HEADER PROTEIN FIBRIL 05-AUG-22 8ANL TITLE STRUCTURE OF THE AMYLOID-FORMING PEPTIDE LFIEWL FROM EXENDIN-4, GROWN TITLE 2 FROM WATER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE LFIEWL FROM EXENDIN-4; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HELODERMA SUSPECTUM; SOURCE 4 ORGANISM_TAXID: 8554 KEYWDS AMYLOID, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR Z.DURVANGER REVDAT 3 19-JUN-24 8ANL 1 REMARK REVDAT 2 09-AUG-23 8ANL 1 JRNL REVDAT 1 02-AUG-23 8ANL 0 JRNL AUTH D.HORVATH,Z.DURVANGER,D.K MENYHARD,M.SULYOK-EILER,F.BENCS, JRNL AUTH 2 G.GYULAI,P.HORVATH,N.TARICSKA,A.PERCZEL JRNL TITL POLYMORPHIC AMYLOID NANOSTRUCTURES OF HORMONE PEPTIDES JRNL TITL 2 INVOLVED IN GLUCOSE HOMEOSTASIS DISPLAY REVERSIBLE AMYLOID JRNL TITL 3 FORMATION. JRNL REF NAT COMMUN V. 14 4621 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37528104 JRNL DOI 10.1038/S41467-023-40294-X REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 1780 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 178 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 14.2100 - 1.7500 0.98 1602 178 0.1761 0.2125 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.187 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.488 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.56 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 : 0.018 250 REMARK 3 ANGLE : 1.779 342 REMARK 3 CHIRALITY : 0.072 38 REMARK 3 PLANARITY : 0.009 37 REMARK 3 DIHEDRAL : 13.753 80 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.1698 0.6966 -1.1209 REMARK 3 T TENSOR REMARK 3 T11: 0.0423 T22: 0.0979 REMARK 3 T33: 0.0891 T12: 0.0040 REMARK 3 T13: -0.0190 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 3.4321 L22: 6.8255 REMARK 3 L33: 7.1508 L12: 0.3083 REMARK 3 L13: -1.0717 L23: -5.2535 REMARK 3 S TENSOR REMARK 3 S11: 0.1212 S12: 0.3882 S13: -0.0521 REMARK 3 S21: 0.0046 S22: -0.1417 S23: 0.0401 REMARK 3 S31: -0.2580 S32: 0.3405 S33: -0.0626 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.8783 -1.2855 1.9750 REMARK 3 T TENSOR REMARK 3 T11: 0.0640 T22: 0.1135 REMARK 3 T33: 0.0729 T12: 0.0069 REMARK 3 T13: -0.0373 T23: 0.0691 REMARK 3 L TENSOR REMARK 3 L11: 3.0556 L22: 4.2305 REMARK 3 L33: 4.3000 L12: -0.8080 REMARK 3 L13: 0.6437 L23: -0.1656 REMARK 3 S TENSOR REMARK 3 S11: -0.0185 S12: -0.7036 S13: -0.3331 REMARK 3 S21: 0.2850 S22: 0.3229 S23: 0.1056 REMARK 3 S31: 0.2868 S32: -0.3143 S33: 0.0681 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.1158 0.9182 -17.9007 REMARK 3 T TENSOR REMARK 3 T11: 0.1364 T22: 0.1083 REMARK 3 T33: 0.1197 T12: 0.0582 REMARK 3 T13: -0.0234 T23: 0.0309 REMARK 3 L TENSOR REMARK 3 L11: 4.1365 L22: 9.0780 REMARK 3 L33: 7.6477 L12: 0.2379 REMARK 3 L13: 0.1895 L23: -6.6532 REMARK 3 S TENSOR REMARK 3 S11: 0.0526 S12: -0.0467 S13: 0.1331 REMARK 3 S21: -0.2561 S22: -0.0852 S23: 0.0180 REMARK 3 S31: 0.2726 S32: -0.0120 S33: -0.0519 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.8143 -1.3684 -15.3345 REMARK 3 T TENSOR REMARK 3 T11: 0.1024 T22: 0.1673 REMARK 3 T33: 0.1108 T12: 0.0272 REMARK 3 T13: 0.0230 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 5.3379 L22: 8.4478 REMARK 3 L33: 9.4142 L12: 1.1647 REMARK 3 L13: -0.9575 L23: -7.0521 REMARK 3 S TENSOR REMARK 3 S11: 0.0645 S12: -0.1788 S13: -0.0401 REMARK 3 S21: 0.3146 S22: -0.1293 S23: 0.0516 REMARK 3 S31: -0.2189 S32: 0.0650 S33: 0.2352 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 8ANL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1292124772. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-AUG-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU PHOTONJET-R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1803 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 14.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.140 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: CRYSTAL STRUCTURE OF LYIQWL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LYOPHILIZED PEPTIDE WAS DISSOLVED IN REMARK 280 WATER (0.15 MG/ML CONCENTRATION), FOLLOWED BY PH ADJUSTMENT WITH REMARK 280 NAOH TO PH 5.50. CRYSTALS APPEARED AFTER INCUBATION AT 310K FOR REMARK 280 SEVERAL DAYS., EVAPORATION, RECRYSTALLIZATION 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, 2 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: DIMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 8ANL A 1 6 PDB 8ANL 8ANL 1 6 DBREF 8ANL B 1 6 PDB 8ANL 8ANL 1 6 DBREF 8ANL C 1 6 PDB 8ANL 8ANL 1 6 DBREF 8ANL D 1 6 PDB 8ANL 8ANL 1 6 SEQRES 1 A 6 LEU PHE ILE GLU TRP LEU SEQRES 1 B 6 LEU PHE ILE GLU TRP LEU SEQRES 1 C 6 LEU PHE ILE GLU TRP LEU SEQRES 1 D 6 LEU PHE ILE GLU TRP LEU FORMUL 5 HOH *2(H2 O) SHEET 1 AA1 2 PHE A 2 TRP A 5 0 SHEET 2 AA1 2 PHE B 2 TRP B 5 -1 O PHE B 2 N TRP A 5 SHEET 1 AA2 2 PHE C 2 TRP C 5 0 SHEET 2 AA2 2 PHE D 2 TRP D 5 -1 O GLU D 4 N ILE C 3 CRYST1 9.520 14.292 34.287 90.59 93.30 95.97 P 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 0.105042 0.010985 0.006238 0.00000 SCALE2 0.000000 0.070351 0.001154 0.00000 SCALE3 0.000000 0.000000 0.029218 0.00000