HEADER PROTEIN FIBRIL 11-APR-26 29WR TITLE STRUCTURE OF THE AMYLOID-FORMING PEPTIDE LLQGLV FROM HUMAN SECRETIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE LLQGLV FROM SECRETIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR Z.DURVANGER REVDAT 1 04-NOV-26 29WR 0 JRNL AUTH D.HORVATH,S.SZANISZLO,Z.DURVANGER,Z.FAZEKAS,K.H.Y.DUONG, JRNL AUTH 2 A.PERCZEL JRNL TITL EVOLUTIONARILY CONSERVED AMYLOID AGGREGATION IN THE PACAP JRNL TITL 2 PEPTIDE FAMILY IS CONTROLLED BY HEPARIN-SENSITIVE LYS/ARG JRNL TITL 3 GATEKEEPER RESIDUES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 9984 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.118 REMARK 3 R VALUE (WORKING SET) : 0.117 REMARK 3 FREE R VALUE : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 488 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 18.9100 - 1.3700 0.99 3394 170 0.0851 0.1033 REMARK 3 2 1.3700 - 1.0900 0.94 3178 169 0.1267 0.1442 REMARK 3 3 1.0800 - 0.9500 0.87 2924 149 0.2227 0.2619 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) : 0.099 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.043 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 6.41 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 : 0.014 222 REMARK 3 ANGLE : 1.894 302 REMARK 3 CHIRALITY : 0.095 45 REMARK 3 PLANARITY : 0.007 35 REMARK 3 DIHEDRAL : 17.930 83 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 29WR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-APR-26. REMARK 100 THE DEPOSITION ID IS D_1292155922. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-24 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 : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10050 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.948 REMARK 200 RESOLUTION RANGE LOW (A) : 18.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PEPTIDE WAS DISSOLVED AT A REMARK 280 CONCENTRATION OF 5 MG / ML IN 30% (V/V) ETHANOL IN AN EPPENDORF REMARK 280 TUBE WITH A PERFORATED CAP AND INCUBATED AT 310 K. CRYSTALS GREW REMARK 280 ON THE WALL OF THE TUBE UPON SOLVENT EVAPORATION., EVAPORATION, REMARK 280 RECRYSTALLIZATION 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 9.87700 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 29WR A 1 6 PDB 29WR 29WR 1 6 DBREF 29WR B 1 6 PDB 29WR 29WR 1 6 DBREF 29WR C 1 6 PDB 29WR 29WR 1 6 DBREF 29WR D 1 6 PDB 29WR 29WR 1 6 SEQRES 1 A 6 LEU LEU GLN GLY LEU VAL SEQRES 1 B 6 LEU LEU GLN GLY LEU VAL SEQRES 1 C 6 LEU LEU GLN GLY LEU VAL SEQRES 1 D 6 LEU LEU GLN GLY LEU VAL HET EOH A 101 9 HET TFA B 101 7 HET EOH C 101 9 HET EOH C 102 9 HET TFA D 101 7 HETNAM EOH ETHANOL HETNAM TFA TRIFLUOROACETIC ACID FORMUL 5 EOH 3(C2 H6 O) FORMUL 6 TFA 2(C2 H F3 O2) FORMUL 10 HOH *6(H2 O) SHEET 1 AA1 4 LEU A 2 LEU A 5 0 SHEET 2 AA1 4 LEU B 2 VAL B 6 -1 O VAL B 6 N LEU A 2 SHEET 3 AA1 4 LEU C 2 LEU C 5 -1 O GLN C 3 N GLN B 3 SHEET 4 AA1 4 GLN D 3 VAL D 6 -1 O VAL D 6 N LEU C 2 CRYST1 19.169 19.754 22.484 90.00 99.43 90.00 P 1 21 1 8 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 0.052168 0.000000 0.008663 0.00000 SCALE2 0.000000 0.050623 0.000000 0.00000 SCALE3 0.000000 0.000000 0.045085 0.00000 CONECT 474 475 476 477 478 CONECT 475 474 479 480 481 CONECT 476 474 482 CONECT 477 474 CONECT 478 474 CONECT 479 475 CONECT 480 475 CONECT 481 475 CONECT 482 476 CONECT 483 484 485 489 CONECT 484 483 486 487 488 CONECT 485 483 CONECT 486 484 CONECT 487 484 CONECT 488 484 CONECT 489 483 CONECT 490 491 492 493 494 CONECT 491 490 495 496 497 CONECT 492 490 498 CONECT 493 490 CONECT 494 490 CONECT 495 491 CONECT 496 491 CONECT 497 491 CONECT 498 492 CONECT 499 500 501 502 503 CONECT 500 499 504 505 506 CONECT 501 499 507 CONECT 502 499 CONECT 503 499 CONECT 504 500 CONECT 505 500 CONECT 506 500 CONECT 507 501 CONECT 508 509 510 514 CONECT 509 508 511 512 513 CONECT 510 508 CONECT 511 509 CONECT 512 509 CONECT 513 509 CONECT 514 508 MASTER 184 0 5 0 4 0 0 6 209 4 41 4 END