PDB Short entry for 1M27 HEADER SIGNALING PROTEIN, TRANSFERASE 21-JUN-02 1M27 TITLE CRYSTAL STRUCTURE OF SAP/FYNSH3/SLAM TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH2 DOMAIN PROTEIN 1A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XLP GENE PRODUCT, SAP, SLAM-ASSOCIATED PROTEIN, T CELL COMPND 5 SIGNAL TRANSDUCTION MOLECULE SAP, DUNCAN'S DISEASE SH2-PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: SLAM PEPTIDE (RESIDUES 276-286); COMPND 11 SYNONYM: SLAM, IPO-3, CD150 ANTIGEN, CDW150; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN; COMPND 15 CHAIN: C; COMPND 16 FRAGMENT: SH3 DOMAIN (RESIDUES 82-143); COMPND 17 SYNONYM: FYN, P59-FYN, SYN, SLK; COMPND 18 EC: 2.7.1.112; COMPND 19 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 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. THIS SOURCE 10 SEQUENCE WAS CHEMICALLY SYNTHESIZED.; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SH2-SH3 INTERACTION, SIGNALING PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.CHAN,J.GRIESBACH,H.K.SONG,F.POY,C.TERHORST,M.J.ECK REVDAT 3 14-FEB-24 1M27 1 REMARK REVDAT 2 24-FEB-09 1M27 1 VERSN REVDAT 1 06-MAY-03 1M27 0 JRNL AUTH B.CHAN,A.LANYI,H.K.SONG,J.GRIESBACH,M.SIMARRO-GRANDE,F.POY, JRNL AUTH 2 D.HOWIE,J.SUMEGI,C.TERHORST,M.J.ECK JRNL TITL SAP COUPLES FYN TO SLAM IMMUNE RECEPTORS. JRNL REF NAT.CELL BIOL. V. 5 155 2003 JRNL REFN ISSN 1465-7392 JRNL PMID 12545174 JRNL DOI 10.1038/NCB920 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8291 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 SET) : 0.213 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 967 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 20.00 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 967 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1407 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 86 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.34 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.45 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.258 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 1M27 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000016505. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 160 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62846 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 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) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TARTRATE, PH 5.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 91.53950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.45450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.45450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.76975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.45450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.45450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 137.30925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.45450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.45450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.76975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.45450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.45450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 137.30925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 91.53950 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 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 A 36 -2.36 -154.69 REMARK 500 THR C 85 -50.79 -138.33 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 FLC A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D4T RELATED DB: PDB REMARK 900 SAP/SLAM COMPLEX DBREF 1M27 A 1 104 UNP O60880 SH21A_HUMAN 1 104 DBREF 1M27 C 84 144 UNP P06241 FYN_HUMAN 83 143 DBREF 1M27 B 276 286 UNP Q13291 SLAF1_HUMAN 276 286 SEQRES 1 A 104 MET ASP ALA VAL ALA VAL TYR HIS GLY LYS ILE SER ARG SEQRES 2 A 104 GLU THR GLY GLU LYS LEU LEU LEU ALA THR GLY LEU ASP SEQRES 3 A 104 GLY SER TYR LEU LEU ARG ASP SER GLU SER VAL PRO GLY SEQRES 4 A 104 VAL TYR CYS LEU CYS VAL LEU TYR HIS GLY TYR ILE TYR SEQRES 5 A 104 THR TYR ARG VAL SER GLN THR GLU THR GLY SER TRP SER SEQRES 6 A 104 ALA GLU THR ALA PRO GLY VAL HIS LYS ARG TYR PHE ARG SEQRES 7 A 104 LYS ILE LYS ASN LEU ILE SER ALA PHE GLN LYS PRO ASP SEQRES 8 A 104 GLN GLY ILE VAL ILE PRO LEU GLN TYR PRO VAL GLU LYS SEQRES 1 B 11 LYS SER LEU THR ILE TYR ALA GLN VAL GLN LYS SEQRES 1 C 61 VAL THR LEU PHE VAL ALA LEU TYR ASP TYR GLU ALA ARG SEQRES 2 C 61 THR GLU ASP ASP LEU SER PHE HIS LYS GLY GLU LYS PHE SEQRES 3 C 61 GLN ILE LEU ASN SER SER GLU GLY ASP TRP TRP GLU ALA SEQRES 4 C 61 ARG SER LEU THR THR GLY GLU THR GLY TYR ILE PRO SER SEQRES 5 C 61 ASN TYR VAL ALA PRO VAL ASP SER ILE HET FLC A 300 13 HETNAM FLC CITRATE ANION FORMUL 4 FLC C6 H5 O7 3- FORMUL 5 HOH *86(H2 O) HELIX 1 1 SER A 12 GLY A 24 1 13 HELIX 2 2 LYS A 79 PHE A 87 1 9 SHEET 1 A 5 TYR A 100 PRO A 101 0 SHEET 2 A 5 SER A 28 ASP A 33 1 N TYR A 29 O TYR A 100 SHEET 3 A 5 VAL A 40 TYR A 47 -1 O CYS A 44 N LEU A 30 SHEET 4 A 5 TYR A 50 GLN A 58 -1 O VAL A 56 N TYR A 41 SHEET 5 A 5 TRP A 64 ALA A 66 -1 O SER A 65 N SER A 57 SHEET 1 B 5 TYR A 100 PRO A 101 0 SHEET 2 B 5 SER A 28 ASP A 33 1 N TYR A 29 O TYR A 100 SHEET 3 B 5 VAL A 40 TYR A 47 -1 O CYS A 44 N LEU A 30 SHEET 4 B 5 TYR A 50 GLN A 58 -1 O VAL A 56 N TYR A 41 SHEET 5 B 5 THR B 279 ALA B 282 1 O ILE B 280 N THR A 53 SHEET 1 C 5 THR C 130 PRO C 134 0 SHEET 2 C 5 TRP C 119 SER C 124 -1 N ALA C 122 O GLY C 131 SHEET 3 C 5 LYS C 108 ASN C 113 -1 N GLN C 110 O ARG C 123 SHEET 4 C 5 LEU C 86 ALA C 89 -1 N PHE C 87 O PHE C 109 SHEET 5 C 5 VAL C 138 PRO C 140 -1 O ALA C 139 N VAL C 88 SITE 1 AC1 8 ARG A 32 SER A 34 GLU A 35 SER A 36 SITE 2 AC1 8 CYS A 42 ARG A 55 HOH A 322 TYR B 281 CRYST1 52.909 52.909 183.079 90.00 90.00 90.00 P 41 21 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 0.018900 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018900 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005462 0.00000