HEADER TRANSPORT PROTEIN 25-JUL-18 6E75 TITLE STRUCTURE OF HUMAN TRANSTHYRETIN ASP38ALA 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, MUTANT, 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 6E75 1 REMARK REVDAT 2 18-DEC-19 6E75 1 REMARK REVDAT 1 31-JUL-19 6E75 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) : 19.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 38583 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3859 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 : 19 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.15 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2929 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2079 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2636 REMARK 3 BIN R VALUE (WORKING SET) : 0.2063 REMARK 3 BIN FREE R VALUE : 0.2231 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 293 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 : 1772 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 86 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.86750 REMARK 3 B22 (A**2) : 2.30600 REMARK 3 B33 (A**2) : 0.56150 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) : 0.180 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.069 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.069 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.069 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.069 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 : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1889 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2589 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 628 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 38 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 287 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1889 ; 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 : 257 ; 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 : 2164 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.04 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.24 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.99 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): 43.9656 29.8625 79.7300 REMARK 3 T TENSOR REMARK 3 T11: -0.0186 T22: -0.0415 REMARK 3 T33: -0.0305 T12: 0.0067 REMARK 3 T13: -0.0008 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.5133 L22: 0.7599 REMARK 3 L33: 0.5150 L12: -0.0510 REMARK 3 L13: -0.1132 L23: -0.0592 REMARK 3 S TENSOR REMARK 3 S11: -0.0484 S12: 0.0110 S13: -0.1335 REMARK 3 S21: -0.0290 S22: -0.0168 S23: -0.0043 REMARK 3 S31: -0.0060 S32: -0.0218 S33: 0.0653 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6E75 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_1000234644. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 : 38583 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.748 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.8300 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.56 REMARK 200 R MERGE FOR SHELL (I) : 0.49900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.210 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 (%): 47.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (V/V) PEG 400, 100 MM SODIUM REMARK 280 ACETATE, 200 MM CALCIUM ACETATE, PH 4.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 21.59500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.87000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.59500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.87000 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: 6640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 86.38000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 85.74000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 308 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 224 LIES ON A SPECIAL POSITION. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 201 DBREF 6E75 A 10 124 UNP P02766 TTHY_HUMAN 30 144 DBREF 6E75 B 10 124 UNP P02766 TTHY_HUMAN 30 144 SEQADV 6E75 ALA A 38 UNP P02766 ASP 58 ENGINEERED MUTATION SEQADV 6E75 ALA B 38 UNP P02766 ASP 58 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 VAL HIS VAL PHE ARG LYS SEQRES 3 A 115 ALA ALA ALA 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 ALA 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 ACT A 201 4 HETNAM ACT ACETATE ION FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *86(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 THR A 119 N ALA A 108 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 ALA B 108 O THR 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 SER A 112 1 O LEU A 111 N LEU A 17 SHEET 4 AA2 8 SER A 115 THR A 123 -1 O THR A 119 N ALA A 108 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 ALA B 108 O THR 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 THR A 40 LYS A 48 0 SHEET 2 AA3 8 ALA A 29 ALA A 36 -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 ALA B 36 -1 N HIS B 31 O GLU B 72 SHEET 8 AA3 8 THR B 40 LYS B 48 -1 O ALA B 45 N VAL B 32 SITE 1 AC1 7 PHE A 44 LEU A 58 GLU A 63 GLU A 66 SITE 2 AC1 7 ASN A 98 ASP A 99 HOH A 312 CRYST1 43.190 85.740 63.900 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 0.023154 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011663 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015649 0.00000