HEADER TRANSPORT PROTEIN 07-OCT-16 5H0Y TITLE CRYSTAL STRUCTURE OF H88Y MUTATED HUMAN TRANSTHYRETIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSTHYRETIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-147; COMPND 5 SYNONYM: ATTR,PREALBUMIN,TBPA; COMPND 6 ENGINEERED: YES; COMPND 7 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 TRANSTHHYRETIN, AMYLOIDOSIS, TRANSPORTER, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.YOKOYAMA,Y.HANAWA,T.OBITA,M.MIZUGUCHI REVDAT 3 20-MAR-24 5H0Y 1 REMARK REVDAT 2 26-JUL-17 5H0Y 1 JRNL REVDAT 1 14-JUN-17 5H0Y 0 JRNL AUTH T.YOKOYAMA,Y.HANAWA,T.OBITA,M.MIZUGUCHI JRNL TITL STABILITY AND CRYSTAL STRUCTURES OF HIS88 MUTANT HUMAN JRNL TITL 2 TRANSTHYRETINS JRNL REF FEBS LETT. V. 591 1862 2017 JRNL REFN ISSN 1873-3468 JRNL PMID 28563699 JRNL DOI 10.1002/1873-3468.12704 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 10534 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 527 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 31.4073 - 2.8571 1.00 2620 138 0.1893 0.2272 REMARK 3 2 2.8571 - 2.2679 1.00 2502 132 0.2317 0.2884 REMARK 3 3 2.2679 - 1.9813 1.00 2495 131 0.2006 0.2168 REMARK 3 4 1.9813 - 1.8002 0.96 2390 126 0.2336 0.2796 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 955 REMARK 3 ANGLE : 0.964 1311 REMARK 3 CHIRALITY : 0.068 149 REMARK 3 PLANARITY : 0.005 166 REMARK 3 DIHEDRAL : 13.211 342 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 5H0Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-13 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 : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10536 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 37.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 25% GLYCEROL, REMARK 280 0.1 M MES, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 20.67450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.40250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.62200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.67450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.40250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.62200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.67450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.40250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.62200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.67450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 31.40250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.62200 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: 7690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 41.34900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 125.61000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 41.34900 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 125.61000 REMARK 350 BIOMT3 4 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 342 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 343 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 ALA A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 PRO A 125 REMARK 465 LYS A 126 REMARK 465 GLU A 127 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 A 343 DISTANCE = 6.20 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H0V RELATED DB: PDB REMARK 900 RELATED ID: 5H0W RELATED DB: PDB REMARK 900 RELATED ID: 5H0X RELATED DB: PDB REMARK 900 RELATED ID: 5H0Z RELATED DB: PDB DBREF 5H0Y A 11 127 UNP P02766 TTHY_HUMAN 31 147 SEQADV 5H0Y ALA A 2 UNP P02766 EXPRESSION TAG SEQADV 5H0Y HIS A 3 UNP P02766 EXPRESSION TAG SEQADV 5H0Y HIS A 4 UNP P02766 EXPRESSION TAG SEQADV 5H0Y HIS A 5 UNP P02766 EXPRESSION TAG SEQADV 5H0Y HIS A 6 UNP P02766 EXPRESSION TAG SEQADV 5H0Y HIS A 7 UNP P02766 EXPRESSION TAG SEQADV 5H0Y HIS A 8 UNP P02766 EXPRESSION TAG SEQADV 5H0Y MET A 9 UNP P02766 EXPRESSION TAG SEQADV 5H0Y SER A 10 UNP P02766 EXPRESSION TAG SEQADV 5H0Y TYR A 88 UNP P02766 HIS 108 ENGINEERED MUTATION SEQRES 1 A 126 ALA HIS HIS HIS HIS HIS HIS MET SER PRO LEU MET VAL SEQRES 2 A 126 LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA ILE ASN SEQRES 3 A 126 VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP ASP THR SEQRES 4 A 126 TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SER GLY SEQRES 5 A 126 GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE VAL GLU SEQRES 6 A 126 GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER TYR TRP SEQRES 7 A 126 LYS ALA LEU GLY ILE SER PRO PHE TYR GLU HIS ALA GLU SEQRES 8 A 126 VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG ARG TYR SEQRES 9 A 126 THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SER THR SEQRES 10 A 126 THR ALA VAL VAL THR ASN PRO LYS GLU HET SO4 A 201 5 HET CL A 202 1 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 CL CL 1- FORMUL 4 HOH *43(H2 O) HELIX 1 AA1 THR A 75 LEU A 82 1 8 SHEET 1 AA1 3 SER A 23 PRO A 24 0 SHEET 2 AA1 3 LEU A 12 ASP A 18 -1 N ASP A 18 O SER A 23 SHEET 3 AA1 3 GLU A 54 LEU A 55 -1 O LEU A 55 N VAL A 14 SHEET 1 AA2 4 SER A 23 PRO A 24 0 SHEET 2 AA2 4 LEU A 12 ASP A 18 -1 N ASP A 18 O SER A 23 SHEET 3 AA2 4 ARG A 104 SER A 112 1 O ILE A 107 N MET A 13 SHEET 4 AA2 4 SER A 115 THR A 123 -1 O SER A 117 N LEU A 110 SHEET 1 AA3 4 TRP A 41 LYS A 48 0 SHEET 2 AA3 4 ALA A 29 LYS A 35 -1 N VAL A 32 O ALA A 45 SHEET 3 AA3 4 GLY A 67 ASP A 74 -1 O GLU A 72 N HIS A 31 SHEET 4 AA3 4 HIS A 90 ALA A 97 -1 O PHE A 95 N TYR A 69 SITE 1 AC1 4 LYS A 76 LYS A 80 HOH A 305 HOH A 308 SITE 1 AC2 4 MET A 9 SER A 10 HIS A 56 GLY A 57 CRYST1 41.349 62.805 85.244 90.00 90.00 90.00 I 2 2 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 0.024184 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015922 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011731 0.00000