HEADER LIPID BINDING PROTEIN 06-OCT-14 4RIL TITLE STRUCTURE OF THE AMYLOID FORMING SEGMENT, GAVVTGVTAVA, FROM THE NAC TITLE 2 DOMAIN OF PARKINSON'S DISEASE PROTEIN ALPHA-SYNUCLEIN, RESIDUES 68- TITLE 3 78, DETERMINED BY ELECTRON DIFFRACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-SYNUCLEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NON-A BETA COMPONENT OF AD AMYLOID, NON-A4 COMPONENT OF COMPND 5 AMYLOID PRECURSOR, NACP; COMPND 6 ENGINEERED: 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; SOURCE 6 OTHER_DETAILS: SYNTHETIC PEPTIDE GAVVTGVTAVA CORRESPONDING TO SOURCE 7 SEGMENT 68-78 OF HUMAN ALPHA-SYNUCLEIN KEYWDS AMYLOID, ALPHA-SYNUCLEIN, PARKINSON'S DISEASE, TOXIC CORE, NACORE, KEYWDS 2 LIPID BINDING PROTEIN EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR J.A.RODRIGUEZ,M.IVANOVA,M.R.SAWAYA,D.CASCIO,F.REYES,D.SHI,L.JOHNSON, AUTHOR 2 E.GUENTHER,S.SANGWAN,J.HATTNE,B.NANNENGA,A.S.BREWSTER, AUTHOR 3 M.MESSERSCHMIDT,S.BOUTET,N.K.SAUTER,T.GONEN,D.S.EISENBERG REVDAT 7 20-SEP-23 4RIL 1 REMARK REVDAT 6 30-JUN-21 4RIL 1 REMARK REVDAT 5 25-APR-18 4RIL 1 REMARK REVDAT 4 07-OCT-15 4RIL 1 JRNL REVDAT 3 23-SEP-15 4RIL 1 JRNL REVDAT 2 09-SEP-15 4RIL 1 JRNL REVDAT 1 26-AUG-15 4RIL 0 JRNL AUTH J.A.RODRIGUEZ,M.I.IVANOVA,M.R.SAWAYA,D.CASCIO,F.E.REYES, JRNL AUTH 2 D.SHI,S.SANGWAN,E.L.GUENTHER,L.M.JOHNSON,M.ZHANG,L.JIANG, JRNL AUTH 3 M.A.ARBING,B.L.NANNENGA,J.HATTNE,J.WHITELEGGE,A.S.BREWSTER, JRNL AUTH 4 M.MESSERSCHMIDT,S.BOUTET,N.K.SAUTER,T.GONEN,D.S.EISENBERG JRNL TITL STRUCTURE OF THE TOXIC CORE OF ALPHA-SYNUCLEIN FROM JRNL TITL 2 INVISIBLE CRYSTALS. JRNL REF NATURE V. 525 486 2015 JRNL REFN ISSN 0028-0836 JRNL PMID 26352473 JRNL DOI 10.1038/NATURE15368 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 1073 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 + TEST SET) : 0.251 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.840 REMARK 3 FREE R VALUE TEST SET COUNT : 127 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.88 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 286 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2642 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 245 REMARK 3 BIN R VALUE (WORKING SET) : 0.2532 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 14.34 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 41 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 66 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.98760 REMARK 3 B22 (A**2) : 3.49080 REMARK 3 B33 (A**2) : 0.49680 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.55090 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.305 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.108 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.913 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 65 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 90 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 16 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 1 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 10 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 65 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 11 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 76 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.65 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.08 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 6.49 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4RIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000087390. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NANOCRYSTALS REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : 28-AUG-14 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 4.00 REMARK 240 NUMBER OF CRYSTALS USED : 4 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 : 1073 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 240 RESOLUTION RANGE LOW (A) : 16.430 REMARK 240 DATA SCALING SOFTWARE : AIMLESS 0.3.11, XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 240 DATA REDUNDANCY : 4.400 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.43 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.60 REMARK 240 COMPLETENESS FOR SHELL (%) : 82.5 REMARK 240 DATA REDUNDANCY IN SHELL : 4.40 REMARK 240 R MERGE FOR SHELL (I) : 0.56500 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER 2.5.6 REMARK 240 STARTING MODEL : 4RIK REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.40500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.41000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.40500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.41000 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 300 REMARK: THE BIOLOGICAL UNIT IS A PAIR OF BETA-SHEETS. ONE SHEET IS REMARK 300 COMPOSED OF CHAIN A AND UNIT CELL TRANSLATIONS ALONG THE B REMARK 300 DIMENSION. THE OTHER SHEET IS COMPOSED OF THE SYMMETRY MATE -X+1/2, REMARK 300 Y+1/2,-Z, AND UNIT CELL TRANSLATIONS ALONG B. 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: DECAMERIC 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -9.64000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -4.82000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 4.82000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 9.64000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 35.40500 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 -7.23000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 35.40500 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 -2.41000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 35.40500 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 2.41000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 35.40500 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 7.23000 REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 35.40500 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 12.05000 REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-3028 RELATED DB: EMDB DBREF 4RIL A 68 78 UNP P37840 SYUA_HUMAN 68 78 SEQRES 1 A 11 GLY ALA VAL VAL THR GLY VAL THR ALA VAL ALA FORMUL 2 HOH *2(H2 O) CRYST1 70.810 4.820 16.790 90.00 105.68 90.00 C 1 2 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 0.014122 0.000000 0.003964 0.00000 SCALE2 0.000000 0.207469 0.000000 0.00000 SCALE3 0.000000 0.000000 0.061861 0.00000