HEADER TRANSPORT PROTEIN 02-AUG-00 1FHN
TITLE TRANSTHYRETIN STABILITY AS A KEY FACTOR IN AMYLOIDOGENESIS
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, TRANSTHYRETIN, PROTEIN STABILITY, TRANSPORT PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR M.P.SEBASTIAO
REVDAT 6 07-FEB-24 1FHN 1 REMARK
REVDAT 5 22-AUG-18 1FHN 1 COMPND SOURCE REMARK SEQADV
REVDAT 4 13-JUL-11 1FHN 1 VERSN
REVDAT 3 24-FEB-09 1FHN 1 VERSN
REVDAT 2 09-OCT-02 1FHN 1 REMARK
REVDAT 1 25-JUL-01 1FHN 0
JRNL AUTH M.P.SEBASTIAO,V.LAMZIN,M.J.SARAIVA,A.M.DAMAS
JRNL TITL TRANSTHYRETIN STABILITY AS A KEY FACTOR IN AMYLOIDOGENESIS:
JRNL TITL 2 X-RAY ANALYSIS AT ATOMIC RESOLUTION.
JRNL REF J.MOL.BIOL. V. 306 733 2001
JRNL REFN ISSN 0022-2836
JRNL PMID 11243784
JRNL DOI 10.1006/JMBI.2000.4415
REMARK 2
REMARK 2 RESOLUTION. 1.75 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SHELXL-97
REMARK 3 AUTHORS : G.M.SHELDRICK
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.173
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.153
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.181
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1261
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 25046
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1780
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 128
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL
REMARK 3 NUMBER OF RESTRAINTS : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 ANGLE DISTANCES (A) : NULL
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1FHN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-00.
REMARK 100 THE DEPOSITION ID IS D_1000011596.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-NOV-94
REMARK 200 TEMPERATURE (KELVIN) : 277
REMARK 200 PH : 4.9
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG
REMARK 200 BEAMLINE : X11
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.93
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 100492
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750
REMARK 200 RESOLUTION RANGE LOW (A) : 12.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 200 DATA REDUNDANCY : 4.000
REMARK 200 R MERGE (I) : 0.06300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3
REMARK 200 DATA REDUNDANCY IN SHELL : 3.00
REMARK 200 R MERGE FOR SHELL (I) : 0.45000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.73
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, CITRATE BUFFER,
REMARK 280 GLYCEROL, PH 4.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 287K
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 21.88500
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.08500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.88500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.08500
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 BIOLOGICAL ASSEMBLY IS A HOMOTETRAMER CONSTRUCTED FROM
REMARK 300 CHAINS A AND B AND A SYMMETRY PARTNER GENERATED BY CRYSTALLOGRAPHIC
REMARK 300 TWO-FOLD SYMMETRY.
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: 6480 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19210 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 43.77000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 86.17000
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 PRO A 125
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 PRO B 125
REMARK 465 LYS B 126
REMARK 465 GLU B 127
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 TYR A 116 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES
REMARK 500 TYR A 116 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 ARG B 21 CD - NE - CZ ANGL. DEV. = 26.3 DEGREES
REMARK 500 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
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 -46.03 -130.12
REMARK 500 SER B 100 -74.11 -51.19
REMARK 500 PRO B 102 167.61 -49.97
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1F86 RELATED DB: PDB
REMARK 900 TTR THR119MET:THYROXINE COMPLEX
REMARK 900 RELATED ID: 1FH2 RELATED DB: PDB
REMARK 900 TTR VAL30MET/THR119MET DOUBLE MUTANT
DBREF 1FHN A 1 127 UNP P02766 TTHY_HUMAN 21 147
DBREF 1FHN B 1 127 UNP P02766 TTHY_HUMAN 21 147
SEQADV 1FHN MET A 119 UNP P02766 THR 139 ENGINEERED MUTATION
SEQADV 1FHN 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 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 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 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 MET ALA VAL VAL THR ASN PRO LYS GLU
FORMUL 3 HOH *128(H2 O)
HELIX 1 1 ASP A 74 LEU A 82 1 9
HELIX 2 2 ASP B 74 LEU B 82 1 9
SHEET 1 A12 GLU A 54 LEU A 55 0
SHEET 2 A12 LEU A 12 ASP A 18 -1 O VAL A 14 N LEU A 55
SHEET 3 A12 SER A 23 PRO A 24 -1 O SER A 23 N ASP A 18
SHEET 4 A12 LEU A 12 ASP A 18 -1 N ASP A 18 O SER A 23
SHEET 5 A12 ARG A 104 SER A 112 1 O TYR A 105 N MET A 13
SHEET 6 A12 SER A 115 THR A 123 -1 O SER A 115 N SER A 112
SHEET 7 A12 SER B 115 THR B 123 -1 O TYR B 116 N THR A 118
SHEET 8 A12 ARG B 104 SER B 112 -1 N ARG B 104 O THR B 123
SHEET 9 A12 LEU B 12 ASP B 18 1 N MET B 13 O TYR B 105
SHEET 10 A12 SER B 23 PRO B 24 -1 O SER B 23 N ASP B 18
SHEET 11 A12 LEU B 12 ASP B 18 -1 N ASP B 18 O SER B 23
SHEET 12 A12 GLU B 54 LEU B 55 -1 N LEU B 55 O VAL B 14
SHEET 1 B 8 TRP A 41 LYS A 48 0
SHEET 2 B 8 ALA A 29 LYS A 35 -1 N VAL A 30 O GLY A 47
SHEET 3 B 8 GLY A 67 ILE A 73 -1 O ILE A 68 N LYS A 35
SHEET 4 B 8 HIS A 88 ALA A 97 -1 O ALA A 91 N ILE A 73
SHEET 5 B 8 HIS B 88 ALA B 97 -1 N GLU B 89 O VAL A 94
SHEET 6 B 8 GLY B 67 ILE B 73 -1 O GLY B 67 N ALA B 97
SHEET 7 B 8 ALA B 29 ALA B 36 -1 O HIS B 31 N GLU B 72
SHEET 8 B 8 THR B 40 LYS B 48 -1 O THR B 40 N ALA B 36
CRYST1 43.770 86.170 65.220 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 0.022847 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011605 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015333 0.00000
(ATOM LINES ARE NOT SHOWN.)
END