PDB Short entry for 1X45 HEADER ENDOCYTOSIS/EXOCYTOSIS 13-MAY-05 1X45 TITLE SOLUTION STRUCTURE OF THE FIRST PDZ DOMAIN OF AMYLOID BETA A4 TITLE 2 PRECURSOR PROTEIN-BINDING FAMILY A, MEMBER 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA (A4) PRECURSOR PROTEIN-BINDING, FAMILY A, COMPND 3 MEMBER 1 (X11); COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: PDZ DOMAIN; COMPND 6 SYNONYM: NEURON-SPECIFIC XII PROTEIN, NEURONAL MUNC18-1-INTERACTING COMPND 7 PROTEIN 1, MINT-1, ADAPTER PROTEIN X11 ALPHA; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: APBA1, MINT1, X11; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050118-02; SOURCE 8 OTHER_DETAILS: CELL FREE PROTEIN SYNTHESIS KEYWDS PDZ DOMAIN, AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY A, KEYWDS 2 MEMBER 1, NEURON-SPECIFIC XII PROTEIN, ADAPTER PROTEIN XII ALPHA, KEYWDS 3 NEURONAL MUNC 18-1-INTERACTING PROTEIN 1 MINT-1, STRUCTURAL KEYWDS 4 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 5 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 6 INITIATIVE, RSGI, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.R.QIN,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 02-MAR-22 1X45 1 REMARK SEQADV REVDAT 2 24-FEB-09 1X45 1 VERSN REVDAT 1 13-NOV-05 1X45 0 JRNL AUTH X.R.QIN,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE FIRST PDZ DOMAIN OF AMYLOID BETA JRNL TITL 2 A4 PRECURSOR PROTEIN-BINDING FAMILY A, MEMBER 1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT,P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1X45 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024355. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.55MM 13C, 15N-LABELED PROTEIN; REMARK 210 20MM D-TRIS-HCL(PH7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9296, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH REMARK 210 THE LOWEST ENERGY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 1 SER A 2 108.78 -39.84 REMARK 500 1 SER A 6 98.84 -42.97 REMARK 500 1 SER A 26 45.96 -78.27 REMARK 500 1 TRP A 28 96.27 -40.49 REMARK 500 1 PRO A 33 93.53 -69.74 REMARK 500 1 THR A 34 -75.60 -111.90 REMARK 500 1 VAL A 35 144.46 -175.61 REMARK 500 1 ILE A 54 106.90 -54.58 REMARK 500 1 SER A 85 -60.02 -95.23 REMARK 500 1 SER A 93 121.64 -38.75 REMARK 500 1 PRO A 95 88.43 -69.80 REMARK 500 2 SER A 5 49.81 -86.13 REMARK 500 2 SER A 26 31.84 -95.61 REMARK 500 2 TRP A 28 94.42 -63.30 REMARK 500 2 PRO A 33 90.32 -69.69 REMARK 500 2 THR A 34 -76.04 -110.97 REMARK 500 2 VAL A 35 140.29 -176.08 REMARK 500 2 HIS A 42 38.20 -82.65 REMARK 500 2 ILE A 54 105.38 -53.05 REMARK 500 2 VAL A 67 119.81 -39.29 REMARK 500 2 SER A 93 114.83 -36.64 REMARK 500 3 TRP A 28 -74.74 -121.18 REMARK 500 3 PRO A 33 87.28 -69.80 REMARK 500 3 THR A 34 -75.56 -104.50 REMARK 500 3 VAL A 35 140.96 -175.52 REMARK 500 3 HIS A 42 74.69 -67.06 REMARK 500 3 ILE A 54 106.67 -47.31 REMARK 500 3 SER A 93 115.18 -34.27 REMARK 500 4 SER A 26 37.50 -82.97 REMARK 500 4 TRP A 28 66.62 -110.47 REMARK 500 4 PRO A 33 86.37 -69.76 REMARK 500 4 THR A 34 -76.10 -105.91 REMARK 500 4 VAL A 35 142.39 -176.18 REMARK 500 4 HIS A 42 36.82 -89.13 REMARK 500 4 ILE A 54 107.38 -57.02 REMARK 500 4 VAL A 67 122.63 -37.54 REMARK 500 4 SER A 93 109.99 -38.92 REMARK 500 4 SER A 96 -51.67 -127.31 REMARK 500 5 SER A 26 30.43 -88.19 REMARK 500 5 SER A 30 -175.11 -60.96 REMARK 500 5 PRO A 33 84.47 -69.73 REMARK 500 5 THR A 34 -76.22 -104.56 REMARK 500 5 VAL A 35 142.78 -176.27 REMARK 500 5 MET A 41 151.85 -48.34 REMARK 500 5 ILE A 54 105.50 -49.32 REMARK 500 5 SER A 93 107.12 -40.22 REMARK 500 6 PRO A 33 87.47 -69.74 REMARK 500 6 THR A 34 -75.77 -107.23 REMARK 500 6 VAL A 35 141.54 -175.77 REMARK 500 6 HIS A 42 45.03 -84.24 REMARK 500 REMARK 500 THIS ENTRY HAS 167 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO001000025.1 RELATED DB: TARGETDB DBREF 1X45 A 8 92 UNP Q02410 APBA1_HUMAN 656 740 SEQADV 1X45 GLY A 1 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 SER A 2 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 SER A 3 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 GLY A 4 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 SER A 5 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 SER A 6 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 GLY A 7 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 SER A 93 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 GLY A 94 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 PRO A 95 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 SER A 96 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 SER A 97 UNP Q02410 CLONING ARTIFACT SEQADV 1X45 GLY A 98 UNP Q02410 CLONING ARTIFACT SEQRES 1 A 98 GLY SER SER GLY SER SER GLY ASP VAL PHE ILE GLU LYS SEQRES 2 A 98 GLN LYS GLY GLU ILE LEU GLY VAL VAL ILE VAL GLU SER SEQRES 3 A 98 GLY TRP GLY SER ILE LEU PRO THR VAL ILE ILE ALA ASN SEQRES 4 A 98 MET MET HIS GLY GLY PRO ALA GLU LYS SER GLY LYS LEU SEQRES 5 A 98 ASN ILE GLY ASP GLN ILE MET SER ILE ASN GLY THR SER SEQRES 6 A 98 LEU VAL GLY LEU PRO LEU SER THR CYS GLN SER ILE ILE SEQRES 7 A 98 LYS GLY LEU LYS ASN GLN SER ARG VAL LYS LEU ASN ILE SEQRES 8 A 98 VAL SER GLY PRO SER SER GLY HELIX 1 1 GLY A 44 GLY A 50 1 7 HELIX 2 2 PRO A 70 GLY A 80 1 11 SHEET 1 A 4 ASP A 8 GLU A 12 0 SHEET 2 A 4 ARG A 86 VAL A 92 -1 O LEU A 89 N VAL A 9 SHEET 3 A 4 GLN A 57 ILE A 61 -1 N GLN A 57 O VAL A 92 SHEET 4 A 4 THR A 64 SER A 65 -1 O THR A 64 N ILE A 61 SHEET 1 B 2 VAL A 21 VAL A 24 0 SHEET 2 B 2 ILE A 36 MET A 40 -1 O ASN A 39 N VAL A 22 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000