PDB Short entry for 1M61 HEADER TRANSFERASE 11-JUL-02 1M61 TITLE CRYSTAL STRUCTURE OF THE APO SH2 DOMAINS OF ZAP-70 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE ZAP-70; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TANDEM SH2 DOMAINS (RESIDUES 1-256); COMPND 5 SYNONYM: 70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE; COMPND 6 EC: 2.7.1.112; COMPND 7 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS APO FORM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.H.A.FOLMER,S.GESCHWINDNER,Y.XUE REVDAT 3 07-MAR-18 1M61 1 REMARK REVDAT 2 24-FEB-09 1M61 1 VERSN REVDAT 1 15-JUL-03 1M61 0 JRNL AUTH R.H.A.FOLMER,S.GESCHWINDNER,Y.XUE JRNL TITL CRYSTAL STRUCTURE AND NMR STUDIES OF THE APO SH2 DOMAINS OF JRNL TITL 2 ZAP-70: TWO BIKES RATHER THAN A TANDEM JRNL REF BIOCHEMISTRY V. 41 14176 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12450381 JRNL DOI 10.1021/BI026465E REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2002 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 591220.750 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 9426 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.900 REMARK 3 FREE R VALUE TEST SET COUNT : 370 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.015 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 9426 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1462 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 66 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.044 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2058 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -12.61000 REMARK 3 B22 (A**2) : 7.89000 REMARK 3 B33 (A**2) : 4.72000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.96000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.38 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) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.180 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.420 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.220 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 26.06 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1M61 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000016642. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-99 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0158 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9426 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.06200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 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) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.52200 REMARK 200 R SYM FOR SHELL (I) : 0.45600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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: PDB ENTRY 1A81 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, SODIUM CHLORIDE, PH 8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 26.11350 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: 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: 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 902 170.56 -50.01 REMARK 500 HIS A 903 114.80 72.33 REMARK 500 PRO A 4 -9.25 -51.31 REMARK 500 LEU A 26 30.18 -94.64 REMARK 500 ASP A 90 114.50 -167.19 REMARK 500 ASP A 92 48.46 24.85 REMARK 500 ASN A 97 175.70 -58.71 REMARK 500 LYS A 100 115.67 71.61 REMARK 500 CYS A 102 68.75 -103.23 REMARK 500 PRO A 105 146.03 -37.21 REMARK 500 SER A 166 -37.29 -34.92 REMARK 500 GLN A 182 50.98 30.47 REMARK 500 LYS A 206 29.88 44.38 REMARK 500 ASP A 244 68.72 -7.68 REMARK 500 LYS A 251 -91.82 -126.57 REMARK 500 PRO A 255 134.18 -31.32 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 PO4 A 300 DBREF 1M61 A 1 256 UNP P43403 ZAP70_HUMAN 1 256 SEQADV 1M61 GLY A 901 UNP P43403 CLONING ARTIFACT SEQADV 1M61 SER A 902 UNP P43403 CLONING ARTIFACT SEQADV 1M61 HIS A 903 UNP P43403 CLONING ARTIFACT SEQRES 1 A 259 GLY SER HIS MET PRO ASP PRO ALA ALA HIS LEU PRO PHE SEQRES 2 A 259 PHE TYR GLY SER ILE SER ARG ALA GLU ALA GLU GLU HIS SEQRES 3 A 259 LEU LYS LEU ALA GLY MET ALA ASP GLY LEU PHE LEU LEU SEQRES 4 A 259 ARG GLN CYS LEU ARG SER LEU GLY GLY TYR VAL LEU SER SEQRES 5 A 259 LEU VAL HIS ASP VAL ARG PHE HIS HIS PHE PRO ILE GLU SEQRES 6 A 259 ARG GLN LEU ASN GLY THR TYR ALA ILE ALA GLY GLY LYS SEQRES 7 A 259 ALA HIS CYS GLY PRO ALA GLU LEU CYS GLU PHE TYR SER SEQRES 8 A 259 ARG ASP PRO ASP GLY LEU PRO CYS ASN LEU ARG LYS PRO SEQRES 9 A 259 CYS ASN ARG PRO SER GLY LEU GLU PRO GLN PRO GLY VAL SEQRES 10 A 259 PHE ASP CYS LEU ARG ASP ALA MET VAL ARG ASP TYR VAL SEQRES 11 A 259 ARG GLN THR TRP LYS LEU GLU GLY GLU ALA LEU GLU GLN SEQRES 12 A 259 ALA ILE ILE SER GLN ALA PRO GLN VAL GLU LYS LEU ILE SEQRES 13 A 259 ALA THR THR ALA HIS GLU ARG MET PRO TRP TYR HIS SER SEQRES 14 A 259 SER LEU THR ARG GLU GLU ALA GLU ARG LYS LEU TYR SER SEQRES 15 A 259 GLY ALA GLN THR ASP GLY LYS PHE LEU LEU ARG PRO ARG SEQRES 16 A 259 LYS GLU GLN GLY THR TYR ALA LEU SER LEU ILE TYR GLY SEQRES 17 A 259 LYS THR VAL TYR HIS TYR LEU ILE SER GLN ASP LYS ALA SEQRES 18 A 259 GLY LYS TYR CYS ILE PRO GLU GLY THR LYS PHE ASP THR SEQRES 19 A 259 LEU TRP GLN LEU VAL GLU TYR LEU LYS LEU LYS ALA ASP SEQRES 20 A 259 GLY LEU ILE TYR CYS LEU LYS GLU ALA CYS PRO ASN HET PO4 A 300 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *36(H2 O) HELIX 1 1 SER A 16 LEU A 26 1 11 HELIX 2 2 GLY A 79 ASP A 90 1 12 HELIX 3 3 GLY A 113 LYS A 132 1 20 HELIX 4 4 GLU A 134 ALA A 154 1 21 HELIX 5 5 ALA A 157 MET A 161 5 5 HELIX 6 6 THR A 169 SER A 179 1 11 HELIX 7 7 THR A 231 LYS A 240 1 10 SHEET 1 A 5 PHE A 11 GLY A 13 0 SHEET 2 A 5 PHE A 34 GLN A 38 1 N GLN A 38 O GLY A 13 SHEET 3 A 5 TYR A 46 HIS A 52 -1 O VAL A 47 N ARG A 37 SHEET 4 A 5 ARG A 55 ARG A 63 -1 O ILE A 61 N TYR A 46 SHEET 5 A 5 TYR A 69 ILE A 71 -1 O ALA A 70 N GLU A 62 SHEET 1 B 4 PHE A 187 PRO A 191 0 SHEET 2 B 4 THR A 197 TYR A 204 -1 O ALA A 199 N ARG A 190 SHEET 3 B 4 THR A 207 GLN A 215 -1 O TYR A 211 N LEU A 200 SHEET 4 B 4 TYR A 221 CYS A 222 -1 O CYS A 222 N SER A 214 SITE 1 AC1 4 ARG A 170 ARG A 190 ARG A 192 ALA A 199 CRYST1 48.851 52.227 54.455 90.00 89.91 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 0.020471 0.000000 -0.000032 0.00000 SCALE2 0.000000 0.019147 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018364 0.00000