HEADER TRANSPORT PROTEIN 03-OCT-11 3U2J TITLE NEUTRON CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN 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 NEUTRON 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 4 01-NOV-23 3U2J 1 SEQADV REVDAT 3 24-JUL-19 3U2J 1 REMARK REVDAT 2 07-MAR-18 3U2J 1 REMARK REVDAT 1 22-FEB-12 3U2J 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 NUMBER OF REFLECTIONS : 15295 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 776 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 12.5602 - 3.6200 0.89 2595 130 0.1805 0.2188 REMARK 3 2 3.6200 - 2.8847 0.98 2726 133 0.1996 0.2589 REMARK 3 3 2.8847 - 2.5234 0.95 2602 145 0.2324 0.2551 REMARK 3 4 2.5234 - 2.2943 0.90 2467 114 0.2541 0.3177 REMARK 3 5 2.2943 - 2.1307 0.87 2338 156 0.2835 0.3042 REMARK 3 6 2.1307 - 2.0056 0.80 2139 115 0.3352 0.3445 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 : 0.49 REMARK 3 B_SOL : 42.82 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.580 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.67140 REMARK 3 B22 (A**2) : 1.40160 REMARK 3 B33 (A**2) : 0.26980 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 : 0.004 3904 REMARK 3 ANGLE : 1.401 7004 REMARK 3 CHIRALITY : 0.096 282 REMARK 3 PLANARITY : 0.004 768 REMARK 3 DIHEDRAL : 16.675 1089 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 3U2J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068224. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 20-NOV-10 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 7.40 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : BL-03 REMARK 230 WAVELENGTH OR RANGE (A) : 3.2 - 6.2 REMARK 230 MONOCHROMATOR : DISK CHOPPER REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : STORAGE PHOSPHORS REMARK 230 DETECTOR MANUFACTURER : WAVELENGTH-SHIFT-FIBER TYPE OF REMARK 230 POSITION-SENSITIVE DETECTOR REMARK 230 INTENSITY-INTEGRATION SOFTWARE : STARGAZER REMARK 230 DATA SCALING SOFTWARE : STARGAZER REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 15307 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 230 RESOLUTION RANGE LOW (A) : 12.100 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 86.4 REMARK 230 DATA REDUNDANCY : 2.600 REMARK 230 R MERGE (I) : NULL REMARK 230 R SYM (I) : 0.19100 REMARK 230 FOR THE DATA SET : 4.3000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 230 COMPLETENESS FOR SHELL (%) : 72.5 REMARK 230 DATA REDUNDANCY IN SHELL : 1.70 REMARK 230 R MERGE FOR SHELL (I) : NULL REMARK 230 R SYM FOR SHELL (I) : 0.30600 REMARK 230 FOR SHELL : 1.500 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : PHENIX REMARK 230 STARTING MODEL: PDB ENTRY 3U2I REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.85M TRI-AMMONIUM CITRATE, PD7.4, REMARK 280 0.4M MGCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH REMARK 280 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 22.04700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.05150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.04700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.05150 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: 6300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 44.09400 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 86.10300 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 LYS A 126 REMARK 465 GLU A 127 REMARK 465 ASN B 98 REMARK 465 ASP B 99 REMARK 465 SER B 100 REMARK 465 GLY B 101 REMARK 465 PRO B 125 REMARK 465 LYS B 126 REMARK 465 GLU B 127 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG B 103 CG CD NE CZ NH1 NH2 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 ASP B 38 -121.05 -63.26 REMARK 500 ASP B 39 34.04 -142.70 REMARK 500 PHE B 44 -44.08 -132.46 REMARK 500 ARG B 103 79.13 166.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG B 103 ARG B 104 149.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3U2I RELATED DB: PDB REMARK 900 STARTING MODEL FOR STRUCTURE REFINEMENT DBREF 3U2J A 12 127 UNP P02766 TTHY_HUMAN 32 147 DBREF 3U2J B 12 127 UNP P02766 TTHY_HUMAN 32 147 SEQADV 3U2J MET A 11 UNP P02766 EXPRESSION TAG SEQADV 3U2J 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 DOD *55(D2 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 123 N ARG A 104 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 TYR B 105 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 123 N ARG A 104 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 TYR B 105 SHEET 8 B 8 GLU B 54 LEU B 55 -1 O LEU B 55 N VAL B 14 SHEET 1 C 4 TRP A 41 LYS A 48 0 SHEET 2 C 4 ALA A 29 LYS A 35 -1 N VAL A 32 O ALA A 45 SHEET 3 C 4 GLY A 67 ILE A 73 -1 O GLU A 72 N HIS A 31 SHEET 4 C 4 ALA A 91 ALA A 97 -1 O ALA A 91 N ILE A 73 SHEET 1 D 4 TRP B 41 LYS B 48 0 SHEET 2 D 4 ALA B 29 LYS B 35 -1 N VAL B 32 O ALA B 45 SHEET 3 D 4 GLY B 67 ILE B 73 -1 O GLU B 72 N HIS B 31 SHEET 4 D 4 ALA B 91 ALA B 97 -1 O ALA B 97 N GLY B 67 CRYST1 44.094 86.103 66.313 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 0.022679 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015080 0.00000