HEADER TRANSPORT PROTEIN 25-JUL-18 6E71 TITLE STRUCTURE OF HUMAN TRANSTHYRETIN VAL30MET/THR119MET MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSTHYRETIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ATTR,PREALBUMIN,TBPA; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24 KEYWDS HUMAN TRANSTHYRETIN, AMYLOID, TRANSTHYRETIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.SAELICES,K.CHUNG,M.R.SAWAYA,D.CASCIO,D.EISENBERG REVDAT 3 13-MAR-24 6E71 1 REMARK REVDAT 2 18-DEC-19 6E71 1 REMARK REVDAT 1 31-JUL-19 6E71 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 38229 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3823 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 : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.03 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 765 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2992 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 689 REMARK 3 BIN R VALUE (WORKING SET) : 0.2931 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.93 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76 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 : 1782 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.15310 REMARK 3 B22 (A**2) : 1.01770 REMARK 3 B33 (A**2) : 0.13540 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) : 0.200 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.074 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.072 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.072 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.072 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 : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1879 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2563 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 635 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 321 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1879 ; 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 : 2169 ; 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) : 3.91 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.04 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { *|* } REMARK 3 ORIGIN FOR THE GROUP (A): 44.0529 30.1465 79.9095 REMARK 3 T TENSOR REMARK 3 T11: -0.0590 T22: -0.0051 REMARK 3 T33: -0.0172 T12: 0.0030 REMARK 3 T13: -0.0049 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.2258 L22: 0.8597 REMARK 3 L33: 0.4334 L12: -0.0514 REMARK 3 L13: -0.1004 L23: -0.0320 REMARK 3 S TENSOR REMARK 3 S11: -0.0332 S12: -0.0012 S13: -0.0828 REMARK 3 S21: -0.0458 S22: -0.0163 S23: -0.0178 REMARK 3 S31: 0.0187 S32: -0.0167 S33: 0.0495 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6E71 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_1000234598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : NULL 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 : 38230 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 43.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.249 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.21 REMARK 200 R MERGE FOR SHELL (I) : 0.90700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.540 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 (%): 47.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 0.1M TRIS, 30% REMARK 280 (W/V) PEG 4000, PH 8.5, 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 21.57000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.27000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.57000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.27000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 86.28000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 86.54000 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 PEG A 201 DBREF 6E71 A 10 124 UNP P02766 TTHY_HUMAN 30 144 DBREF 6E71 B 10 124 UNP P02766 TTHY_HUMAN 30 144 SEQADV 6E71 MET A 30 UNP P02766 VAL 50 ENGINEERED MUTATION SEQADV 6E71 MET A 119 UNP P02766 THR 139 ENGINEERED MUTATION SEQADV 6E71 MET B 30 UNP P02766 VAL 50 ENGINEERED MUTATION SEQADV 6E71 MET B 119 UNP P02766 THR 139 ENGINEERED MUTATION 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 MET 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 MET 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 MET 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 MET ALA VAL VAL THR ASN HET PEG A 201 7 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 PEG C4 H10 O3 FORMUL 4 HOH *106(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 LEU A 111 1 O LEU A 111 N LEU A 17 SHEET 4 AA1 8 SER A 115 THR A 123 -1 O MET A 119 N ALA A 108 SHEET 5 AA1 8 SER B 115 THR B 123 -1 O THR B 118 N TYR A 116 SHEET 6 AA1 8 ARG B 104 SER B 112 -1 N ALA B 108 O MET B 119 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 LEU A 111 1 O LEU A 111 N LEU A 17 SHEET 4 AA2 8 SER A 115 THR A 123 -1 O MET A 119 N ALA A 108 SHEET 5 AA2 8 SER B 115 THR B 123 -1 O THR B 118 N TYR A 116 SHEET 6 AA2 8 ARG B 104 SER B 112 -1 N ALA B 108 O MET B 119 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 PHE A 95 N TYR A 69 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 11 LEU A 110 LEU A 111 SER A 112 SER A 115 SITE 2 AC1 11 TYR A 116 SER A 117 LEU B 110 SER B 112 SITE 3 AC1 11 SER B 115 TYR B 116 SER B 117 CRYST1 43.140 86.540 63.880 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 0.023180 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011555 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015654 0.00000