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- PDB-6gn9: Crystal structure of a thioredoxin from Clostridium acetobutylicu... -

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Basic information

Entry
Database: PDB / ID: 6gn9
TitleCrystal structure of a thioredoxin from Clostridium acetobutylicum at 1.75 A resolution
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin
Function / homology
Function and homology information


protein-disulfide reductase activity
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
ACETATE ION / Thioredoxin
Similarity search - Component
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBuey, R.M. / Fernandez-Justel, D. / Balsera, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBFU2016-80343-P Spain
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Ferredoxin-linked flavoenzyme defines a family of pyridine nucleotide-independent thioredoxin reductases.
Authors: Buey, R.M. / Fernandez-Justel, D. / de Pereda, J.M. / Revuelta, J.L. / Schurmann, P. / Buchanan, B.B. / Balsera, M.
History
DepositionMay 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0995
Polymers11,8631
Non-polymers2364
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area5500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.031, 42.388, 84.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Thioredoxin


Mass: 11862.610 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Gene: CA_C3083 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97EM7
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate pH 6.5, 40% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.75→42.261 Å / Num. obs: 11442 / % possible obs: 99.82 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08933 / Rrim(I) all: 0.09336 / Net I/σ(I): 15.95
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 12.6 % / Rmerge(I) obs: 2.37 / Num. unique obs: 1112 / CC1/2: 0.398 / Rrim(I) all: 2.47 / % possible all: 99.19

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DYR

3dyr


Resolution: 1.75→42.261 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.86
RfactorNum. reflection% reflection
Rfree0.2179 555 4.86 %
Rwork0.2019 --
obs0.2027 11428 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→42.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 16 42 813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002799
X-RAY DIFFRACTIONf_angle_d0.5111082
X-RAY DIFFRACTIONf_dihedral_angle_d17.368471
X-RAY DIFFRACTIONf_chiral_restr0.045125
X-RAY DIFFRACTIONf_plane_restr0.003142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.92620.33121360.29332657X-RAY DIFFRACTION100
1.9262-2.20490.24011580.23272644X-RAY DIFFRACTION100
2.2049-2.77790.21731270.21532725X-RAY DIFFRACTION100
2.7779-42.27330.20091340.18362848X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.776-0.23510.41353.3158-3.33643.33490.22850.2883-0.2172-0.7882-0.415-0.2268-0.1598-0.0436-0.13790.62010.03680.06880.47630.05630.4312-19.826553.75583.3366
25.66441.50322.04033.07320.58054.1223-0.07430.47480.0822-0.026-0.0616-0.2523-0.14510.19620.010.22630.02740.02790.3058-0.02040.2939-14.032451.58813.8562
35.24172.46153.69717.03514.64384.3583-0.06910.2819-0.0587-0.41110.0337-0.35930.19390.4341-0.02320.39-0.00410.03020.30280.01580.3177-12.133242.214912.8624
43.36350.72590.66852.79042.34953.658-0.13690.19870.3805-0.3305-0.10510.0821-0.2874-0.02710.23770.31570.0169-0.02250.30980.00960.3027-17.826453.732412.1645
53.8506-4.07913.23796.828-3.29183.03310.33890.0979-0.23680.15350.05230.4406-0.3893-0.3979-0.1660.27380.05220.08450.41940.00460.2915-26.048950.846311.827
63.9815-0.83360.30944.9585-1.77163.5696-0.0973-0.4587-0.07150.40280.23020.3689-0.138-0.7044-0.09630.2590.00370.02220.3356-0.02460.2401-23.057447.380718.4669
72.5166-2.24372.48038.6552-2.41147.50860.1670.2792-0.26990.0577-0.0631.07790.60350.0852-0.11220.3149-0.0193-0.01780.31970.00040.4034-24.555738.942114.6593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 93 )
7X-RAY DIFFRACTION7chain 'A' and (resid 94 through 104 )

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