HEADER PROTEIN FIBRIL 18-AUG-21 7RVK TITLE SEGMENT FROM Y169G MUTANT OF THE HUMAN PRION PROTEIN 169-175 GSNQNNF COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 169-175; COMPND 5 SYNONYM: PRP,ASCR,PRP27-30,PRP33-35C; COMPND 6 ENGINEERED: YES; COMPND 7 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, PRION, FIBRIL, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR C.GLYNN,J.A.RODRIGUEZ,E.HERNANDEZ REVDAT 1 24-AUG-22 7RVK 0 JRNL AUTH C.GLYNN,E.HERNANDEZ,M.GALLAGHER-JONES,J.MIAO,J.A.RODRIGUEZ JRNL TITL STRUCTURAL AND BIOPHYSICAL CONSEQUENCES OF SEQUENCE JRNL TITL 2 VARIATION IN THE B2A2 LOOP OF MAMMALIAN PRIONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.3 REMARK 3 NUMBER OF REFLECTIONS : 2075 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 208 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) : 1.00 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.12 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.30 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 550 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2084 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 495 REMARK 3 BIN R VALUE (WORKING SET) : 0.2067 REMARK 3 BIN FREE R VALUE : 0.2223 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 55 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 55 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 3.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01650 REMARK 3 B22 (A**2) : 0.23530 REMARK 3 B33 (A**2) : -0.21880 REMARK 3 B12 (A**2) : 0.11790 REMARK 3 B13 (A**2) : 0.21730 REMARK 3 B23 (A**2) : -0.10160 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.189 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.040 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.045 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.043 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.045 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 : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 103 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 175 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 19 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 5 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 18 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 103 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 6 ; 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 : 93 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.94 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.14 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 24.60 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 7RVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000259073. 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 : 22-SEP-16 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 6.00 REMARK 240 NUMBER OF CRYSTALS USED : 1 REMARK 240 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 300 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 2076 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 240 RESOLUTION RANGE LOW (A) : 13.840 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 80.3 REMARK 240 DATA REDUNDANCY : 6.217 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.00 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.03 REMARK 240 COMPLETENESS FOR SHELL (%) : 64.7 REMARK 240 DATA REDUNDANCY IN SHELL : 4.26 REMARK 240 R MERGE FOR SHELL (I) : 0.43000 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 240 SOFTWARE USED : SHELXD REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 169 N REMARK 620 2 GLY A 169 O 76.4 REMARK 620 3 PHE A 175 OXT 114.3 49.5 REMARK 620 4 ACT A 201 OXT 111.3 96.6 54.2 REMARK 620 5 ACT A 201 O 67.8 90.6 77.4 43.7 REMARK 620 N 1 2 3 4 DBREF 7RVK A 169 175 UNP P04156 PRIO_HUMAN 169 175 SEQADV 7RVK GLY A 169 UNP P04156 TYR 169 ENGINEERED MUTATION SEQRES 1 A 7 GLY SER ASN GLN ASN ASN PHE HET ACT A 201 7 HET ZN A 202 1 HETNAM ACT ACETATE ION HETNAM ZN ZINC ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *6(H2 O) LINK N GLY A 169 ZN ZN A 202 1555 1555 2.10 LINK O GLY A 169 ZN ZN A 202 1555 1555 2.26 LINK OXT PHE A 175 ZN ZN A 202 1555 1564 2.20 LINK OXT ACT A 201 ZN ZN A 202 1555 1555 1.95 LINK O ACT A 201 ZN ZN A 202 1555 1455 1.88 CRYST1 4.860 14.110 18.410 90.00 93.71 101.21 P 1 1 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 0.205761 0.040779 0.013867 0.00000 SCALE2 0.000000 0.072250 0.000929 0.00000 SCALE3 0.000000 0.000000 0.054437 0.00000