PDB Short entry for 2FK1 HEADER METAL BINDING PROTEIN 03-JAN-06 2FK1 TITLE STRUCTURE OF THE ALZHEIMER'S AMYLOID PRECURSOR PROTEIN (APP) COPPER TITLE 2 BINDING DOMAIN IN 'SMALL UNIT CELL' FORM, CU(II)-BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN PRECURSOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 133 TO 189; COMPND 5 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: APP; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPIC-9 KEYWDS ALPHA-BETA TWO-LAYERED SANDWICH, CU(II) COORDINATION, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.K.-W.KONG,M.W.PARKER REVDAT 4 30-AUG-23 2FK1 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2FK1 1 VERSN REVDAT 2 27-MAR-07 2FK1 1 JRNL REVDAT 1 16-JAN-07 2FK1 0 JRNL AUTH G.K.KONG,J.J.ADAMS,H.H.HARRIS,J.F.BOAS,C.C.CURTAIN, JRNL AUTH 2 D.GALATIS,C.L.MASTERS,K.J.BARNHAM,W.J.MCKINSTRY,R.CAPPAI, JRNL AUTH 3 M.W.PARKER JRNL TITL STRUCTURAL STUDIES OF THE ALZHEIMER'S AMYLOID PRECURSOR JRNL TITL 2 PROTEIN COPPER-BINDING DOMAIN REVEAL HOW IT BINDS COPPER JRNL TITL 3 IONS JRNL REF J.MOL.BIOL. V. 367 148 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17239395 JRNL DOI 10.1016/J.JMB.2006.12.041 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 624974.470 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 6912 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) : 0.188 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 675 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 784 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 100 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 475 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 68 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82000 REMARK 3 B22 (A**2) : -1.48000 REMARK 3 B33 (A**2) : 0.66000 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) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : -0.0 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.920 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) : 1.390 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.060 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.480 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.530 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 36.19 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_ED.PARAM REMARK 3 PARAMETER FILE 2 : WATER.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 2FK1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000035969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3784 REMARK 200 MONOCHROMATOR : DIAMOND (111) DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : BENT CYLINDRICAL SI-MIRROR (RH REMARK 200 COATED) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7238 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1000 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 (%) : 66.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.12900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2FJZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 8.0, 28 - 32 % (W/V) REMARK 280 PEG 10000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 15.71850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.20100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.27250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.20100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.71850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.27250 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: 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 LEU A 172 62.94 60.50 REMARK 500 ASP A 177 23.23 -141.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 54 O REMARK 620 2 HOH A 55 O 80.6 REMARK 620 3 HIS A 147 NE2 106.6 105.0 REMARK 620 4 HIS A 151 ND1 72.1 103.3 151.0 REMARK 620 5 TYR A 168 OH 174.3 97.7 79.1 103.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OWT RELATED DB: PDB REMARK 900 RELATED ID: 2FJZ RELATED DB: PDB REMARK 900 RELATED ID: 2FK2 RELATED DB: PDB REMARK 900 RELATED ID: 2FK3 RELATED DB: PDB DBREF 2FK1 A 133 189 UNP P05067 A4_HUMAN 133 189 SEQADV 2FK1 GLU A 131 UNP P05067 CLONING ARTIFACT SEQADV 2FK1 ALA A 132 UNP P05067 CLONING ARTIFACT SEQRES 1 A 59 GLU ALA CYS LYS PHE LEU HIS GLN GLU ARG MET ASP VAL SEQRES 2 A 59 CYS GLU THR HIS LEU HIS TRP HIS THR VAL ALA LYS GLU SEQRES 3 A 59 THR CYS SER GLU LYS SER THR ASN LEU HIS ASP TYR GLY SEQRES 4 A 59 MET LEU LEU PRO CYS GLY ILE ASP LYS PHE ARG GLY VAL SEQRES 5 A 59 GLU PHE VAL CYS CYS PRO LEU HET CU A 101 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ FORMUL 3 HOH *68(H2 O) HELIX 1 1 THR A 146 LYS A 161 1 16 SHEET 1 A 3 LYS A 134 GLU A 139 0 SHEET 2 A 3 LYS A 178 PRO A 188 -1 O PHE A 184 N LEU A 136 SHEET 3 A 3 THR A 163 CYS A 174 -1 N ASN A 164 O CYS A 187 SSBOND 1 CYS A 133 CYS A 187 1555 1555 2.06 SSBOND 2 CYS A 144 CYS A 174 1555 1555 2.02 SSBOND 3 CYS A 158 CYS A 186 1555 1555 2.04 LINK O HOH A 54 CU CU A 101 1555 1555 2.52 LINK O HOH A 55 CU CU A 101 1555 1555 2.39 LINK CU CU A 101 NE2 HIS A 147 1555 1555 2.31 LINK CU CU A 101 ND1 HIS A 151 1555 1555 1.95 LINK CU CU A 101 OH TYR A 168 1555 1555 1.92 SITE 1 AC1 5 HOH A 54 HOH A 55 HIS A 147 HIS A 151 SITE 2 AC1 5 TYR A 168 CRYST1 31.437 32.545 50.402 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 0.031810 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030727 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019840 0.00000