HEADER MEMBRANE PROTEIN 28-JUN-99 1QTP TITLE CRYSTAL STRUCTURE OF THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT (ALPHA-ADAPTIN C); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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: BL4; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-2T; SOURCE 10 OTHER_DETAILS: MUS MUSCULUS KEYWDS FOUR-WAVELENGTH MAD, SELENOMETHIONINE, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.M.TRAUB,M.A.DOWNS,J.L.WESTRICH,D.H.FREMONT REVDAT 6 21-DEC-22 1QTP 1 SEQADV LINK REVDAT 5 24-FEB-09 1QTP 1 VERSN REVDAT 4 01-APR-03 1QTP 1 JRNL REVDAT 3 23-JUN-00 1QTP 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQADV REVDAT 2 31-AUG-99 1QTP 1 JRNL REVDAT 1 12-JUL-99 1QTP 0 JRNL AUTH L.M.TRAUB,M.A.DOWNS,J.L.WESTRICH,D.H.FREMONT JRNL TITL CRYSTAL STRUCTURE OF THE ALPHA APPENDAGE OF AP-2 REVEALS A JRNL TITL 2 RECRUITMENT PLATFORM FOR CLATHRIN-COAT ASSEMBLY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 8907 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 10430869 JRNL DOI 10.1073/PNAS.96.16.8907 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0100 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 29053 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 5% REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1487 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2695 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 155 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1957 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : -0.05000 REMARK 3 B13 (A**2) : -0.08000 REMARK 3 B23 (A**2) : 0.02000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.15 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) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.260 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) : 1.410 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.090 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.480 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.830 ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QTP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000009255. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-98; NULL; NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 110; NULL; NULL; NULL REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y; Y REMARK 200 RADIATION SOURCE : APS; APS; APS; APS REMARK 200 BEAMLINE : 19-ID; 19-ID; 19-ID; 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07813; 0.97956; 0.97945; REMARK 200 0.94645 REMARK 200 MONOCHROMATOR : NULL; NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL; NULL; NULL REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE; NULL; NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57749 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 2.580 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH; SINGLE REMARK 200 WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M MAGNESIUM SULFATE, 100 MM MES, REMARK 280 10MM SPERMINE TETRA-HCL, PH 6.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 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 ARG A 697 79.06 -100.68 REMARK 500 ASN A 719 -161.08 -119.39 REMARK 500 GLN A 732 -130.19 55.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QTP A 692 938 UNP P17427 AP2A2_MOUSE 692 938 SEQADV 1QTP GLY A 692 UNP P17427 SER 692 CONFLICT SEQADV 1QTP SER A 693 UNP P17427 ALA 693 CONFLICT SEQADV 1QTP PRO A 694 UNP P17427 VAL 694 CONFLICT SEQADV 1QTP GLY A 695 UNP P17427 ALA 695 CONFLICT SEQADV 1QTP ILE A 696 UNP P17427 PRO 696 CONFLICT SEQADV 1QTP ARG A 697 UNP P17427 LEU 697 CONFLICT SEQADV 1QTP LEU A 698 UNP P17427 ALA 698 CONFLICT SEQADV 1QTP GLY A 699 UNP P17427 PRO 699 CONFLICT SEQADV 1QTP SER A 700 UNP P17427 GLY 700 CONFLICT SEQADV 1QTP MSE A 737 UNP P17427 MET 737 MODIFIED RESIDUE SEQADV 1QTP MSE A 831 UNP P17427 MET 831 MODIFIED RESIDUE SEQADV 1QTP MSE A 860 UNP P17427 MET 860 MODIFIED RESIDUE SEQADV 1QTP MSE A 914 UNP P17427 MET 914 MODIFIED RESIDUE SEQRES 1 A 247 GLY SER PRO GLY ILE ARG LEU GLY SER SER GLU ASP ASN SEQRES 2 A 247 PHE ALA ARG PHE VAL CYS LYS ASN ASN GLY VAL LEU PHE SEQRES 3 A 247 GLU ASN GLN LEU LEU GLN ILE GLY LEU LYS SER GLU PHE SEQRES 4 A 247 ARG GLN ASN LEU GLY ARG MSE PHE ILE PHE TYR GLY ASN SEQRES 5 A 247 LYS THR SER THR GLN PHE LEU ASN PHE THR PRO THR LEU SEQRES 6 A 247 ILE CYS ALA ASP ASP LEU GLN THR ASN LEU ASN LEU GLN SEQRES 7 A 247 THR LYS PRO VAL ASP PRO THR VAL ASP GLY GLY ALA GLN SEQRES 8 A 247 VAL GLN GLN VAL VAL ASN ILE GLU CYS ILE SER ASP PHE SEQRES 9 A 247 THR GLU ALA PRO VAL LEU ASN ILE GLN PHE ARG TYR GLY SEQRES 10 A 247 GLY THR PHE GLN ASN VAL SER VAL LYS LEU PRO ILE THR SEQRES 11 A 247 LEU ASN LYS PHE PHE GLN PRO THR GLU MSE ALA SER GLN SEQRES 12 A 247 ASP PHE PHE GLN ARG TRP LYS GLN LEU SER ASN PRO GLN SEQRES 13 A 247 GLN GLU VAL GLN ASN ILE PHE LYS ALA LYS HIS PRO MSE SEQRES 14 A 247 ASP THR GLU ILE THR LYS ALA LYS ILE ILE GLY PHE GLY SEQRES 15 A 247 SER ALA LEU LEU GLU GLU VAL ASP PRO ASN PRO ALA ASN SEQRES 16 A 247 PHE VAL GLY ALA GLY ILE ILE HIS THR LYS THR THR GLN SEQRES 17 A 247 ILE GLY CYS LEU LEU ARG LEU GLU PRO ASN LEU GLN ALA SEQRES 18 A 247 GLN MSE TYR ARG LEU THR LEU ARG THR SER LYS ASP THR SEQRES 19 A 247 VAL SER GLN ARG LEU CYS GLU LEU LEU SER GLU GLN PHE MODRES 1QTP MSE A 737 MET SELENOMETHIONINE MODRES 1QTP MSE A 831 MET SELENOMETHIONINE MODRES 1QTP MSE A 860 MET SELENOMETHIONINE MODRES 1QTP MSE A 914 MET SELENOMETHIONINE HET MSE A 737 8 HET MSE A 831 8 HET MSE A 860 8 HET MSE A 914 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 HOH *266(H2 O) HELIX 1 1 ASN A 704 VAL A 709 5 6 HELIX 2 2 ALA A 759 ASN A 765 1 7 HELIX 3 3 THR A 821 LYS A 824 5 4 HELIX 4 4 ALA A 832 LYS A 841 1 10 HELIX 5 5 ASN A 845 GLN A 847 5 3 HELIX 6 6 ASP A 861 GLY A 873 1 13 HELIX 7 7 LYS A 923 GLU A 936 1 14 SHEET 1 A 5 ASN A 713 GLU A 718 0 SHEET 2 A 5 LEU A 722 ARG A 731 -1 N ILE A 724 O PHE A 717 SHEET 3 A 5 LEU A 734 ASN A 743 -1 N LEU A 734 O ARG A 731 SHEET 4 A 5 GLN A 782 CYS A 791 -1 O VAL A 783 N TYR A 741 SHEET 5 A 5 LEU A 766 THR A 770 -1 N ASN A 767 O GLU A 790 SHEET 1 B 3 LEU A 750 ILE A 757 0 SHEET 2 B 3 VAL A 800 TYR A 807 -1 O VAL A 800 N ILE A 757 SHEET 3 B 3 THR A 810 LYS A 817 -1 O THR A 810 N TYR A 807 SHEET 1 C 5 GLU A 849 LYS A 855 0 SHEET 2 C 5 MSE A 914 THR A 921 -1 N TYR A 915 O PHE A 854 SHEET 3 C 5 GLN A 899 ASN A 909 -1 N LEU A 903 O ARG A 920 SHEET 4 C 5 PHE A 887 HIS A 894 -1 O PHE A 887 N LEU A 906 SHEET 5 C 5 PHE A 826 PRO A 828 -1 O GLN A 827 N ILE A 892 SHEET 1 C1 5 GLU A 849 LYS A 855 0 SHEET 2 C1 5 MSE A 914 THR A 921 -1 N TYR A 915 O PHE A 854 SHEET 3 C1 5 GLN A 899 ASN A 909 -1 N LEU A 903 O ARG A 920 SHEET 4 C1 5 PHE A 887 HIS A 894 -1 O PHE A 887 N LEU A 906 SHEET 5 C1 5 ALA A 875 LEU A 877 -1 N ALA A 875 O ALA A 890 LINK C ARG A 736 N MSE A 737 1555 1555 1.33 LINK C MSE A 737 N PHE A 738 1555 1555 1.33 LINK C GLU A 830 N MSE A 831 1555 1555 1.32 LINK C MSE A 831 N ALA A 832 1555 1555 1.33 LINK C PRO A 859 N MSE A 860 1555 1555 1.32 LINK C MSE A 860 N ASP A 861 1555 1555 1.32 LINK C GLN A 913 N MSE A 914 1555 1555 1.33 LINK C MSE A 914 N TYR A 915 1555 1555 1.33 CRYST1 38.700 40.730 41.840 99.68 95.81 113.60 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 0.025840 0.011289 0.005355 0.00000 SCALE2 0.000000 0.026793 0.006300 0.00000 SCALE3 0.000000 0.000000 0.024679 0.00000