PDB Short entry for 2FMA HEADER METAL BINDING PROTEIN 08-JAN-06 2FMA TITLE STRUCTURE OF THE ALZHEIMER'S AMYLOID PRECURSOR PROTEIN (APP) COPPER TITLE 2 BINDING DOMAIN IN 'SMALL UNIT CELL' FORM, ATOMIC RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN PRECURSOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: COPPER BINDING DOMAIN(RESIDUES 133-189); COMPND 5 SYNONYM: AMYLOID PRECURSOR PROTEIN, AMYLOID BETA A4 PROTEIN, SOLUBLE COMPND 6 APP-ALPHA, SOLUBLE APP-BETA; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPIC-9 KEYWDS ALPHA-BETA TWO-LAYERED SANDWICH, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.K.-W.KONG REVDAT 5 25-OCT-23 2FMA 1 REMARK SEQADV REVDAT 4 13-JUL-11 2FMA 1 VERSN REVDAT 3 26-JAN-10 2FMA 1 JRNL REVDAT 2 24-FEB-09 2FMA 1 VERSN REVDAT 1 16-JAN-07 2FMA 0 JRNL AUTH G.K.KONG,J.J.ADAMS,R.CAPPAI,M.W.PARKER JRNL TITL STRUCTURE OF ALZHEIMER'S DISEASE AMYLOID PRECURSOR PROTEIN JRNL TITL 2 COPPER-BINDING DOMAIN AT ATOMIC RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 63 819 2007 JRNL REFN ESSN 1744-3091 JRNL PMID 17909280 JRNL DOI 10.1107/S1744309107041139 REMARK 2 REMARK 2 RESOLUTION. 0.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.131 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.131 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2107 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 41418 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.124 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 31537 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 : 6 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 596.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 449.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5469 REMARK 3 NUMBER OF RESTRAINTS : 5492 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.026 REMARK 3 ANGLE DISTANCES (A) : 0.036 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.105 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.105 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.113 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.027 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.094 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FMA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000036047. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-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-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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41418 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.850 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 (%) : 90.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REFINEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: PDB ENTRY 2FJZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 8.0, 28-32% (W/V) PEG REMARK 280 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 15.64450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.04400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.24400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.04400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.64450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.24400 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 155 CD LYS A 155 CE -0.177 REMARK 500 GLU A 160 CD GLU A 160 OE2 -0.073 REMARK 500 GLY A 175 N GLY A 175 CA -0.093 REMARK 500 GLU A 183 CD GLU A 183 OE1 0.093 REMARK 500 GLU A 183 CD GLU A 183 OE2 -0.142 REMARK 500 LEU A 189 C LEU A 189 OXT 0.230 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 ASP A 177 18.52 -152.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1001 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 REMARK 900 RELATED ID: 2FKL RELATED DB: PDB DBREF 2FMA A 133 189 UNP P05067 A4_HUMAN 133 189 SEQADV 2FMA GLU A 131 UNP P05067 CLONING ARTIFACT SEQADV 2FMA 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 GOL A1001 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *115(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 VAL A 182 N GLN A 138 SHEET 3 A 3 THR A 163 CYS A 174 -1 N HIS A 166 O VAL A 185 SSBOND 1 CYS A 133 CYS A 187 1555 1555 2.07 SSBOND 2 CYS A 144 CYS A 174 1555 1555 2.03 SSBOND 3 CYS A 158 CYS A 186 1555 1555 2.03 SITE 1 AC1 9 ALA A 132 HIS A 147 GLY A 169 GLU A 183 SITE 2 AC1 9 VAL A 185 HOH A2005 HOH A2010 HOH A2085 SITE 3 AC1 9 HOH A2088 CRYST1 31.289 32.488 50.088 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 0.031960 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019965 0.00000