HEADER PROTEIN FIBRIL 27-DEC-14 4XFO TITLE STRUCTURE OF AN AMYLOID-FORMING SEGMENT TAVVTN FROM HUMAN TITLE 2 TRANSTHYRETIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-FORMING PEPTIDE TAVVTN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: THIS SEQUENCE CORRESPONDS TO A SEGMENT FROM HUMAN SOURCE 6 TRANSTHYRETIN KEYWDS AMYLOID, TRANSTHYRETIN, FIBRIL, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR L.SAELICES,M.SAWAYA,D.CASCIO,D.S.EISENBERG REVDAT 4 28-FEB-24 4XFO 1 JRNL REMARK REVDAT 3 09-DEC-15 4XFO 1 JRNL REVDAT 2 28-OCT-15 4XFO 1 JRNL REVDAT 1 21-OCT-15 4XFO 0 JRNL AUTH L.SAELICES,L.M.JOHNSON,W.Y.LIANG,M.R.SAWAYA,D.CASCIO, JRNL AUTH 2 P.RUCHALA,J.WHITELEGGE,L.JIANG,R.RIEK,D.S.EISENBERG JRNL TITL UNCOVERING THE MECHANISM OF AGGREGATION OF HUMAN JRNL TITL 2 TRANSTHYRETIN. JRNL REF J.BIOL.CHEM. V. 290 28932 2015 JRNL REFN ESSN 1083-351X JRNL PMID 26459562 JRNL DOI 10.1074/JBC.M115.659912 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 624 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 63 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.009 41 REMARK 3 ANGLE : 1.270 57 REMARK 3 CHIRALITY : 0.052 10 REMARK 3 PLANARITY : 0.004 7 REMARK 3 DIHEDRAL : 12.584 12 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 4XFO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205587. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 0.9792 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 629 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 16.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 21.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 6.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS REMARK 280 PH 5.5, 25% W/V POLYETHYLENE GLYCOL 3,350, 25% GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A PAIR OF INDEFINITELY LONG BETA REMARK 300 SHEETS CONSTRUCTED FROM CHAIN A AND UNIT CELL TRANSLATIONS ALONG REMARK 300 THE "A" DIRECTION (THAT IS, THE "A" DIRECTION CORRESPONDS TO THE REMARK 300 FIBER AXIS) (I.E. X,Y,Z; X+1,Y,Z; X+2,Y,Z; ETC.) TOGETHER WITH A REMARK 300 COMPLEMENTARY SHEET FORMED FROM X,Y+1,Z AND ITS UNIT CELL REMARK 300 TRANSLATIONS ALONG THE "A" DIRECTION (I.E. X+1,Y+1,Z; X+2,Y+1,Z; X+ REMARK 300 3,Y+1,Z;, ETC.) 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 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 4.75000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 9.50000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 14.25000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XFN RELATED DB: PDB DBREF 4XFO A 1 6 PDB 4XFO 4XFO 1 6 SEQRES 1 A 6 THR ALA VAL VAL THR ASN CRYST1 4.750 10.660 16.390 77.64 87.81 77.61 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 0.210526 -0.046264 0.001755 0.00000 SCALE2 0.000000 0.096047 -0.020718 0.00000 SCALE3 0.000000 0.000000 0.062462 0.00000 ATOM 1 N THR A 1 0.496 -0.528 -2.304 1.00 1.55 N ATOM 2 CA THR A 1 0.217 -0.538 -3.735 1.00 1.55 C ATOM 3 C THR A 1 0.863 -1.737 -4.414 1.00 2.55 C ATOM 4 O THR A 1 2.075 -1.899 -4.378 1.00 1.94 O ATOM 5 CB THR A 1 0.711 0.769 -4.396 1.00 2.85 C ATOM 6 OG1 THR A 1 0.144 1.886 -3.696 1.00 3.35 O ATOM 7 CG2 THR A 1 0.300 0.824 -5.868 1.00 3.18 C ATOM 8 N ALA A 2 0.030 -2.576 -5.023 1.00 1.18 N ATOM 9 CA ALA A 2 0.499 -3.729 -5.770 1.00 1.03 C ATOM 10 C ALA A 2 -0.111 -3.669 -7.153 1.00 1.24 C ATOM 11 O ALA A 2 -1.334 -3.531 -7.295 1.00 2.05 O ATOM 12 CB ALA A 2 0.118 -5.041 -5.070 1.00 1.74 C ATOM 13 N VAL A 3 0.743 -3.766 -8.169 1.00 0.47 N ATOM 14 CA VAL A 3 0.322 -3.667 -9.556 1.00 0.39 C ATOM 15 C VAL A 3 0.951 -4.820 -10.318 1.00 0.52 C ATOM 16 O VAL A 3 2.171 -4.950 -10.363 1.00 0.52 O ATOM 17 CB VAL A 3 0.735 -2.306 -10.193 1.00 0.47 C ATOM 18 CG1 VAL A 3 0.224 -2.207 -11.635 1.00 0.54 C ATOM 19 CG2 VAL A 3 0.247 -1.129 -9.327 1.00 0.79 C ATOM 20 N VAL A 4 0.107 -5.666 -10.903 1.00 0.34 N ATOM 21 CA VAL A 4 0.571 -6.889 -11.538 1.00 0.39 C ATOM 22 C VAL A 4 -0.018 -7.055 -12.916 1.00 0.53 C ATOM 23 O VAL A 4 -1.225 -6.906 -13.093 1.00 0.46 O ATOM 24 CB VAL A 4 0.191 -8.153 -10.703 1.00 0.70 C ATOM 25 CG1 VAL A 4 0.590 -9.437 -11.437 1.00 1.04 C ATOM 26 CG2 VAL A 4 0.831 -8.093 -9.328 1.00 1.15 C ATOM 27 N THR A 5 0.842 -7.375 -13.880 1.00 0.32 N ATOM 28 CA THR A 5 0.433 -7.881 -15.191 1.00 0.72 C ATOM 29 C THR A 5 1.026 -9.269 -15.339 1.00 0.93 C ATOM 30 O THR A 5 2.207 -9.472 -15.092 1.00 1.03 O ATOM 31 CB THR A 5 0.898 -6.972 -16.337 1.00 1.15 C ATOM 32 OG1 THR A 5 0.038 -5.829 -16.389 1.00 2.12 O ATOM 33 CG2 THR A 5 0.820 -7.688 -17.673 1.00 1.44 C ATOM 34 N ASN A 6 0.174 -10.225 -15.693 1.00 0.89 N ATOM 35 CA ASN A 6 0.565 -11.615 -15.856 1.00 1.76 C ATOM 36 C ASN A 6 -0.257 -12.201 -17.006 1.00 2.47 C ATOM 37 O ASN A 6 -0.042 -13.334 -17.424 1.00 3.59 O ATOM 38 CB ASN A 6 0.341 -12.389 -14.553 1.00 1.49 C ATOM 39 CG ASN A 6 0.960 -13.790 -14.556 1.00 1.48 C ATOM 40 OD1 ASN A 6 2.141 -13.976 -14.857 1.00 2.17 O ATOM 41 ND2 ASN A 6 0.156 -14.780 -14.180 1.00 1.46 N ATOM 42 OXT ASN A 6 -1.156 -11.510 -17.524 1.00 3.92 O TER 43 ASN A 6 MASTER 197 0 0 0 0 0 0 6 42 1 0 1 END