HEADER TRANSPORT PROTEIN 16-FEB-24 8W1N TITLE STRUCTURE OF TRANSTHYRETIN PATHOGENIC MUTATION A120S 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS TETRAMER, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.A.FERGUSON,R.L.STANFIELD,P.E.WRIGHT REVDAT 1 28-FEB-24 8W1N 0 JRNL AUTH X.SUN,J.A.FERGUSON,K.YANG,R.L.STANFIELD,H.J.DYSON,P.E.WRIGHT JRNL TITL THE MISPACKED F87 SIDECHAIN DRIVES AGGREGATION-PROMOTING JRNL TITL 2 CONFORMATIONAL FLUCTUATIONS IN TRANSTHYRETIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21RC1_5127 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 31104 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1605 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 38.5700 - 3.5600 0.98 2934 142 0.1918 0.2244 REMARK 3 2 3.5600 - 2.8300 0.99 2810 144 0.2004 0.2197 REMARK 3 3 2.8200 - 2.4700 0.99 2749 170 0.2245 0.2953 REMARK 3 4 2.4700 - 2.2400 0.96 2677 145 0.2748 0.3294 REMARK 3 5 2.2400 - 2.0800 0.96 2672 139 0.2647 0.2739 REMARK 3 6 2.0800 - 1.9600 0.98 2636 167 0.2568 0.3056 REMARK 3 7 1.9600 - 1.8600 0.92 2562 134 0.4553 0.5399 REMARK 3 8 1.8600 - 1.7800 0.97 2653 142 0.3241 0.3319 REMARK 3 9 1.7800 - 1.7100 0.97 2662 135 0.3192 0.3544 REMARK 3 10 1.7100 - 1.6500 0.96 2627 148 0.3174 0.3684 REMARK 3 11 1.6500 - 1.6000 0.93 2517 139 0.3230 0.3805 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.261 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.321 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.99 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 : 0.006 1894 REMARK 3 ANGLE : 0.829 2602 REMARK 3 CHIRALITY : 0.055 298 REMARK 3 PLANARITY : 0.007 333 REMARK 3 DIHEDRAL : 14.863 684 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 8W1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281657. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9765 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V722 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31452 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 38.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.21 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES AT PH 6.0, 10% (V/V) REMARK 280 GLYCEROL, 5% (W/V) PEG 1000, AND 30% (V/V) PEG 600, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 21.55700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.55700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.14000 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 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 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 287 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 221 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 271 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 297 LIES ON A SPECIAL POSITION. 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 MET A 0 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 MET B 0 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 PRO B 125 REMARK 465 LYS B 126 REMARK 465 GLU B 127 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE B 44 -54.63 -132.88 REMARK 500 SER B 100 82.57 -47.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 299 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH B 300 DISTANCE = 7.17 ANGSTROMS REMARK 525 HOH B 301 DISTANCE = 7.84 ANGSTROMS DBREF 8W1N A 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 8W1N B 1 127 UNP P02766 TTHY_HUMAN 21 147 SEQADV 8W1N MET A 0 UNP P02766 INITIATING METHIONINE SEQADV 8W1N SER A 120 UNP P02766 ALA 140 ENGINEERED MUTATION SEQADV 8W1N MET B 0 UNP P02766 INITIATING METHIONINE SEQADV 8W1N SER B 120 UNP P02766 ALA 140 ENGINEERED MUTATION SEQRES 1 A 128 MET GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU SEQRES 2 A 128 MET VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA SEQRES 3 A 128 ILE ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP SEQRES 4 A 128 ASP THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SEQRES 5 A 128 SER GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE SEQRES 6 A 128 VAL GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER SEQRES 7 A 128 TYR TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS SEQRES 8 A 128 ALA GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG SEQRES 9 A 128 ARG TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SEQRES 10 A 128 SER THR THR SER VAL VAL THR ASN PRO LYS GLU SEQRES 1 B 128 MET GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU SEQRES 2 B 128 MET VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA SEQRES 3 B 128 ILE ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP SEQRES 4 B 128 ASP THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SEQRES 5 B 128 SER GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE SEQRES 6 B 128 VAL GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER SEQRES 7 B 128 TYR TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS SEQRES 8 B 128 ALA GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG SEQRES 9 B 128 ARG TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SEQRES 10 B 128 SER THR THR SER VAL VAL THR ASN PRO LYS GLU FORMUL 3 HOH *218(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 THR B 118 N TYR A 116 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 THR B 118 N TYR A 116 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 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 91 N ILE A 73 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 VAL B 71 O VAL B 93 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 CRYST1 43.114 86.280 64.088 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 0.023194 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011590 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015604 0.00000