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- PDB-2cvj: Crystal Structure of thioredoxin reductase-related protein TTHA03... -

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Basic information

Entry
Database: PDB / ID: 2cvj
TitleCrystal Structure of thioredoxin reductase-related protein TTHA0370 from Thermus thermophilus HB8
Componentsthioredoxin reductase related protein
KeywordsOXIDOREDUCTASE / thioredoxin reductase-related protein / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / nucleotide binding
Similarity search - Function
: / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD binding domain / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase related protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKashihara, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of thioredoxin reductase-related protein TTHA0370 from Thermus thermophilus HB8
Authors: Kashihara, A. / Yokoyama, S. / Kuramitsu, S.
History
DepositionJun 4, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thioredoxin reductase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0322
Polymers19,2471
Non-polymers7861
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: thioredoxin reductase related protein
hetero molecules

A: thioredoxin reductase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0654
Polymers38,4932
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area6650 Å2
ΔGint-31 kcal/mol
Surface area13640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.050, 79.690, 83.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein thioredoxin reductase related protein


Mass: 19246.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SLC3
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.3M NaH2 Phosphate, 0.9M K2H Phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97909, 0.9, 0.97933
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 9, 2004
RadiationMonochromator: Si Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979091
20.91
30.979331
ReflectionResolution: 1.7→31.97 Å / Num. all: 164790 / Num. obs: 23729 / % possible obs: 99.8 % / Redundancy: 6.94 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 21.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 10.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.38 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1766148.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1487 10.2 %RANDOM
Rwork0.203 ---
all0.206 14646 --
obs0.203 14646 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.6635 Å2 / ksol: 0.413362 e/Å3
Displacement parametersBiso mean: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---1.73 Å20 Å2
3---2.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å-0.06 Å
Refinement stepCycle: LAST / Resolution: 2→19.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 0 53 133 1534
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 239 9.9 %
Rwork0.189 2185 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3fad_xplor_param.txtfad_xplor_top.txt

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