PDB Short entry for 2DIZ HEADER ELECTRON TRANSPORT 30-MAR-06 2DIZ TITLE THE SOLUTION STRUCTURE OF THE THIRD THIOREDOXIN DOMAIN OF HUMAN TITLE 2 THIOREDOXIN DOMAIN-CONTAINING PROTEIN 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN DOMAIN-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 3RD THIOREDOXIN DOMAIN; COMPND 5 SYNONYM: THIOREDOXIN-LIKE PROTEIN P46, ENDOPLASMIC RETICULUM PROTEIN COMPND 6 ERP46; COMPND 7 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: TXNDC5; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P050302-28; SOURCE 9 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS THIOREDOXIN-LIKE PROTEIN P46, ENDOPLASMIC RETICULUM PROTEIN ERP46, KEYWDS 2 TLP46, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 3 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DIZ 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DIZ 1 VERSN REVDAT 1 30-SEP-06 2DIZ 0 JRNL AUTH N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL THE SOLUTION STRUCTURE OF THE THIRD THIOREDOXIN DOMAIN OF JRNL TITL 2 HUMAN THIOREDOXIN DOMAIN-CONTAINING PROTEIN 5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DIZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025468. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.3MM THIOREDOXIN DOMAIN U REMARK 210 -15N,13C; 20MM D-TRIS HCL; 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.955, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH REMARK 210 THE LEAST RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 1 SER A 2 153.34 -48.40 REMARK 500 1 PRO A 33 1.44 -69.78 REMARK 500 1 SER A 77 45.55 34.93 REMARK 500 1 VAL A 93 -61.56 -105.06 REMARK 500 1 LEU A 102 -36.52 -36.56 REMARK 500 1 LYS A 114 112.51 -37.05 REMARK 500 2 SER A 5 92.93 -68.55 REMARK 500 2 SER A 6 171.37 -54.85 REMARK 500 2 PRO A 33 2.51 -69.69 REMARK 500 2 LYS A 51 157.96 -43.35 REMARK 500 2 GLU A 69 74.34 -118.21 REMARK 500 2 SER A 77 47.62 34.51 REMARK 500 2 ALA A 113 31.89 -92.90 REMARK 500 3 SER A 3 99.78 -60.85 REMARK 500 3 THR A 8 -68.47 -128.20 REMARK 500 3 GLU A 69 69.25 -111.27 REMARK 500 3 SER A 77 40.90 34.42 REMARK 500 3 VAL A 93 -56.67 -128.48 REMARK 500 4 SER A 3 153.11 -47.23 REMARK 500 4 THR A 8 -52.04 -129.76 REMARK 500 4 ALA A 11 92.31 -57.90 REMARK 500 4 THR A 20 -70.22 -61.34 REMARK 500 4 PRO A 33 1.70 -69.76 REMARK 500 4 SER A 77 31.16 38.40 REMARK 500 4 VAL A 93 -58.80 -122.83 REMARK 500 4 HIS A 96 103.14 -46.74 REMARK 500 4 SER A 97 76.96 -109.22 REMARK 500 4 LYS A 114 99.30 -47.19 REMARK 500 5 THR A 8 -57.23 -130.73 REMARK 500 5 PRO A 33 2.49 -69.85 REMARK 500 5 SER A 77 48.00 34.29 REMARK 500 5 VAL A 93 -60.86 -108.49 REMARK 500 5 HIS A 96 108.62 -59.78 REMARK 500 5 ARG A 100 44.37 -85.85 REMARK 500 5 LYS A 114 113.03 -38.22 REMARK 500 6 SER A 5 131.58 -172.12 REMARK 500 6 LYS A 51 177.62 -56.61 REMARK 500 6 SER A 77 27.58 42.16 REMARK 500 6 LYS A 92 158.55 -39.18 REMARK 500 6 VAL A 93 -59.43 -123.10 REMARK 500 6 ALA A 113 31.22 -87.93 REMARK 500 6 ASP A 115 38.99 -87.86 REMARK 500 7 SER A 3 108.56 -58.90 REMARK 500 7 PRO A 33 1.45 -69.74 REMARK 500 7 LYS A 51 164.34 -49.38 REMARK 500 7 GLU A 69 68.79 -111.86 REMARK 500 7 ARG A 100 49.54 -99.87 REMARK 500 8 ALA A 11 98.20 -67.73 REMARK 500 8 PRO A 33 1.00 -69.74 REMARK 500 8 CYS A 66 33.65 -84.87 REMARK 500 REMARK 500 THIS ENTRY HAS 151 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002004474.1 RELATED DB: TARGETDB DBREF 2DIZ A 8 117 UNP Q8NBS9 TXND5_HUMAN 288 315 SEQADV 2DIZ GLY A 1 UNP Q8NBS9 CLONING ARTIFACT SEQADV 2DIZ SER A 2 UNP Q8NBS9 CLONING ARTIFACT SEQADV 2DIZ SER A 3 UNP Q8NBS9 CLONING ARTIFACT SEQADV 2DIZ GLY A 4 UNP Q8NBS9 CLONING ARTIFACT SEQADV 2DIZ SER A 5 UNP Q8NBS9 CLONING ARTIFACT SEQADV 2DIZ SER A 6 UNP Q8NBS9 CLONING ARTIFACT SEQADV 2DIZ GLY A 7 UNP Q8NBS9 CLONING ARTIFACT SEQRES 1 A 117 GLY SER SER GLY SER SER GLY THR VAL LEU ALA LEU THR SEQRES 2 A 117 GLU ASN ASN PHE ASP ASP THR ILE ALA GLU GLY ILE THR SEQRES 3 A 117 PHE ILE LYS PHE TYR ALA PRO TRP CYS GLY HIS CYS LYS SEQRES 4 A 117 THR LEU ALA PRO THR TRP GLU GLU LEU SER LYS LYS GLU SEQRES 5 A 117 PHE PRO GLY LEU ALA GLY VAL LYS ILE ALA GLU VAL ASP SEQRES 6 A 117 CYS THR ALA GLU ARG ASN ILE CYS SER LYS TYR SER VAL SEQRES 7 A 117 ARG GLY TYR PRO THR LEU LEU LEU PHE ARG GLY GLY LYS SEQRES 8 A 117 LYS VAL SER GLU HIS SER GLY GLY ARG ASP LEU ASP SER SEQRES 9 A 117 LEU HIS ARG PHE VAL LEU SER GLN ALA LYS ASP GLU LEU HELIX 1 1 PHE A 17 GLU A 23 1 7 HELIX 2 2 GLY A 36 LYS A 51 1 16 HELIX 3 3 GLU A 69 TYR A 76 1 8 HELIX 4 4 ASP A 101 LYS A 114 1 14 SHEET 1 A 4 LEU A 10 ALA A 11 0 SHEET 2 A 4 LYS A 60 ASP A 65 1 O ILE A 61 N LEU A 10 SHEET 3 A 4 THR A 26 TYR A 31 1 N PHE A 27 O LYS A 60 SHEET 4 A 4 THR A 83 LEU A 85 -1 O THR A 83 N PHE A 30 SSBOND 1 CYS A 66 CYS A 73 1555 1555 2.00 CISPEP 1 TYR A 81 PRO A 82 1 -0.03 CISPEP 2 TYR A 81 PRO A 82 2 -0.04 CISPEP 3 TYR A 81 PRO A 82 3 -0.07 CISPEP 4 TYR A 81 PRO A 82 4 -0.06 CISPEP 5 TYR A 81 PRO A 82 5 0.00 CISPEP 6 TYR A 81 PRO A 82 6 -0.02 CISPEP 7 TYR A 81 PRO A 82 7 -0.10 CISPEP 8 TYR A 81 PRO A 82 8 -0.01 CISPEP 9 TYR A 81 PRO A 82 9 -0.03 CISPEP 10 TYR A 81 PRO A 82 10 -0.02 CISPEP 11 TYR A 81 PRO A 82 11 0.01 CISPEP 12 TYR A 81 PRO A 82 12 -0.06 CISPEP 13 TYR A 81 PRO A 82 13 -0.01 CISPEP 14 TYR A 81 PRO A 82 14 -0.11 CISPEP 15 TYR A 81 PRO A 82 15 -0.01 CISPEP 16 TYR A 81 PRO A 82 16 -0.14 CISPEP 17 TYR A 81 PRO A 82 17 0.02 CISPEP 18 TYR A 81 PRO A 82 18 -0.19 CISPEP 19 TYR A 81 PRO A 82 19 0.06 CISPEP 20 TYR A 81 PRO A 82 20 -0.08 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000