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- PDB-6kil: N21Q mutant thioredoxin from Halobacterium salinarum NRC-1 -

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Basic information

Entry
Database: PDB / ID: 6kil
TitleN21Q mutant thioredoxin from Halobacterium salinarum NRC-1
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / halophile
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / glycerol ether metabolic process / protein-disulfide reductase (NAD(P)H) activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsArai, S. / Shibazaki, C. / Shimizu, R. / Adachi, M. / Ishibashi, M. / Tokunaga, H. / Tokunaga, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2020
Title: Catalytic mechanism and evolutional characteristics of thioredoxin from Halobacterium salinarum NRC-1.
Authors: Arai, S. / Shibazaki, C. / Shimizu, R. / Adachi, M. / Ishibashi, M. / Tokunaga, H. / Tokunaga, M.
History
DepositionJul 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)13,1861
Polymers13,1861
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.917, 43.283, 54.435
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Thioredoxin / TrxA


Mass: 13186.258 Da / Num. of mol.: 1 / Mutation: N21Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile)
Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: trxA, trxA1_1, trxA1_2, VNG_6073G, VNG_6453G / Plasmid: pCold-I / Production host: Escherichia coli (E. coli) / References: UniProt: O46709
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl buffer (pH8.5), 2.0 M ammonium sulfate, 12.7 mg/mL of protein
PH range: 8 - 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 30, 2015
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 13317 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Χ2: 1.79 / Net I/av σ(I): 12.9 / Net I/σ(I): 12.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7 % / Rmerge(I) obs: 0.383 / Num. unique obs: 647 / CC1/2: 0.939 / Rpim(I) all: 0.154 / Rrim(I) all: 0.413 / Χ2: 1.345 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E0Q

2e0q


Resolution: 1.6→32.71 Å / SU ML: 0.0745 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.3461
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 662 4.99 %Random selection
Rwork0.1766 ---
obs0.1771 13275 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 0 94 946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054908
X-RAY DIFFRACTIONf_angle_d1.0511257
X-RAY DIFFRACTIONf_chiral_restr0.0555149
X-RAY DIFFRACTIONf_plane_restr0.0082174
X-RAY DIFFRACTIONf_dihedral_angle_d2.323740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.720.24141260.19952482X-RAY DIFFRACTION99.92
1.72-1.90.2091330.18182471X-RAY DIFFRACTION100
1.9-2.170.20011290.18142509X-RAY DIFFRACTION99.96
2.17-2.730.17921350.18152523X-RAY DIFFRACTION100
2.73-32.710.17011390.16712628X-RAY DIFFRACTION99.6
Refinement TLS params.Method: refined / Origin x: 32.8646478415 Å / Origin y: 26.4296171813 Å / Origin z: 22.4906493733 Å
111213212223313233
T0.0472041998018 Å2-0.00331623524155 Å2-0.00421894634038 Å2-0.0676832374691 Å2-0.00835781043977 Å2--0.0600547714676 Å2
L2.48942215389 °2-0.426305158421 °2-0.623362132825 °2-2.42528371364 °20.214532616104 °2--2.69651504758 °2
S-0.0313716851468 Å °0.0349230934543 Å °-0.0768250833243 Å °0.0494052974813 Å °0.00960098187698 Å °0.00369682524833 Å °0.053748820309 Å °-0.0548245342948 Å °-0.00858592150225 Å °
Refinement TLS groupSelection details: all

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