PDB Short entry for 1D4T HEADER SIGNALING PROTEIN 06-OCT-99 1D4T TITLE CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH A SLAM TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: T CELL SIGNAL TRANSDUCTION MOLECULE SAP; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH2 DOMAIN (RESIDUES 1-104); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: SLAM TAIL PEPTIDE (RESIDUES 276 TO 286); COMPND 10 SYNONYM: SLAM; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BLOOD; SOURCE 6 CELL: T CELL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: T7-PRSET; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 14 OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS) KEYWDS SH2 DOMAIN, TYROSINE KINASE, SIGNAL TRANSDUCTION, PEPTIDE KEYWDS 2 RECOGNITION, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.POY,M.B.YAFFE,J.SAYOS,K.SAXENA,M.J.ECK REVDAT 5 07-FEB-24 1D4T 1 REMARK REVDAT 4 31-JAN-18 1D4T 1 REMARK REVDAT 3 24-FEB-09 1D4T 1 VERSN REVDAT 2 10-APR-00 1D4T 1 JRNL REVDAT 1 14-OCT-99 1D4T 0 JRNL AUTH F.POY,M.B.YAFFE,J.SAYOS,K.SAXENA,M.MORRA,J.SUMEGI, JRNL AUTH 2 L.C.CANTLEY,C.TERHORST,M.J.ECK JRNL TITL CRYSTAL STRUCTURES OF THE XLP PROTEIN SAP REVEAL A CLASS OF JRNL TITL 2 SH2 DOMAINS WITH EXTENDED, PHOSPHOTYROSINE-INDEPENDENT JRNL TITL 3 SEQUENCE RECOGNITION. JRNL REF MOL.CELL V. 4 555 1999 JRNL REFN ISSN 1097-2765 JRNL PMID 10549287 JRNL DOI 10.1016/S1097-2765(00)80206-3 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.SAYOS,C.WU,M.MORRA,N.WANG,C.TERHOSRT REMARK 1 TITL THE X-LINKED LYMPHOPROLIFERATIVE DISEASE GENE PRODUCT SAP REMARK 1 TITL 2 REGULATES SIGNALS INDUCED THROUGH THE CO-RECEPTOR SLAM REMARK 1 REF NATURE V. 395 462 1998 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/26683 REMARK 2 REMARK 2 RESOLUTION. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R 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) : 0.127 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.130 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 171 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.115 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.117 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 149 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 2809 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 915 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 236 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1147.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 957.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1032 REMARK 3 NUMBER OF RESTRAINTS : 1219 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.080 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.130 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.070 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.040 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.080 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D4T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 22.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04300 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: AB INITIO REMARK 200 SOFTWARE USED: ARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000, 20% GLYCEROL, 100 MM REMARK 280 HEPES PH 8.0, AND 100 MM DTT, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 22K, TEMPERATURE 295.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.45500 REMARK 290 SMTRY3 2 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: 1640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LEU B 278 CG LEU B 278 CD2 0.234 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 13 NH1 - CZ - NH2 ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 13 NE - CZ - NH1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 75 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 LYS B 276 CA - CB - CG ANGL. DEV. = 20.8 DEGREES REMARK 500 LEU B 278 CB - CG - CD1 ANGL. DEV. = -10.4 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 10 43.45 -91.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D1Z RELATED DB: PDB REMARK 900 STRUCTURE OF THE UNLIGANDED SAP SH2 DOMAIN REMARK 900 RELATED ID: 1D4W RELATED DB: PDB REMARK 900 SAP SH2 DOMAIN IN COMPLEX WITH SYNTHETIC PHOSPHOPEPTIDE DBREF 1D4T A 1 104 UNP O60880 SH21A_HUMAN 1 104 DBREF 1D4T 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 FORMUL 3 HOH *236(H2 O) HELIX 1 1 SER A 12 GLY A 24 1 13 HELIX 2 2 LYS A 79 GLN A 88 1 10 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 TYR A 41 TYR A 47 -1 N CYS A 42 O ARG A 32 SHEET 4 A 5 TYR A 50 GLN A 58 -1 O TYR A 50 N TYR A 47 SHEET 5 A 5 TRP A 64 ALA A 66 -1 O SER A 65 N SER A 57 SHEET 1 A1 5 TYR A 100 PRO A 101 0 SHEET 2 A1 5 SER A 28 ASP A 33 1 N TYR A 29 O TYR A 100 SHEET 3 A1 5 TYR A 41 TYR A 47 -1 N CYS A 42 O ARG A 32 SHEET 4 A1 5 TYR A 50 GLN A 58 -1 O TYR A 50 N TYR A 47 SHEET 5 A1 5 THR B 279 TYR B 281 1 O ILE B 280 N THR A 53 CRYST1 25.870 42.910 44.950 90.00 98.26 90.00 P 1 21 1 2 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 0.038655 0.000000 0.005612 0.00000 SCALE2 0.000000 0.023305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022480 0.00000