HEADER ENDOCYTOSIS/EXOCYTOSIS 11-FEB-99 1B9K TITLE ALPHA-ADAPTIN APPENDAGE DOMAIN, FROM CLATHRIN ADAPTOR AP2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ALPHA-ADAPTIN APPENDAGE DOMAIN); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: APPENDAGE DOMAIN; COMPND 5 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX 4T2; SOURCE 11 EXPRESSION_SYSTEM_GENE: ALPHA-ADAPTIN C KEYWDS ENDOCYTOSIS, ADAPTOR, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.J.OWEN,P.R.EVANS REVDAT 5 27-DEC-23 1B9K 1 REMARK REVDAT 4 24-FEB-09 1B9K 1 VERSN REVDAT 3 01-APR-03 1B9K 1 JRNL REVDAT 2 09-JUN-00 1B9K 1 DBREF REVDAT 1 06-JUL-99 1B9K 0 JRNL AUTH D.J.OWEN,Y.VALLIS,M.E.NOBLE,J.B.HUNTER,T.R.DAFFORN, JRNL AUTH 2 P.R.EVANS,H.T.MCMAHON JRNL TITL A STRUCTURAL EXPLANATION FOR THE BINDING OF MULTIPLE LIGANDS JRNL TITL 2 BY THE ALPHA-ADAPTIN APPENDAGE DOMAIN. JRNL REF CELL(CAMBRIDGE,MASS.) V. 97 805 1999 JRNL REFN ISSN 0092-8674 JRNL PMID 10380931 JRNL DOI 10.1016/S0092-8674(00)80791-6 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 18198 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1444 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1875 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 302 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.41000 REMARK 3 B22 (A**2) : -0.60000 REMARK 3 B33 (A**2) : -0.40000 REMARK 3 B12 (A**2) : 0.14000 REMARK 3 B13 (A**2) : 0.04000 REMARK 3 B23 (A**2) : 0.13000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.013 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.032 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.034 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.010 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.123 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.180 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.245 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.109 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : 0.300 ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 15.000; NULL REMARK 3 PLANAR (DEGREES) : 4.400 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 13.000; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 21.000; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.500 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.200 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.400 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.000 ; 6.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B9K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000477. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 180 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51805 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 15.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.23500 REMARK 200 R SYM FOR SHELL (I) : 0.23500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SHARP SOLOMON, SOLOMON REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 10% ISOPROPANOL, 100MM REMARK 280 NA CITRATE PH 6.0, 10MM DTT, 6MG/ML PROTEIN REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 701 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 702 CG CD OE1 OE2 REMARK 470 ARG A 707 CD NE CZ NH1 NH2 REMARK 470 LYS A 771 CD CE NZ REMARK 470 GLN A 838 CD OE1 NE2 REMARK 470 GLU A 879 CG CD OE1 OE2 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 GLU A 907 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ASP A 924 CB - CG - OD1 ANGL. DEV. = 6.8 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 ASN A 719 -159.58 -118.25 REMARK 500 GLN A 732 -126.87 57.59 REMARK 500 ALA A 759 151.97 -45.54 REMARK 500 REMARK 500 REMARK: NULL DBREF 1B9K A 701 938 UNP P17427 AP2A2_MOUSE 701 938 SEQRES 1 A 238 SER GLU ASP ASN PHE ALA ARG PHE VAL CYS LYS ASN ASN SEQRES 2 A 238 GLY VAL LEU PHE GLU ASN GLN LEU LEU GLN ILE GLY LEU SEQRES 3 A 238 LYS SER GLU PHE ARG GLN ASN LEU GLY ARG MET PHE ILE SEQRES 4 A 238 PHE TYR GLY ASN LYS THR SER THR GLN PHE LEU ASN PHE SEQRES 5 A 238 THR PRO THR LEU ILE CYS ALA ASP ASP LEU GLN THR ASN SEQRES 6 A 238 LEU ASN LEU GLN THR LYS PRO VAL ASP PRO THR VAL ASP SEQRES 7 A 238 GLY GLY ALA GLN VAL GLN GLN VAL ILE ASN ILE GLU CYS SEQRES 8 A 238 ILE SER ASP PHE THR GLU ALA PRO VAL LEU ASN ILE GLN SEQRES 9 A 238 PHE ARG TYR GLY GLY THR PHE GLN ASN VAL SER VAL LYS SEQRES 10 A 238 LEU PRO ILE THR LEU ASN LYS PHE PHE GLN PRO THR GLU SEQRES 11 A 238 MET ALA SER GLN ASP PHE PHE GLN ARG TRP LYS GLN LEU SEQRES 12 A 238 SER ASN PRO GLN GLN GLU VAL GLN ASN ILE PHE LYS ALA SEQRES 13 A 238 LYS HIS PRO MET ASP THR GLU ILE THR LYS ALA LYS ILE SEQRES 14 A 238 ILE GLY PHE GLY SER ALA LEU LEU GLU GLU VAL ASP PRO SEQRES 15 A 238 ASN PRO ALA ASN PHE VAL GLY ALA GLY ILE ILE HIS THR SEQRES 16 A 238 LYS THR THR GLN ILE GLY CYS LEU LEU ARG LEU GLU PRO SEQRES 17 A 238 ASN LEU GLN ALA GLN MET TYR ARG LEU THR LEU ARG THR SEQRES 18 A 238 SER LYS ASP THR VAL SER GLN ARG LEU CYS GLU LEU LEU SEQRES 19 A 238 SER GLU GLN PHE FORMUL 2 HOH *302(H2 O) HELIX 1 1 PHE A 705 PHE A 708 5 4 HELIX 2 2 ASP A 760 GLN A 763 1 4 HELIX 3 3 LEU A 822 PHE A 825 5 4 HELIX 4 4 SER A 833 GLN A 842 1 10 HELIX 5 5 PRO A 846 GLN A 848 5 3 HELIX 6 6 THR A 862 PHE A 872 1 11 HELIX 7 7 ASP A 924 GLU A 936 1 13 SHEET 1 A 5 LEU A 766 THR A 770 0 SHEET 2 A 5 GLN A 782 CYS A 791 -1 N GLU A 790 O ASN A 767 SHEET 3 A 5 LEU A 734 ASN A 743 -1 N TYR A 741 O VAL A 783 SHEET 4 A 5 LEU A 722 ARG A 731 -1 N ARG A 731 O LEU A 734 SHEET 5 A 5 GLY A 714 GLU A 718 -1 N PHE A 717 O ILE A 724 SHEET 1 B 3 THR A 753 ILE A 757 0 SHEET 2 B 3 VAL A 800 TYR A 807 -1 N GLN A 804 O THR A 753 SHEET 3 B 3 THR A 810 LYS A 817 -1 N VAL A 816 O LEU A 801 SHEET 1 C 5 PHE A 826 PRO A 828 0 SHEET 2 C 5 ASN A 886 HIS A 894 -1 N ILE A 892 O GLN A 827 SHEET 3 C 5 GLN A 899 ASN A 909 -1 N LEU A 906 O PHE A 887 SHEET 4 C 5 MET A 914 THR A 921 -1 N ARG A 920 O LEU A 903 SHEET 5 C 5 GLU A 849 LYS A 855 -1 N PHE A 854 O TYR A 915 SHEET 1 D 2 ALA A 875 LEU A 877 0 SHEET 2 D 2 VAL A 888 ALA A 890 -1 N ALA A 890 O ALA A 875 CRYST1 39.860 40.870 42.470 99.40 95.29 113.69 P 1 1 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 0.025088 0.011007 0.004860 0.00000 SCALE2 0.000000 0.026719 0.006018 0.00000 SCALE3 0.000000 0.000000 0.024239 0.00000