HEADER METAL BINDING PROTEIN 04-JAN-06 2FKL TITLE STRUCTURE OF THE ALZHEIMER'S AMYLOID PRECURSOR PROTEIN (APP) COPPER TITLE 2 BINDING DOMAIN (RESIDUES 126- 189 OF APP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN PRECURSOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 124 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, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.K.-W.KONG,M.W.PARKER REVDAT 5 30-OCT-24 2FKL 1 REMARK REVDAT 4 30-AUG-23 2FKL 1 REMARK REVDAT 3 24-FEB-09 2FKL 1 VERSN REVDAT 2 27-MAR-07 2FKL 1 JRNL REVDAT 1 16-JAN-07 2FKL 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. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 402853.510 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 82.8 REMARK 3 NUMBER OF REFLECTIONS : 4562 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 : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 199 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.019 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 57.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 501 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE : 0.4100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 17 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.099 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1026 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.74000 REMARK 3 B22 (A**2) : -1.39000 REMARK 3 B33 (A**2) : -1.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.96000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.24 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) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 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) : 1.630 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.870 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.210 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.560 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 41.29 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 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000035988. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-03 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 4.05 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : BENT GE(111) MONOCHROMATOR REMARK 200 OPTICS : BENT CONICAL SI-MIRROR (RH REMARK 200 COATED) REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR 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 : 5731 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07700 REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.17300 REMARK 200 FOR SHELL : 3.300 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 (%): 52.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M (NH4)H2PO4, PH 4.05, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 17.41150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: MONOMER (THE PACKING ARRANGEMENT WITHIN THE ASYMMETRIC UNIT REMARK 300 IS LIKELY TO BE AN ARTEFACT OF CRYSTALLISATION ONLY) 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 124 REMARK 465 ASP A 125 REMARK 465 SER B 124 REMARK 465 ASP B 125 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 ASP A 131 51.01 26.98 REMARK 500 ASP A 167 171.01 177.45 REMARK 500 LEU A 172 88.15 50.34 REMARK 500 ASP B 131 -57.56 -6.70 REMARK 500 LEU B 172 68.31 62.60 REMARK 500 ILE B 176 79.10 -65.15 REMARK 500 REMARK 500 REMARK: NULL 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: 2FK1 RELATED DB: PDB REMARK 900 RELATED ID: 2FK2 RELATED DB: PDB REMARK 900 RELATED ID: 2FK3 RELATED DB: PDB DBREF 2FKL A 124 189 UNP P05067 A4_HUMAN 124 189 DBREF 2FKL B 124 189 UNP P05067 A4_HUMAN 124 189 SEQRES 1 A 66 SER ASP ALA LEU LEU VAL PRO ASP LYS CYS LYS PHE LEU SEQRES 2 A 66 HIS GLN GLU ARG MET ASP VAL CYS GLU THR HIS LEU HIS SEQRES 3 A 66 TRP HIS THR VAL ALA LYS GLU THR CYS SER GLU LYS SER SEQRES 4 A 66 THR ASN LEU HIS ASP TYR GLY MET LEU LEU PRO CYS GLY SEQRES 5 A 66 ILE ASP LYS PHE ARG GLY VAL GLU PHE VAL CYS CYS PRO SEQRES 6 A 66 LEU SEQRES 1 B 66 SER ASP ALA LEU LEU VAL PRO ASP LYS CYS LYS PHE LEU SEQRES 2 B 66 HIS GLN GLU ARG MET ASP VAL CYS GLU THR HIS LEU HIS SEQRES 3 B 66 TRP HIS THR VAL ALA LYS GLU THR CYS SER GLU LYS SER SEQRES 4 B 66 THR ASN LEU HIS ASP TYR GLY MET LEU LEU PRO CYS GLY SEQRES 5 B 66 ILE ASP LYS PHE ARG GLY VAL GLU PHE VAL CYS CYS PRO SEQRES 6 B 66 LEU FORMUL 3 HOH *19(H2 O) HELIX 1 1 HIS A 147 LYS A 161 1 15 HELIX 2 2 HIS B 147 LYS B 161 1 15 SHEET 1 A 4 VAL A 129 PRO A 130 0 SHEET 2 A 4 ASN B 164 PRO B 173 -1 O MET B 170 N VAL A 129 SHEET 3 A 4 LYS B 178 CYS B 187 -1 O CYS B 187 N ASN B 164 SHEET 4 A 4 LYS B 134 GLU B 139 -1 N LEU B 136 O PHE B 184 SHEET 1 B 4 VAL A 129 PRO A 130 0 SHEET 2 B 4 ASN B 164 PRO B 173 -1 O MET B 170 N VAL A 129 SHEET 3 B 4 LYS B 178 CYS B 187 -1 O CYS B 187 N ASN B 164 SHEET 4 B 4 GLU B 145 THR B 146 -1 N GLU B 145 O PHE B 179 SHEET 1 C 3 LYS A 134 GLU A 139 0 SHEET 2 C 3 LYS A 178 PRO A 188 -1 O CYS A 186 N LYS A 134 SHEET 3 C 3 GLU A 145 THR A 146 -1 N GLU A 145 O PHE A 179 SHEET 1 D 3 LYS A 134 GLU A 139 0 SHEET 2 D 3 LYS A 178 PRO A 188 -1 O CYS A 186 N LYS A 134 SHEET 3 D 3 THR A 163 PRO A 173 -1 N HIS A 166 O VAL A 185 SSBOND 1 CYS A 133 CYS A 187 1555 1555 2.02 SSBOND 2 CYS A 144 CYS A 174 1555 1555 2.03 SSBOND 3 CYS A 158 CYS A 186 1555 1555 2.03 SSBOND 4 CYS B 133 CYS B 187 1555 1555 2.03 SSBOND 5 CYS B 144 CYS B 174 1555 1555 2.02 SSBOND 6 CYS B 158 CYS B 186 1555 1555 2.03 CRYST1 44.694 34.823 50.810 90.00 98.53 90.00 P 1 21 1 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 0.022374 0.000000 0.003357 0.00000 SCALE2 0.000000 0.028717 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019901 0.00000