HEADER TRANSPORT PROTEIN 25-JUL-18 6E6Z TITLE STRUCTURE OF WILD TYPE HUMAN TRANSTHYRETIN IN COMPLEX WITH TAFAMIDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSTHYRETIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ATTR,PREALBUMIN,TBPA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TTR, PALB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3) P:L KEYWDS HUMAN TRANSTHYRETIN, AMYLOID, TRANSTHYRETIN, TAFAMIDIS, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.CHUNG,L.SAELICES,M.R.SAWAYA,D.CASCIO,D.EISENBERG REVDAT 3 13-MAR-24 6E6Z 1 REMARK REVDAT 2 18-DEC-19 6E6Z 1 REMARK REVDAT 1 31-JUL-19 6E6Z 0 JRNL AUTH L.SAELICES,K.CHUNG,S.ESSWEIN,J.CHOU,W.LIANG,J.H.LI, JRNL AUTH 2 M.R.SAWAYA,D.CASCIO,D.EISENBERG JRNL TITL STRUCTURAL VARIANTS OF TRANSTHYRETIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22975 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2298 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 12 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2765 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1979 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2488 REMARK 3 BIN R VALUE (WORKING SET) : 0.1935 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.02 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 277 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1778 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.14630 REMARK 3 B22 (A**2) : 2.87990 REMARK 3 B33 (A**2) : -8.02620 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.230 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.118 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.111 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.118 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.112 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1916 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2632 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 620 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 39 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 285 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1916 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 251 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2123 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.05 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.66 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.65 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 44.1781 29.7307 69.5817 REMARK 3 T TENSOR REMARK 3 T11: -0.0490 T22: 0.0125 REMARK 3 T33: -0.0469 T12: -0.0169 REMARK 3 T13: 0.0155 T23: -0.0375 REMARK 3 L TENSOR REMARK 3 L11: 1.1254 L22: 1.4034 REMARK 3 L33: 0.7766 L12: 0.2157 REMARK 3 L13: 0.3362 L23: 0.7140 REMARK 3 S TENSOR REMARK 3 S11: -0.0424 S12: 0.0878 S13: -0.1731 REMARK 3 S21: -0.1465 S22: -0.0598 S23: 0.0211 REMARK 3 S31: -0.0220 S32: -0.1801 S33: 0.1022 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 41.8415 29.0266 89.0933 REMARK 3 T TENSOR REMARK 3 T11: -0.0108 T22: -0.0261 REMARK 3 T33: -0.0127 T12: 0.0041 REMARK 3 T13: 0.0090 T23: 0.0219 REMARK 3 L TENSOR REMARK 3 L11: 0.6564 L22: 0.7192 REMARK 3 L33: 0.6970 L12: -0.4051 REMARK 3 L13: 0.0775 L23: -0.0215 REMARK 3 S TENSOR REMARK 3 S11: -0.0975 S12: -0.0017 S13: -0.0771 REMARK 3 S21: 0.1082 S22: 0.0223 S23: 0.0236 REMARK 3 S31: 0.0317 S32: 0.0384 S33: 0.0751 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6E6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000234527. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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-C 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 : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23032 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 63.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.81 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.5700 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) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 12.43 REMARK 200 R MERGE FOR SHELL (I) : 0.71400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.640 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG-1000, 0.1M IMIDAZOLE, REMARK 280 0.2M CALCIUM ACETATE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 20.62000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.62000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.13000 REMARK 290 SMTRY3 4 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 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, B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 82.48000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 84.26000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3MI A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3MI B 201 DBREF 6E6Z A 10 124 UNP P02766 TTHY_HUMAN 30 144 DBREF 6E6Z B 10 124 UNP P02766 TTHY_HUMAN 30 144 SEQRES 1 A 115 CYS PRO LEU MET VAL LYS VAL LEU ASP ALA VAL ARG GLY SEQRES 2 A 115 SER PRO ALA ILE ASN VAL ALA VAL HIS VAL PHE ARG LYS SEQRES 3 A 115 ALA ALA ASP ASP THR TRP GLU PRO PHE ALA SER GLY LYS SEQRES 4 A 115 THR SER GLU SER GLY GLU LEU HIS GLY LEU THR THR GLU SEQRES 5 A 115 GLU GLU PHE VAL GLU GLY ILE TYR LYS VAL GLU ILE ASP SEQRES 6 A 115 THR LYS SER TYR TRP LYS ALA LEU GLY ILE SER PRO PHE SEQRES 7 A 115 HIS GLU HIS ALA GLU VAL VAL PHE THR ALA ASN ASP SER SEQRES 8 A 115 GLY PRO ARG ARG TYR THR ILE ALA ALA LEU LEU SER PRO SEQRES 9 A 115 TYR SER TYR SER THR THR ALA VAL VAL THR ASN SEQRES 1 B 115 CYS PRO LEU MET VAL LYS VAL LEU ASP ALA VAL ARG GLY SEQRES 2 B 115 SER PRO ALA ILE ASN VAL ALA VAL HIS VAL PHE ARG LYS SEQRES 3 B 115 ALA ALA ASP ASP THR TRP GLU PRO PHE ALA SER GLY LYS SEQRES 4 B 115 THR SER GLU SER GLY GLU LEU HIS GLY LEU THR THR GLU SEQRES 5 B 115 GLU GLU PHE VAL GLU GLY ILE TYR LYS VAL GLU ILE ASP SEQRES 6 B 115 THR LYS SER TYR TRP LYS ALA LEU GLY ILE SER PRO PHE SEQRES 7 B 115 HIS GLU HIS ALA GLU VAL VAL PHE THR ALA ASN ASP SER SEQRES 8 B 115 GLY PRO ARG ARG TYR THR ILE ALA ALA LEU LEU SER PRO SEQRES 9 B 115 TYR SER TYR SER THR THR ALA VAL VAL THR ASN HET 3MI A 201 26 HET 3MI B 201 26 HETNAM 3MI 2-(3,5-DICHLOROPHENYL)-1,3-BENZOXAZOLE-6-CARBOXYLIC HETNAM 2 3MI ACID HETSYN 3MI TAFAMIDIS FORMUL 3 3MI 2(C14 H7 CL2 N O3) FORMUL 5 HOH *51(H2 O) HELIX 1 AA1 ASP A 74 LEU A 82 1 9 HELIX 2 AA2 ASP B 74 LEU B 82 1 9 SHEET 1 AA1 8 SER A 23 PRO A 24 0 SHEET 2 AA1 8 LEU A 12 ASP A 18 -1 N ASP A 18 O SER A 23 SHEET 3 AA1 8 ARG A 104 SER A 112 1 O LEU A 111 N LEU A 17 SHEET 4 AA1 8 SER A 115 THR A 123 -1 O SER A 115 N SER A 112 SHEET 5 AA1 8 SER B 115 THR B 123 -1 O TYR B 116 N THR A 118 SHEET 6 AA1 8 ARG B 104 SER B 112 -1 N ARG B 104 O THR B 123 SHEET 7 AA1 8 LEU B 12 ASP B 18 1 N LEU B 17 O LEU B 111 SHEET 8 AA1 8 SER B 23 PRO B 24 -1 O SER B 23 N ASP B 18 SHEET 1 AA2 8 GLU A 54 LEU A 55 0 SHEET 2 AA2 8 LEU A 12 ASP A 18 -1 N VAL A 14 O LEU A 55 SHEET 3 AA2 8 ARG A 104 SER A 112 1 O LEU A 111 N LEU A 17 SHEET 4 AA2 8 SER A 115 THR A 123 -1 O SER A 115 N SER A 112 SHEET 5 AA2 8 SER B 115 THR B 123 -1 O TYR B 116 N THR A 118 SHEET 6 AA2 8 ARG B 104 SER B 112 -1 N ARG B 104 O THR B 123 SHEET 7 AA2 8 LEU B 12 ASP B 18 1 N LEU B 17 O LEU B 111 SHEET 8 AA2 8 GLU B 54 LEU B 55 -1 O LEU B 55 N VAL B 14 SHEET 1 AA3 8 TRP A 41 LYS A 48 0 SHEET 2 AA3 8 ALA A 29 LYS A 35 -1 N VAL A 32 O ALA A 45 SHEET 3 AA3 8 GLY A 67 ILE A 73 -1 O GLU A 72 N HIS A 31 SHEET 4 AA3 8 HIS A 88 ALA A 97 -1 O ALA A 97 N GLY A 67 SHEET 5 AA3 8 HIS B 88 ALA B 97 -1 O VAL B 94 N GLU A 89 SHEET 6 AA3 8 GLY B 67 ILE B 73 -1 N ILE B 73 O ALA B 91 SHEET 7 AA3 8 ALA B 29 LYS B 35 -1 N HIS B 31 O GLU B 72 SHEET 8 AA3 8 TRP B 41 LYS B 48 -1 O ALA B 45 N VAL B 32 SITE 1 AC1 6 LYS A 15 LEU A 17 ALA A 108 LEU A 110 SITE 2 AC1 6 SER A 117 THR A 118 SITE 1 AC2 6 LYS B 15 LEU B 17 ALA B 108 LEU B 110 SITE 2 AC2 6 SER B 117 THR B 118 CRYST1 41.240 84.260 63.430 90.00 90.00 90.00 P 21 21 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 0.024248 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015765 0.00000