HEADER TRANSPORT PROTEIN 15-MAR-18 6FZL TITLE CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN DOUBLE MUTANT K35T/T119M 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 KEYWDS AMYLOID, GATEKEEPER, AGGREGATION, STABILITY, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.ESPERANTE,S.VENTURA,D.REVERTER,N.VAREJAO REVDAT 3 07-FEB-24 6FZL 1 REMARK REVDAT 2 12-APR-23 6FZL 1 JRNL REVDAT 1 27-MAR-19 6FZL 0 JRNL AUTH S.A.ESPERANTE,N.VAREJAO,F.PINHEIRO,R.SANT'ANNA, JRNL AUTH 2 J.R.LUQUE-ORTEGA,C.ALFONSO,V.SORA,E.PAPALEO,G.RIVAS, JRNL AUTH 3 D.REVERTER,S.VENTURA JRNL TITL DISEASE-ASSOCIATED MUTATIONS IMPACTING BC-LOOP FLEXIBILITY JRNL TITL 2 TRIGGER LONG-RANGE TRANSTHYRETIN TETRAMER DESTABILIZATION JRNL TITL 3 AND AGGREGATION. JRNL REF J.BIOL.CHEM. V. 297 01039 2021 JRNL REFN ESSN 1083-351X JRNL PMID 34343569 JRNL DOI 10.1016/J.JBC.2021.101039 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 41398 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2093 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 42.9975 - 3.5665 0.94 2717 160 0.1801 0.1615 REMARK 3 2 3.5665 - 2.8310 0.97 2713 141 0.1755 0.1888 REMARK 3 3 2.8310 - 2.4732 0.93 2570 131 0.1800 0.2031 REMARK 3 4 2.4732 - 2.2471 1.00 2708 155 0.1699 0.1681 REMARK 3 5 2.2471 - 2.0860 1.00 2713 162 0.1653 0.2005 REMARK 3 6 2.0860 - 1.9630 1.00 2699 145 0.1672 0.1765 REMARK 3 7 1.9630 - 1.8647 1.00 2702 129 0.1682 0.2120 REMARK 3 8 1.8647 - 1.7836 1.00 2677 154 0.1810 0.2133 REMARK 3 9 1.7836 - 1.7149 0.98 2224 124 0.1894 0.2431 REMARK 3 10 1.7149 - 1.6557 0.98 2161 135 0.2012 0.2309 REMARK 3 11 1.6557 - 1.6039 1.00 2682 138 0.2004 0.2320 REMARK 3 12 1.6039 - 1.5581 1.00 2709 122 0.2158 0.2743 REMARK 3 13 1.5581 - 1.5171 1.00 2678 141 0.2282 0.2630 REMARK 3 14 1.5171 - 1.4801 1.00 2654 139 0.2420 0.2402 REMARK 3 15 1.4801 - 1.4464 1.00 2698 117 0.2708 0.3164 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 46.70 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13140 REMARK 3 B22 (A**2) : 3.32720 REMARK 3 B33 (A**2) : -3.19580 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 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 : 0.016 1863 REMARK 3 ANGLE : 1.691 2548 REMARK 3 CHIRALITY : 0.114 289 REMARK 3 PLANARITY : 0.010 328 REMARK 3 DIHEDRAL : 15.204 656 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -22.6552 -15.7818 -13.0577 REMARK 3 T TENSOR REMARK 3 T11: 0.0814 T22: 0.1090 REMARK 3 T33: 0.0844 T12: 0.0081 REMARK 3 T13: -0.0034 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.6815 L22: 1.0733 REMARK 3 L33: 1.1046 L12: 0.3349 REMARK 3 L13: 0.0579 L23: 0.0030 REMARK 3 S TENSOR REMARK 3 S11: -0.0253 S12: 0.1033 S13: -0.0437 REMARK 3 S21: -0.0212 S22: 0.0587 S23: -0.0458 REMARK 3 S31: 0.0653 S32: -0.0104 S33: -0.0307 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 6FZL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-16 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.446 REMARK 200 RESOLUTION RANGE LOW (A) : 63.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.84900 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 1.7.3-928 REMARK 200 STARTING MODEL: 1F41 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7% GLYCEROL, 1.3 M SODIUM CITRATE, PH REMARK 280 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 21.52800 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.97850 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 21.52800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.97850 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: 6350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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 -43.05600 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 PRO A 2 REMARK 465 THR A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 GLU A 7 REMARK 465 SER A 8 REMARK 465 LYS A 9 REMARK 465 LYS A 126 REMARK 465 GLU A 127 REMARK 465 GLY B 1 REMARK 465 PRO B 2 REMARK 465 THR B 3 REMARK 465 GLY B 4 REMARK 465 THR B 5 REMARK 465 GLY B 6 REMARK 465 GLU B 7 REMARK 465 SER B 8 REMARK 465 LYS B 9 REMARK 465 GLY B 101 REMARK 465 PRO B 102 REMARK 465 LYS B 126 REMARK 465 GLU B 127 DBREF 6FZL A 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 6FZL B 1 127 UNP P02766 TTHY_HUMAN 21 147 SEQADV 6FZL THR A 35 UNP P02766 LYS 55 ENGINEERED MUTATION SEQADV 6FZL MET A 119 UNP P02766 THR 139 ENGINEERED MUTATION SEQADV 6FZL THR B 35 UNP P02766 LYS 55 ENGINEERED MUTATION SEQADV 6FZL MET B 119 UNP P02766 THR 139 ENGINEERED MUTATION SEQRES 1 A 127 GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU MET SEQRES 2 A 127 VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA ILE SEQRES 3 A 127 ASN VAL ALA VAL HIS VAL PHE ARG THR ALA ALA ASP ASP SEQRES 4 A 127 THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SER SEQRES 5 A 127 GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE VAL SEQRES 6 A 127 GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER TYR SEQRES 7 A 127 TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS ALA SEQRES 8 A 127 GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG ARG SEQRES 9 A 127 TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SER SEQRES 10 A 127 THR MET ALA VAL VAL THR ASN PRO LYS GLU SEQRES 1 B 127 GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU MET SEQRES 2 B 127 VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA ILE SEQRES 3 B 127 ASN VAL ALA VAL HIS VAL PHE ARG THR ALA ALA ASP ASP SEQRES 4 B 127 THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SER SEQRES 5 B 127 GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE VAL SEQRES 6 B 127 GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER TYR SEQRES 7 B 127 TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS ALA SEQRES 8 B 127 GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG ARG SEQRES 9 B 127 TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SER SEQRES 10 B 127 THR MET ALA VAL VAL THR ASN PRO LYS GLU FORMUL 3 HOH *190(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 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 SER A 112 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 THR 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 91 N ILE A 73 SHEET 5 AA3 8 HIS B 88 ALA B 97 -1 O GLU B 89 N VAL A 94 SHEET 6 AA3 8 GLY B 67 ILE B 73 -1 N TYR B 69 O PHE B 95 SHEET 7 AA3 8 ALA B 29 THR 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 CRYST1 43.056 63.580 85.957 90.00 90.00 90.00 P 21 2 21 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 0.023226 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011634 0.00000