HEADER TRANSPORT(THYROXINE) 02-NOV-92 1TTC TITLE THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYRETIN TITLE 2 AND THE AMYLOIDOGENIC VAL30MET VARIANT TO 1.7 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSTHYRETIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ATTR, PREALBUMIN, TBPA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: PLASMA; SOURCE 6 GENE: TTR, PALB KEYWDS TRANSPORT(THYROXINE) EXPDTA X-RAY DIFFRACTION AUTHOR J.A.HAMILTON,L.K.STEINRAUF,B.C.BRADEN REVDAT 9 14-FEB-24 1TTC 1 REMARK SEQADV REVDAT 8 29-NOV-17 1TTC 1 REMARK HELIX REVDAT 7 05-OCT-11 1TTC 1 SEQADV REVDAT 6 13-JUL-11 1TTC 1 VERSN REVDAT 5 24-FEB-09 1TTC 1 VERSN REVDAT 4 01-APR-03 1TTC 1 JRNL REVDAT 3 15-JAN-95 1TTC 1 SOURCE REVDAT 2 31-JAN-94 1TTC 1 REMARK REVDAT 1 31-OCT-93 1TTC 0 JRNL AUTH J.A.HAMILTON,L.K.STEINRAUF,B.C.BRADEN,J.LIEPNIEKS, JRNL AUTH 2 M.D.BENSON,G.HOLMGREN,O.SANDGREN,L.STEEN JRNL TITL THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN JRNL TITL 2 TRANSTHYRETIN AND THE AMYLOIDOGENIC VAL-30-->MET VARIANT TO JRNL TITL 3 1.7-A RESOLUTION. JRNL REF J.BIOL.CHEM. V. 268 2416 1993 JRNL REFN ISSN 0021-9258 JRNL PMID 8428915 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.A.HAMILTON,L.K.STEINRAUF,J.LIEPNIEKS,M.D.BENSON, REMARK 1 AUTH 2 G.HOLMGREN,O.SANDGREN,L.STEEN REMARK 1 TITL ALTERATION IN MOLECULAR STRUCTURE WHICH RESULTS IN DISEASE: REMARK 1 TITL 2 THE MET-30 VARIANT OF HUMAN PLASMA TRANSTHYRETIN REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V.1139 9 1992 REMARK 1 REFN ISSN 0006-3002 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1946 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 319 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.022 ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 OCCUPANCIES OF DISORDERED SIDE CHAINS AND ATOMS WITH LESS REMARK 3 THAN UNIT OCCUPANCIES WERE SELECTED ON THE BASIS OF REMARK 3 DIFFERENCE FOURIER MAPS. ATOMS WITH OCCUPANCIES OF 0.00 REMARK 3 HAVE NO OBSERVABLE ELECTRON DENSITY. OCCUPANCIES OF REMARK 3 SOLVENT MOLECULES WERE REFINED WITH PROLSQ. REMARK 3 REMARK 3 A NUMBER OF WATER MOLECULE SITES WHICH ARE ONLY PARTIALLY REMARK 3 OCCUPIED WERE INCLUDED IN THIS STRUCTURE. BECAUSE OF REMARK 3 THIS, SHORT CONTACT DISTANCES ARE FOUND BETWEEN SOME OF REMARK 3 THESE WATER MOLECULES. REMARK 4 REMARK 4 1TTC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL 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 (%): 45.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 22.00500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.14500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.00500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.14500 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 300 REMARK: THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL REMARK 300 YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO REMARK 300 CHAIN *A*. 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 6230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 44.01000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 86.29000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY B 1 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 48 CG CD CE NZ REMARK 480 PRO B 2 N CA C DBREF 1TTC A 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 1TTC B 1 127 UNP P02766 TTHY_HUMAN 21 147 SEQADV 1TTC MET A 30 UNP P02766 VAL 50 ENGINEERED MUTATION SEQADV 1TTC MET B 30 UNP P02766 VAL 50 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 MET HIS VAL PHE ARG LYS 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 THR 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 MET HIS VAL PHE ARG LYS 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 THR ALA VAL VAL THR ASN PRO LYS GLU FORMUL 3 HOH *319(H2 O) HELIX 1 1HX THR A 75 GLY A 83 1 9 HELIX 2 2HX THR B 75 GLY B 83 1 9 SHEET 1 INT 8 GLY A 53 HIS A 56 0 SHEET 2 INT 8 PRO A 11 ASP A 18 -1 N VAL A 14 O LEU A 55 SHEET 3 INT 8 ARG A 103 SER A 112 1 O ILE A 107 N MET A 13 SHEET 4 INT 8 SER A 115 THR A 123 -1 O THR A 119 N ALA A 108 SHEET 5 INT 8 SER B 115 THR B 123 -1 N THR A 118 O TYR B 116 SHEET 6 INT 8 ARG B 103 SER B 112 -1 O ALA B 108 N THR B 119 SHEET 7 INT 8 PRO B 11 ASP B 18 1 O MET B 13 N ILE B 107 SHEET 8 INT 8 GLY B 53 HIS B 56 -1 N LEU B 55 O VAL B 14 SHEET 1 X1A 4 THR A 40 GLU A 42 0 SHEET 2 X1A 4 VAL A 28 ALA A 36 -1 N ARG A 34 O GLU A 42 SHEET 3 X1A 4 GLU A 66 ASP A 74 -1 O GLU A 72 N HIS A 31 SHEET 4 X1A 4 HIS A 90 ALA A 97 -1 O VAL A 93 N VAL A 71 SHEET 1 X2A 4 ALA A 45 THR A 49 0 SHEET 2 X2A 4 VAL A 28 ALA A 36 -1 N MET A 30 O GLY A 47 SHEET 3 X2A 4 GLU A 66 ASP A 74 -1 O GLU A 72 N HIS A 31 SHEET 4 X2A 4 HIS A 90 ALA A 97 -1 O VAL A 93 N VAL A 71 SHEET 1 X1B 4 THR B 40 GLU B 42 0 SHEET 2 X1B 4 VAL B 28 ALA B 36 -1 N ARG B 34 O GLU B 42 SHEET 3 X1B 4 GLU B 66 ASP B 74 -1 O GLU B 72 N HIS B 31 SHEET 4 X1B 4 HIS B 90 ALA B 97 -1 O VAL B 93 N VAL B 71 SHEET 1 X2B 4 ALA B 45 THR B 49 0 SHEET 2 X2B 4 VAL B 28 ALA B 36 -1 N MET B 30 O GLY B 47 SHEET 3 X2B 4 GLU B 66 ASP B 74 -1 O GLU B 72 N HIS B 31 SHEET 4 X2B 4 HIS B 90 ALA B 97 -1 O VAL B 93 N VAL B 71 CRYST1 44.010 86.290 65.370 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 0.022722 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015298 0.00000 MTRIX1 1 -0.989090 0.146670 0.013790 36.39515 1 MTRIX2 1 0.146960 0.988870 0.023060 -3.40894 1 MTRIX3 1 -0.010260 0.024840 -0.999640 98.11504 1