HEADER TRANSPORT PROTEIN 03-OCT-11 3U2I
TITLE X-RAY CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN AT ROOM TEMPERATURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRANSTHYRETIN;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 32-147;
COMPND 5 SYNONYM: ATTR, PREALBUMIN, TBPA;
COMPND 6 ENGINEERED: 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;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M-15;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE-30
KEYWDS TRANSPORTER, THYROXINE BINDING, TRANSPORT PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR T.YOKOYAMA,M.MIZUGUCHI,Y.NABESHIMA,K.KUSAKA,T.YAMADA,T.HOSOYA,
AUTHOR 2 T.OHHARA,K.KURIHARA,K.TOMOYORI,I.TANAKA,N.NIIMURA
REVDAT 2 01-NOV-23 3U2I 1 SEQADV
REVDAT 1 22-FEB-12 3U2I 0
JRNL AUTH T.YOKOYAMA,M.MIZUGUCHI,Y.NABESHIMA,K.KUSAKA,T.YAMADA,
JRNL AUTH 2 T.HOSOYA,T.OHHARA,K.KURIHARA,K.TOMOYORI,I.TANAKA,N.NIIMURA
JRNL TITL HYDROGEN-BOND NETWORK AND PH SENSITIVITY IN TRANSTHYRETIN:
JRNL TITL 2 NEUTRON CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN
JRNL REF J.STRUCT.BIOL. V. 177 283 2012
JRNL REFN ISSN 1047-8477
JRNL PMID 22248451
JRNL DOI 10.1016/J.JSB.2011.12.022
REMARK 2
REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743)
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) : 1.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.80
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7
REMARK 3 NUMBER OF REFLECTIONS : 26473
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.197
REMARK 3 R VALUE (WORKING SET) : 0.195
REMARK 3 FREE R VALUE : 0.239
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050
REMARK 3 FREE R VALUE TEST SET COUNT : 1337
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 38.8115 - 3.6607 0.94 2665 131 0.1554 0.1734
REMARK 3 2 3.6607 - 2.9059 0.98 2635 131 0.1633 0.2279
REMARK 3 3 2.9059 - 2.5387 0.97 2584 146 0.1809 0.2207
REMARK 3 4 2.5387 - 2.3066 0.96 2544 150 0.1758 0.2267
REMARK 3 5 2.3066 - 2.1413 0.96 2555 121 0.1833 0.2420
REMARK 3 6 2.1413 - 2.0150 0.96 2511 119 0.1978 0.2297
REMARK 3 7 2.0150 - 1.9141 0.95 2489 136 0.2200 0.2342
REMARK 3 8 1.9141 - 1.8308 0.94 2443 135 0.2512 0.3490
REMARK 3 9 1.8308 - 1.7603 0.92 2396 144 0.3606 0.3674
REMARK 3 10 1.7603 - 1.6996 0.89 2314 124 0.5595 0.6309
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 : 0.83
REMARK 3 K_SOL : 0.34
REMARK 3 B_SOL : 32.23
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.510
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.970
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.51
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.46920
REMARK 3 B22 (A**2) : -1.95040
REMARK 3 B33 (A**2) : 1.48120
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
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 : 0.007 1820
REMARK 3 ANGLE : 1.029 2480
REMARK 3 CHIRALITY : 0.070 283
REMARK 3 PLANARITY : 0.005 314
REMARK 3 DIHEDRAL : 13.092 638
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 3U2I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-OCT-11.
REMARK 100 THE DEPOSITION ID IS D_1000068223.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 09-SEP-10
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 7.4
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 : MACSCIENCE
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2000
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26473
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7
REMARK 200 DATA REDUNDANCY : 19.30
REMARK 200 R MERGE (I) : 0.09200
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) : 1.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76
REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.57300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: 2ROX
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.54
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M TRI-AMMONIUM CITRATE(PD7.4), 0.4M
REMARK 280 MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 7.4
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 21.71550
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.18400
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.71550
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.18400
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
REMARK 350 TOTAL BURIED SURFACE AREA: 6220 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19420 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 43.43100
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 86.36800
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 144 LIES ON A SPECIAL POSITION.
REMARK 375 HOH B 134 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 LYS A 126
REMARK 465 GLU A 127
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 -44.37 -133.46
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3U2J RELATED DB: PDB
DBREF 3U2I A 12 127 UNP P02766 TTHY_HUMAN 32 147
DBREF 3U2I B 12 127 UNP P02766 TTHY_HUMAN 32 147
SEQADV 3U2I MET A 11 UNP P02766 EXPRESSION TAG
SEQADV 3U2I MET B 11 UNP P02766 EXPRESSION TAG
SEQRES 1 A 117 MET LEU MET VAL LYS VAL LEU ASP ALA VAL ARG GLY SER
SEQRES 2 A 117 PRO ALA ILE ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA
SEQRES 3 A 117 ALA ASP ASP THR TRP GLU PRO PHE ALA SER GLY LYS THR
SEQRES 4 A 117 SER GLU SER GLY GLU LEU HIS GLY LEU THR THR GLU GLU
SEQRES 5 A 117 GLU PHE VAL GLU GLY ILE TYR LYS VAL GLU ILE ASP THR
SEQRES 6 A 117 LYS SER TYR TRP LYS ALA LEU GLY ILE SER PRO PHE HIS
SEQRES 7 A 117 GLU HIS ALA GLU VAL VAL PHE THR ALA ASN ASP SER GLY
SEQRES 8 A 117 PRO ARG ARG TYR THR ILE ALA ALA LEU LEU SER PRO TYR
SEQRES 9 A 117 SER TYR SER THR THR ALA VAL VAL THR ASN PRO LYS GLU
SEQRES 1 B 117 MET LEU MET VAL LYS VAL LEU ASP ALA VAL ARG GLY SER
SEQRES 2 B 117 PRO ALA ILE ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA
SEQRES 3 B 117 ALA ASP ASP THR TRP GLU PRO PHE ALA SER GLY LYS THR
SEQRES 4 B 117 SER GLU SER GLY GLU LEU HIS GLY LEU THR THR GLU GLU
SEQRES 5 B 117 GLU PHE VAL GLU GLY ILE TYR LYS VAL GLU ILE ASP THR
SEQRES 6 B 117 LYS SER TYR TRP LYS ALA LEU GLY ILE SER PRO PHE HIS
SEQRES 7 B 117 GLU HIS ALA GLU VAL VAL PHE THR ALA ASN ASP SER GLY
SEQRES 8 B 117 PRO ARG ARG TYR THR ILE ALA ALA LEU LEU SER PRO TYR
SEQRES 9 B 117 SER TYR SER THR THR ALA VAL VAL THR ASN PRO LYS GLU
FORMUL 3 HOH *84(H2 O)
HELIX 1 1 ASP A 74 ALA A 81 1 8
HELIX 2 2 ASP B 74 LEU B 82 1 9
SHEET 1 A 8 SER A 23 PRO A 24 0
SHEET 2 A 8 LEU A 12 ASP A 18 -1 N ASP A 18 O SER A 23
SHEET 3 A 8 ARG A 104 SER A 112 1 O ILE A 107 N MET A 13
SHEET 4 A 8 SER A 115 THR A 123 -1 O THR A 119 N ALA A 108
SHEET 5 A 8 SER B 115 THR B 123 -1 O THR B 118 N TYR A 116
SHEET 6 A 8 ARG B 104 SER B 112 -1 N ALA B 108 O THR B 119
SHEET 7 A 8 LEU B 12 ASP B 18 1 N MET B 13 O ILE B 107
SHEET 8 A 8 SER B 23 PRO B 24 -1 O SER B 23 N ASP B 18
SHEET 1 B 8 GLU A 54 LEU A 55 0
SHEET 2 B 8 LEU A 12 ASP A 18 -1 N VAL A 14 O LEU A 55
SHEET 3 B 8 ARG A 104 SER A 112 1 O ILE A 107 N MET A 13
SHEET 4 B 8 SER A 115 THR A 123 -1 O THR A 119 N ALA A 108
SHEET 5 B 8 SER B 115 THR B 123 -1 O THR B 118 N TYR A 116
SHEET 6 B 8 ARG B 104 SER B 112 -1 N ALA B 108 O THR B 119
SHEET 7 B 8 LEU B 12 ASP B 18 1 N MET B 13 O ILE B 107
SHEET 8 B 8 GLU B 54 LEU B 55 -1 O LEU B 55 N VAL B 14
SHEET 1 C 8 TRP A 41 LYS A 48 0
SHEET 2 C 8 ALA A 29 LYS A 35 -1 N VAL A 32 O ALA A 45
SHEET 3 C 8 GLY A 67 ILE A 73 -1 O GLU A 72 N HIS A 31
SHEET 4 C 8 HIS A 88 ALA A 97 -1 O ALA A 91 N ILE A 73
SHEET 5 C 8 ALA B 91 ALA B 97 -1 O VAL B 94 N GLU A 89
SHEET 6 C 8 GLY B 67 ILE B 73 -1 N TYR B 69 O PHE B 95
SHEET 7 C 8 ALA B 29 LYS B 35 -1 N HIS B 31 O GLU B 72
SHEET 8 C 8 TRP B 41 LYS B 48 -1 O ALA B 45 N VAL B 32
CISPEP 1 SER B 100 GLY B 101 0 -5.16
CRYST1 43.431 86.368 65.716 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 0.023025 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011578 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015217 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
