HEADER TRANSPORT 16-OCT-96 2TRH TITLE TERTIARY STRUCTURES OF THREE AMYLOIDOGENIC TRANSTHYRETIN VARIANTS AND TITLE 2 IMPLICATIONS FOR AMYLOID FIBRIL FORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSTHYRETIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PREALBUMIN; 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 CELL_LINE: HB101; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HB101; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCZ11 KEYWDS ALBUMIN, TRANSPORT, RETINOL-BINDING, VITAMIN A, AMYLOID, THYROID KEYWDS 2 HORMONE, LIVER, PLASMA, CEREBROSPINAL FLUID, POLYNEUROPATHY, DISEASE KEYWDS 3 MUTATION, THYROXINE, PREALBUMIN EXPDTA X-RAY DIFFRACTION AUTHOR N.SCHORMANN,J.R.MURRELL,M.D.BENSON REVDAT 3 13-JUL-11 2TRH 1 VERSN REVDAT 2 24-FEB-09 2TRH 1 VERSN REVDAT 1 21-APR-97 2TRH 0 JRNL AUTH N.SCHORMANN,J.R.MURRELL,M.D.BENSON JRNL TITL TERTIARY STRUCTURES OF AMYLOIDOGENIC AND NON-AMYLOIDOGENIC JRNL TITL 2 TRANSTHYRETIN VARIANTS: NEW MODEL FOR AMYLOID FIBRIL JRNL TITL 3 FORMATION. JRNL REF AMYLOID V. 5 175 1998 JRNL REFN ISSN 1350-6129 JRNL PMID 9818054 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 16842 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 SET) : 0.219 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1009 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.08 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1827 REMARK 3 BIN R VALUE (WORKING SET) : 0.3510 REMARK 3 BIN FREE R VALUE : 0.3950 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 96 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1954 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.60 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.34 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.87 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.57 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.220 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.410 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.410 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.580 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 RESIDUES IN REGIONS WITH LOW ELECTRON DENSITY (RESIDUES REMARK 3 1 - 9 AT N-TERMINUS AND RESIDUES 124 - 127 AT C-TERMINUS) REMARK 3 WERE REFINED WITH OCCUPANCIES SET TO 0.5. REMARK 4 REMARK 4 2TRH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-95 REMARK 200 TEMPERATURE (KELVIN) : 296 REMARK 200 PH : 5.5-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX REMARK 200 DATA SCALING SOFTWARE : BIOTEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20855 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 52.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : 0.22000 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: PDB ENTRY 1TTA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PURIFIED PROTEIN (20MG/ML IN 100MM REMARK 280 TRIS BUFFER, PH 7.5) WAS CRYSTALLIZED FROM\\ 2.25M AMMONIUM REMARK 280 SULFATE, 100MM CITRATE BUFFER, PH 5.5 AT ROOM TEMPERATURE.\\, PH REMARK 280 6.5 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 21.69000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.17000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.69000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.17000 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 6190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 43.38000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 86.34000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 PRO A 2 106.69 -47.58 REMARK 500 GLU A 7 39.75 -156.66 REMARK 500 SER A 8 -88.35 -16.79 REMARK 500 GLU B 7 65.68 -170.14 REMARK 500 LYS B 9 -0.37 -157.16 REMARK 500 ARG B 10 68.10 65.82 REMARK 500 ASP B 39 6.03 80.68 REMARK 500 PHE B 44 -54.09 -123.06 REMARK 500 ASP B 74 76.56 -69.62 REMARK 500 HIS B 90 -178.21 -175.05 REMARK 500 ASP B 99 -33.23 -38.42 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 A 130 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 154 DISTANCE = 5.21 ANGSTROMS DBREF 2TRH A 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 2TRH B 1 127 UNP P02766 TTHY_HUMAN 21 147 SEQADV 2TRH ARG A 10 UNP P02766 CYS 30 VARIANT SEQADV 2TRH ARG B 10 UNP P02766 CYS 30 VARIANT SEQRES 1 A 127 GLY PRO THR GLY THR GLY GLU SER LYS ARG 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 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 ARG 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 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 *71(H2 O) HELIX 1 1 THR A 75 LEU A 82 1 8 HELIX 2 2 THR B 75 LEU B 82 1 8 SHEET 1 A 7 LEU A 12 ASP A 18 0 SHEET 2 A 7 ARG A 103 SER A 112 1 N TYR A 105 O MET A 13 SHEET 3 A 7 SER A 115 ASN A 124 -1 N THR A 123 O ARG A 104 SHEET 4 A 7 SER B 115 THR B 123 -1 N THR B 118 O TYR A 116 SHEET 5 A 7 ARG B 104 SER B 112 -1 N SER B 112 O SER B 115 SHEET 6 A 7 LEU B 12 ASP B 18 1 N MET B 13 O TYR B 105 SHEET 7 A 7 GLU B 54 HIS B 56 -1 N LEU B 55 O VAL B 14 SHEET 1 B 4 ALA A 91 ALA A 97 0 SHEET 2 B 4 GLY A 67 ILE A 73 -1 N ILE A 73 O ALA A 91 SHEET 3 B 4 ALA A 29 LYS A 35 -1 N PHE A 33 O LYS A 70 SHEET 4 B 4 TRP A 41 LYS A 48 -1 N GLY A 47 O VAL A 30 SHEET 1 C 4 ALA B 91 ALA B 97 0 SHEET 2 C 4 GLY B 67 ILE B 73 -1 N ILE B 73 O ALA B 91 SHEET 3 C 4 ALA B 29 LYS B 35 -1 N PHE B 33 O LYS B 70 SHEET 4 C 4 TRP B 41 LYS B 48 -1 N GLY B 47 O VAL B 30 CRYST1 43.380 86.340 65.580 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 0.023052 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011582 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015249 0.00000 MTRIX1 1 -0.990020 0.140910 -0.001970 36.88590 1 MTRIX2 1 0.140920 0.989970 -0.009950 -2.01740 1 MTRIX3 1 0.000550 -0.010130 -0.999950 98.54830 1 MASTER 257 0 0 2 15 0 0 9 0 0 0 20 END