 O AHOH A3682 1555 1555 2.58 LINK NA NA A2001 O BHOH A3690 1555 1555 2.85 LINK NA NA A2001 O HOH A3698 1555 1555 2.93 SITE 1 AC1 8 PHE A 832 ASN A 833 ASP A 835 HOH A3611 SITE 2 AC1 8 HOH A3617 HOH A3682 HOH A3690 HOH A3698 SITE 1 AC2 3 THR A 836 GLU A 839 HOH A3736 SITE 1 AC3 6 ASN A 833 ARG A 852 THR A 866 SER A 867 SITE 2 AC3 6 HOH A3682 HOH A3697 SITE 1 AC4 9 ASN A 831 ARG A 868 GLN A 869 HOH A3620 SITE 2 AC4 9 HOH A3625 HOH A3648 HOH A3677 HOH A3678 SITE 3 AC4 9 HOH A3685 CRYST1 24.743 36.562 69.124 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 0.040415 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027351 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014467 0.00000