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- PDB-6gnc: Crystal structure of a Ferredoxin-Flavin Thioredoxin Reductase fr... -

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Basic information

Entry
Database: PDB / ID: 6gnc
TitleCrystal structure of a Ferredoxin-Flavin Thioredoxin Reductase from Clostridium acetobutylicum at 1.64 A resolution
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Flavoprotein / thioredoxin reductase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / 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 / DI(HYDROXYETHYL)ETHER / Thioredoxin reductase
Similarity search - Component
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.639 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 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0234
Polymers32,0251
Non-polymers9983
Water4,540252
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0468
Polymers64,0502
Non-polymers1,9966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area6930 Å2
ΔGint-27 kcal/mol
Surface area24180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.805, 175.784, 67.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Thioredoxin reductase


Mass: 32025.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Gene: trxB, CA_C1548 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97IU2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium chloride, 0.1 M HEPES pH 7.5, 28% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.639→53.34 Å / Num. obs: 58960 / % possible obs: 99.87 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.03511 / Rrim(I) all: 0.03656 / Net I/σ(I): 34.62
Reflection shellResolution: 1.639→1.698 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.9636 / Mean I/σ(I) obs: 2.95 / Num. unique obs: 5784 / CC1/2: 0.943 / Rrim(I) all: 1.002 / % possible all: 99.52

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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: 6GNA

6gna


Resolution: 1.639→53.34 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.82
RfactorNum. reflection% reflection
Rfree0.2056 2889 4.91 %
Rwork0.182 --
obs0.1832 58903 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.639→53.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 67 252 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092232
X-RAY DIFFRACTIONf_angle_d1.3633019
X-RAY DIFFRACTIONf_dihedral_angle_d18.6371321
X-RAY DIFFRACTIONf_chiral_restr0.061344
X-RAY DIFFRACTIONf_plane_restr0.007376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.639-1.66590.33241290.24892613X-RAY DIFFRACTION100
1.6659-1.69460.25021270.24042631X-RAY DIFFRACTION99
1.6946-1.72540.22311430.23092606X-RAY DIFFRACTION99
1.7254-1.75860.20211200.22412667X-RAY DIFFRACTION100
1.7586-1.79450.25641290.2352614X-RAY DIFFRACTION100
1.7945-1.83350.2571300.23412625X-RAY DIFFRACTION100
1.8335-1.87620.2711280.22642685X-RAY DIFFRACTION100
1.8762-1.92310.23941260.21822654X-RAY DIFFRACTION100
1.9231-1.97510.26491290.21832654X-RAY DIFFRACTION100
1.9751-2.03320.2511330.21472654X-RAY DIFFRACTION100
2.0332-2.09890.21961550.20322646X-RAY DIFFRACTION100
2.0989-2.17390.20841490.20352633X-RAY DIFFRACTION100
2.1739-2.26090.2151340.19782667X-RAY DIFFRACTION100
2.2609-2.36380.22011450.18652649X-RAY DIFFRACTION100
2.3638-2.48840.23151470.19292665X-RAY DIFFRACTION100
2.4884-2.64430.21061280.18882676X-RAY DIFFRACTION100
2.6443-2.84850.22461410.18852691X-RAY DIFFRACTION100
2.8485-3.13510.22411420.19532692X-RAY DIFFRACTION100
3.1351-3.58870.18841690.18032681X-RAY DIFFRACTION100
3.5887-4.5210.17161460.14062734X-RAY DIFFRACTION100
4.521-53.36780.19541390.17262861X-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)
12.0876-0.0753-0.53311.30520.11112.38670.06280.6020.184-0.0572-0.03890.2425-0.1661-0.30610.03310.19660.0488-0.0360.37790.08080.32035.782849.128312.379
20.9581-0.9362-0.19850.97940.06570.7816-0.2891-0.2538-0.37631.3423-0.11660.43020.2785-0.0502-0.52411.25440.00540.1410.251-0.030.1679-1.435774.094515.7829
31.7229-0.8492-0.01670.87070.48392.43960.02290.01270.00160.1330.04960.1980.0503-0.034100.23460.01260.0250.30020.03720.35510.880945.98123.8964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 225 )
3X-RAY DIFFRACTION3chain 'A' and (resid 226 through 290 )

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