HEADER CHAPERONE 26-JUL-22 8DTS TITLE X-RAY CRYSTAL STRUCTURE OF AFSSFN FROM CHAPERONE DNAJB8. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNAJB8 PEPTIDE AFSSFN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J, K, L; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CHAPERONE, AMYLOID EXPDTA X-RAY DIFFRACTION AUTHOR D.R.BOYER,B.RYDER,M.R.SAWAYA,L.A.JOACHIMIAK REVDAT 2 14-AUG-24 8DTS 1 JRNL REVDAT 1 31-JAN-24 8DTS 0 JRNL AUTH B.D.RYDER,E.USTYANTSEVA,D.R.BOYER,A.MENDOZA-OLIVA,M.I.KUSKA, JRNL AUTH 2 P.M.WYDORSKI,P.MACIERZYNSKA,N.MORGAN,M.R.SAWAYA,M.I.DIAMOND, JRNL AUTH 3 H.H.KAMPINGA,L.A.JOACHIMIAK JRNL TITL DNAJB8 OLIGOMERIZATION IS MEDIATED BY AN AROMATIC-RICH MOTIF JRNL TITL 2 THAT IS DISPENSABLE FOR SUBSTRATE ACTIVITY. JRNL REF STRUCTURE V. 32 662 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 38508190 JRNL DOI 10.1016/J.STR.2024.02.015 REMARK 2 REMARK 2 RESOLUTION. 0.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.3 REMARK 3 NUMBER OF REFLECTIONS : 48485 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4849 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 19.1900 - 2.3300 0.95 1548 174 0.1934 0.2246 REMARK 3 2 2.3300 - 1.8500 0.97 1609 179 0.1912 0.2200 REMARK 3 3 1.8500 - 1.6200 0.94 1538 172 0.2000 0.2333 REMARK 3 4 1.6200 - 1.4700 0.97 1632 180 0.1828 0.1919 REMARK 3 5 1.4700 - 1.3600 0.98 1575 175 0.1891 0.2238 REMARK 3 6 1.3600 - 1.2800 0.95 1593 178 0.1920 0.2252 REMARK 3 7 1.2800 - 1.2200 0.94 1542 171 0.1880 0.2029 REMARK 3 8 1.2200 - 1.1700 0.94 1541 171 0.1823 0.1765 REMARK 3 9 1.1700 - 1.1200 0.94 1588 176 0.1709 0.1780 REMARK 3 10 1.1200 - 1.0800 0.96 1570 174 0.1791 0.1915 REMARK 3 11 1.0800 - 1.0500 0.95 1511 167 0.1714 0.1910 REMARK 3 12 1.0500 - 1.0200 0.90 1524 170 0.1865 0.2065 REMARK 3 13 1.0200 - 0.9900 0.94 1549 172 0.1971 0.2185 REMARK 3 14 0.9900 - 0.9700 0.96 1571 174 0.1959 0.2004 REMARK 3 15 0.9700 - 0.9500 0.95 1506 168 0.1936 0.2320 REMARK 3 16 0.9500 - 0.9200 0.88 1512 167 0.2092 0.2050 REMARK 3 17 0.9200 - 0.9100 0.91 1487 166 0.2134 0.2237 REMARK 3 18 0.9100 - 0.8900 0.91 1514 168 0.2351 0.2636 REMARK 3 19 0.8900 - 0.8700 0.94 1484 165 0.2385 0.2755 REMARK 3 20 0.8700 - 0.8600 0.93 1506 168 0.2480 0.2528 REMARK 3 21 0.8600 - 0.8400 0.84 1452 161 0.2524 0.2731 REMARK 3 22 0.8400 - 0.8300 0.83 1379 153 0.2680 0.3338 REMARK 3 23 0.8300 - 0.8200 0.83 1390 155 0.2688 0.3155 REMARK 3 24 0.8200 - 0.8100 0.83 1358 151 0.3014 0.3371 REMARK 3 25 0.8100 - 0.8000 0.81 1259 139 0.2760 0.3036 REMARK 3 26 0.8000 - 0.7900 0.80 1336 149 0.2762 0.3146 REMARK 3 27 0.7900 - 0.7800 0.71 1166 130 0.2821 0.3027 REMARK 3 28 0.7800 - 0.7700 0.70 1212 134 0.2995 0.3354 REMARK 3 29 0.7700 - 0.7600 0.69 1107 123 0.2967 0.2984 REMARK 3 30 0.7600 - 0.7500 0.65 1077 119 0.3068 0.3474 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.095 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.49 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 : 0.008 921 REMARK 3 ANGLE : 1.114 1239 REMARK 3 CHIRALITY : 0.086 112 REMARK 3 PLANARITY : 0.008 171 REMARK 3 DIHEDRAL : 10.563 271 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8DTS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000267276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48640 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.750 REMARK 200 RESOLUTION RANGE LOW (A) : 38.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.58200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.310 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 10.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AFSSFN SYNTHETIC PEPTIDE (GENSCRIPT) REMARK 280 WAS DISSOLVED TO 30 MG/ML IN WATER AND CRYSTALLIZED BY HANGING REMARK 280 DROP AT A 1:2 RATIO WITH 20% PEG 8000, 100 MM HEPES PH 7.5., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, L 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 DBREF 8DTS A 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS B 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS C 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS D 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS E 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS F 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS G 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS H 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS I 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS J 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS K 147 152 PDB 8DTS 8DTS 147 152 DBREF 8DTS L 147 152 PDB 8DTS 8DTS 147 152 SEQRES 1 A 6 ALA PHE SER SER PHE ASN SEQRES 1 B 6 ALA PHE SER SER PHE ASN SEQRES 1 C 6 ALA PHE SER SER PHE ASN SEQRES 1 D 6 ALA PHE SER SER PHE ASN SEQRES 1 E 6 ALA PHE SER SER PHE ASN SEQRES 1 F 6 ALA PHE SER SER PHE ASN SEQRES 1 G 6 ALA PHE SER SER PHE ASN SEQRES 1 H 6 ALA PHE SER SER PHE ASN SEQRES 1 I 6 ALA PHE SER SER PHE ASN SEQRES 1 J 6 ALA PHE SER SER PHE ASN SEQRES 1 K 6 ALA PHE SER SER PHE ASN SEQRES 1 L 6 ALA PHE SER SER PHE ASN FORMUL 13 HOH *32(H2 O) SHEET 1 AA1 2 PHE A 148 SER A 150 0 SHEET 2 AA1 2 PHE L 148 SER L 150 -1 O SER L 149 N SER A 149 SHEET 1 AA2 2 PHE B 148 SER B 150 0 SHEET 2 AA2 2 PHE K 148 SER K 150 -1 O SER K 150 N PHE B 148 SHEET 1 AA3 2 PHE C 148 SER C 150 0 SHEET 2 AA3 2 PHE J 148 SER J 150 -1 O SER J 150 N PHE C 148 SHEET 1 AA4 2 PHE D 148 SER D 150 0 SHEET 2 AA4 2 PHE H 148 SER H 150 -1 O SER H 149 N SER D 149 SHEET 1 AA5 2 PHE E 148 SER E 150 0 SHEET 2 AA5 2 PHE F 148 SER F 150 -1 O SER F 149 N SER E 149 SHEET 1 AA6 2 PHE G 148 SER G 150 0 SHEET 2 AA6 2 PHE I 148 SER I 150 -1 O PHE I 148 N SER G 150 CRYST1 38.380 9.480 30.400 90.00 90.00 90.01 P 1 12 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 0.026055 0.000005 0.000000 0.00000 SCALE2 0.000000 0.105485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032895 0.00000 MASTER 207 0 0 0 12 0 0 6 608 12 0 12 END