HEADER PROTEIN FIBRIL 10-JAN-18 6C3S TITLE AMYLOID FORMING PEPTIDE YTIAAL FROM TRANSTHYRETIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYR-THR-ILE-ALA-ALA-LEU; COMPND 3 CHAIN: A; 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, TRANSTHYRETIN, FIBRIL, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR S.A.SIEVERS,M.R.SAWAYA,L.SAELICES,D.S.EISENBERG REVDAT 4 03-APR-24 6C3S 1 REMARK REVDAT 3 13-MAR-24 6C3S 1 REMARK REVDAT 2 18-JUL-18 6C3S 1 JRNL REVDAT 1 18-APR-18 6C3S 0 JRNL AUTH L.SAELICES,S.A.SIEVERS,M.R.SAWAYA,D.S.EISENBERG JRNL TITL CRYSTAL STRUCTURES OF AMYLOIDOGENIC SEGMENTS OF HUMAN JRNL TITL 2 TRANSTHYRETIN. JRNL REF PROTEIN SCI. V. 27 1295 2018 JRNL REFN ESSN 1469-896X JRNL PMID 29626847 JRNL DOI 10.1002/PRO.3420 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1555 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 620 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.190 REMARK 3 FREE R VALUE TEST SET COUNT : 57 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 1.6590 - 1.6022 0.98 563 0 0.2888 0.1911 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.43 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 : 0.007 46 REMARK 3 ANGLE : 0.896 63 REMARK 3 CHIRALITY : 0.031 9 REMARK 3 PLANARITY : 0.003 7 REMARK 3 DIHEDRAL : 12.595 14 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 6C3S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000232003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.895432 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 625 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 90.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.31800 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: IDEAL BETA STRAND REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: YTIAAL CRYSTALS WERE GROWN FROM A REMARK 280 SOLUTION CONTAINING 10MG/ML PEPTIDE. THE RESERVOIR CONTAINED REMARK 280 100MM BIS-TRIS PH 5.5 AND 3 M SODIUM CHLORIDE. CRYSTALS WERE REMARK 280 SOAKED ON 25% GLYCEROL, PRIOR TO DIFFRACTION, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 9.37300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 4.78900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.39800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 9.37300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 4.78900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.39800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 9.37300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 4.78900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 22.39800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 9.37300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 4.78900 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 22.39800 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: EICOSAMERIC 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 -9.57800 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 9.57800 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 19.15600 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 -19.15600 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 -18.74600 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 -18.74600 REMARK 350 BIOMT2 7 0.000000 -1.000000 0.000000 9.57800 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 -18.74600 REMARK 350 BIOMT2 8 0.000000 -1.000000 0.000000 -9.57800 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 -18.74600 REMARK 350 BIOMT2 9 0.000000 -1.000000 0.000000 -19.15600 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 -18.74600 REMARK 350 BIOMT2 10 0.000000 -1.000000 0.000000 19.15600 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 11 -1.000000 0.000000 0.000000 -9.37300 REMARK 350 BIOMT2 11 0.000000 1.000000 0.000000 4.78900 REMARK 350 BIOMT3 11 0.000000 0.000000 -1.000000 -22.39800 REMARK 350 BIOMT1 12 -1.000000 0.000000 0.000000 -9.37300 REMARK 350 BIOMT2 12 0.000000 1.000000 0.000000 -4.78900 REMARK 350 BIOMT3 12 0.000000 0.000000 -1.000000 -22.39800 REMARK 350 BIOMT1 13 -1.000000 0.000000 0.000000 -9.37300 REMARK 350 BIOMT2 13 0.000000 1.000000 0.000000 14.36700 REMARK 350 BIOMT3 13 0.000000 0.000000 -1.000000 -22.39800 REMARK 350 BIOMT1 14 -1.000000 0.000000 0.000000 -9.37300 REMARK 350 BIOMT2 14 0.000000 1.000000 0.000000 -14.36700 REMARK 350 BIOMT3 14 0.000000 0.000000 -1.000000 -22.39800 REMARK 350 BIOMT1 15 -1.000000 0.000000 0.000000 -9.37300 REMARK 350 BIOMT2 15 0.000000 1.000000 0.000000 23.94500 REMARK 350 BIOMT3 15 0.000000 0.000000 -1.000000 -22.39800 REMARK 350 BIOMT1 16 1.000000 0.000000 0.000000 -9.37300 REMARK 350 BIOMT2 16 0.000000 -1.000000 0.000000 -4.78900 REMARK 350 BIOMT3 16 0.000000 0.000000 -1.000000 -22.39800 REMARK 350 BIOMT1 17 1.000000 0.000000 0.000000 -9.37300 REMARK 350 BIOMT2 17 0.000000 -1.000000 0.000000 4.78900 REMARK 350 BIOMT3 17 0.000000 0.000000 -1.000000 -22.39800 REMARK 350 BIOMT1 18 1.000000 0.000000 0.000000 -9.37300 REMARK 350 BIOMT2 18 0.000000 -1.000000 0.000000 -14.36700 REMARK 350 BIOMT3 18 0.000000 0.000000 -1.000000 -22.39800 REMARK 350 BIOMT1 19 1.000000 0.000000 0.000000 -9.37300 REMARK 350 BIOMT2 19 0.000000 -1.000000 0.000000 14.36700 REMARK 350 BIOMT3 19 0.000000 0.000000 -1.000000 -22.39800 REMARK 350 BIOMT1 20 1.000000 0.000000 0.000000 -9.37300 REMARK 350 BIOMT2 20 0.000000 -1.000000 0.000000 -23.94500 REMARK 350 BIOMT3 20 0.000000 0.000000 -1.000000 -22.39800 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 102 LIES ON A SPECIAL POSITION. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6C3F RELATED DB: PDB REMARK 900 RELATED ID: 6C3G RELATED DB: PDB DBREF 6C3S A 1 6 PDB 6C3S 6C3S 1 6 SEQRES 1 A 6 TYR THR ILE ALA ALA LEU FORMUL 2 HOH *4(H2 O) CRYST1 18.746 9.578 44.796 90.00 90.00 90.00 I 2 2 2 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 0.053345 0.000000 0.000000 0.00000 SCALE2 0.000000 0.104406 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022323 0.00000