HEADER PROTEIN FIBRIL 28-FEB-19 6O4J TITLE AMYLOID BETA KLVFFAENVGS 16-26 D23N IOWA MUTATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PRECURSOR PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 687-697; COMPND 5 SYNONYM: APP, ABPP, APPI, ALZHEIMER DISEASE AMYLOID PROTEIN, AMYLOID COMPND 6 PRECURSOR PROTEIN, AMYLOID-BETA A4 PROTEIN, CEREBRAL VASCULAR AMYLOID COMPND 7 PEPTIDE, CVAP, PREA4, PROTEASE NEXIN-II, PN-II; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR S.L.GRINER,M.R.SAWAYA,J.A.RODRIGUEZ,D.CASCIO,T.GONEN REVDAT 3 11-OCT-23 6O4J 1 REMARK REVDAT 2 18-DEC-19 6O4J 1 REMARK REVDAT 1 30-OCT-19 6O4J 0 JRNL AUTH S.L.GRINER,P.SEIDLER,J.BOWLER,K.A.MURRAY,T.P.YANG,S.SAHAY, JRNL AUTH 2 M.R.SAWAYA,D.CASCIO,J.A.RODRIGUEZ,S.PHILIPP,J.SOSNA, JRNL AUTH 3 C.G.GLABE,T.GONEN,D.S.EISENBERG JRNL TITL STRUCTURE BASED INHIBITORS OF AMYLOID BETA CORE SUGGEST A JRNL TITL 2 COMMON INTERFACE WITH TAU. JRNL REF ELIFE V. 8 2019 JRNL REFN ESSN 2050-084X JRNL PMID 31612856 JRNL DOI 10.7554/ELIFE.46924 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.520 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 3 NUMBER OF REFLECTIONS : 2354 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 11.6409 - 1.7650 0.87 1080 121 0.2187 0.2623 REMARK 3 2 1.7650 - 1.4017 0.86 1038 115 0.2802 0.3334 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.014 180 REMARK 3 ANGLE : 1.458 240 REMARK 3 CHIRALITY : 0.067 26 REMARK 3 PLANARITY : 0.006 32 REMARK 3 DIHEDRAL : 15.776 60 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 80 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6O4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1000239957. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : 07-NOV-14 REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : 1 REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 2355 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 240 RESOLUTION RANGE LOW (A) : 11.640 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 85.4 REMARK 240 DATA REDUNDANCY : 20.21 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.40 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.44 REMARK 240 COMPLETENESS FOR SHELL (%) : 78.0 REMARK 240 DATA REDUNDANCY IN SHELL : 12.06 REMARK 240 R MERGE FOR SHELL (I) : 0.65200 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER REMARK 240 STARTING MODEL : PDB ENTRY 2Y2A 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 25.95500 REMARK 290 SMTRY3 2 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -11.67000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 11.67000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 -5.22655 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 11.64048 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 -16.89655 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 11.64048 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 6.44345 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 11.64048 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-0619 RELATED DB: EMDB REMARK 900 AMYLOID BETA KLVFFAENVGS 16-26 D23N IOWA MUTATION DBREF 6O4J A 16 26 UNP P05067 A4_HUMAN 687 697 DBREF 6O4J B 16 26 UNP P05067 A4_HUMAN 687 697 SEQADV 6O4J ACE A 15 UNP P05067 ACETYLATION SEQADV 6O4J ASN A 23 UNP P05067 ASP 694 ENGINEERED MUTATION SEQADV 6O4J NH2 A 27 UNP P05067 AMIDATION SEQADV 6O4J ACE B 15 UNP P05067 ACETYLATION SEQADV 6O4J ASN B 23 UNP P05067 ASP 694 ENGINEERED MUTATION SEQADV 6O4J NH2 B 27 UNP P05067 AMIDATION SEQRES 1 A 13 ACE LYS LEU VAL PHE PHE ALA GLU ASN VAL GLY SER NH2 SEQRES 1 B 13 ACE LYS LEU VAL PHE PHE ALA GLU ASN VAL GLY SER NH2 HET ACE A 15 3 HET NH2 A 27 1 HET ACE B 15 3 HET NH2 B 27 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 NH2 2(H2 N) SHEET 1 AA1 2 LEU A 17 ALA A 21 0 SHEET 2 AA1 2 LYS B 16 PHE B 20 -1 O LYS B 16 N ALA A 21 LINK C ACE A 15 N LYS A 16 1555 1555 1.33 LINK C SER A 26 N NH2 A 27 1555 1555 1.23 LINK C ACE B 15 N LYS B 16 1555 1555 1.33 LINK C SER B 26 N NH2 B 27 1555 1555 1.24 CRYST1 11.670 51.910 12.760 90.00 114.18 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 0.085690 0.000000 0.038475 0.00000 SCALE2 0.000000 0.019264 0.000000 0.00000 SCALE3 0.000000 0.000000 0.085907 0.00000 HETATM 1 C ACE A 15 5.068 8.573 8.839 1.00 11.66 C HETATM 2 O ACE A 15 6.002 8.093 9.466 1.00 14.02 O HETATM 3 CH3 ACE A 15 5.313 9.279 7.510 1.00 7.84 C