HEADER SIGNALING PROTEIN 30-JAN-03 1NTV TITLE CRYSTAL STRUCTURE OF THE DISABLED-1 (DAB1) PTB DOMAIN-APOER2 PEPTIDE TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISABLED HOMOLOG 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 23-174; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: APOLIPOPROTEIN E RECEPTOR-2 PEPTIDE; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: DAB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3), B834; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: GATEWAY PDEST15; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS BETA-SANDWICH, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.C.STOLT,H.JEON,H.K.SONG,J.HERZ,M.J.ECK,S.C.BLACKLOW REVDAT 5 14-FEB-24 1NTV 1 REMARK REVDAT 4 31-JAN-18 1NTV 1 REMARK REVDAT 3 24-FEB-09 1NTV 1 VERSN REVDAT 2 27-MAY-03 1NTV 1 JRNL REVDAT 1 15-APR-03 1NTV 0 JRNL AUTH P.C.STOLT,H.JEON,H.K.SONG,J.HERZ,M.J.ECK,S.C.BLACKLOW JRNL TITL ORIGINS OF PEPTIDE SELECTIVITY AND PHOSPHOINOSITIDE BINDING JRNL TITL 2 REVEALED BY STRUCTURES OF DISABLED-1 PTB DOMAIN COMPLEXES JRNL REF STRUCTURE V. 11 569 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12737822 JRNL DOI 10.1016/S0969-2126(03)00068-6 REMARK 2 REMARK 2 RESOLUTION. 1.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 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) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 24472 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) : 0.222 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2412 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 12 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1669 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 192 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1290 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.00000 REMARK 3 B22 (A**2) : 2.08000 REMARK 3 B33 (A**2) : -1.09000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : -0.0 REMARK 3 LOW RESOLUTION CUTOFF (A) : 40.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.05 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.640 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 50.51 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : I3P.PAR REMARK 3 PARAMETER FILE 4 : WATER.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : I3P.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NTV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018198. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-02; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; NULL REMARK 200 RADIATION SOURCE : CHESS; NULL REMARK 200 BEAMLINE : F1; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.909; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24472 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.23500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, PEG8000, ETHANOL, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 25K, PH 7.50, TEMPERATURE REMARK 280 298.0K 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 18.12350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.06200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.86200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.06200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.12350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.86200 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: 1610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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: 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 GLN A 145 -164.29 -113.17 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 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NU2 RELATED DB: PDB DBREF 1NTV A 23 174 UNP P97318 DAB1_MOUSE 23 174 DBREF 1NTV B 5 14 PDB 1NTV 1NTV 5 14 SEQRES 1 A 152 GLY GLN ASP ARG SER GLU ALA THR LEU ILE LYS ARG PHE SEQRES 2 A 152 LYS GLY GLU GLY VAL ARG TYR LYS ALA LYS LEU ILE GLY SEQRES 3 A 152 ILE ASP GLU VAL SER ALA ALA ARG GLY ASP LYS LEU CYS SEQRES 4 A 152 GLN ASP SER MET MET LYS LEU LYS GLY VAL VAL ALA GLY SEQRES 5 A 152 ALA ARG SER LYS GLY GLU HIS LYS GLN LYS ILE PHE LEU SEQRES 6 A 152 THR ILE SER PHE GLY GLY ILE LYS ILE PHE ASP GLU LYS SEQRES 7 A 152 THR GLY ALA LEU GLN HIS HIS HIS ALA VAL HIS GLU ILE SEQRES 8 A 152 SER TYR ILE ALA LYS ASP ILE THR ASP HIS ARG ALA PHE SEQRES 9 A 152 GLY TYR VAL CYS GLY LYS GLU GLY ASN HIS ARG PHE VAL SEQRES 10 A 152 ALA ILE LYS THR ALA GLN ALA ALA GLU PRO VAL ILE LEU SEQRES 11 A 152 ASP LEU ARG ASP LEU PHE GLN LEU ILE TYR GLU LEU LYS SEQRES 12 A 152 GLN ARG GLU GLU LEU GLU LYS LYS ALA SEQRES 1 B 10 ASN PHE ASP ASN PRO VAL TYR ARG LYS THR HET PO4 A 200 5 HETNAM PO4 PHOSPHATE ION FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *139(H2 O) HELIX 1 1 SER A 27 LYS A 36 1 10 HELIX 2 2 GLY A 57 SER A 77 1 21 HELIX 3 3 ALA A 109 HIS A 111 5 3 HELIX 4 4 ALA A 147 ARG A 167 1 21 HELIX 5 5 GLU A 169 ALA A 174 1 6 SHEET 1 A 8 LEU A 104 HIS A 108 0 SHEET 2 A 8 GLY A 93 ASP A 98 -1 N ILE A 96 O GLN A 105 SHEET 3 A 8 GLN A 83 SER A 90 -1 N PHE A 86 O PHE A 97 SHEET 4 A 8 VAL A 40 GLU A 51 -1 N ALA A 44 O ILE A 85 SHEET 5 A 8 ARG A 137 THR A 143 -1 O PHE A 138 N ASP A 50 SHEET 6 A 8 ALA A 125 CYS A 130 -1 N PHE A 126 O ILE A 141 SHEET 7 A 8 ILE A 113 LYS A 118 -1 N ALA A 117 O GLY A 127 SHEET 8 A 8 PHE B 6 ASP B 7 -1 O PHE B 6 N ILE A 116 SITE 1 AC1 7 LYS A 45 HIS A 81 LYS A 82 HOH A 218 SITE 2 AC1 7 HOH A 297 HOH A 318 HOH A 324 CRYST1 36.247 45.724 90.124 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 0.027588 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011096 0.00000