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- PDB-6gnd: Crystal structure of the complex of a Ferredoxin-Flavin Thioredox... -

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Basic information

Entry
Database: PDB / ID: 6gnd
TitleCrystal structure of the complex of a Ferredoxin-Flavin Thioredoxin Reductase and a Thioredoxin from Clostridium acetobutylicum at 2.9 A resolution
Components
  • Thioredoxin
  • Thioredoxin reductase
KeywordsOXIDOREDUCTASE / Flavoprotein / thioredoxin reductase / thioredoxin
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / cell redox homeostasis / nucleotide binding / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Thioredoxin / Thioredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin / Thioredoxin reductase
Similarity search - Component
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.889 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
B: Thioredoxin
C: Thioredoxin reductase
D: Thioredoxin
E: Thioredoxin reductase
F: Thioredoxin
G: Thioredoxin reductase
H: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,41814
Polymers174,1528
Non-polymers3,2666
Water1,20767
1
A: Thioredoxin reductase
B: Thioredoxin
G: Thioredoxin reductase
H: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7097
Polymers87,0764
Non-polymers1,6333
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-64 kcal/mol
Surface area32540 Å2
MethodPISA
2
C: Thioredoxin reductase
D: Thioredoxin
hetero molecules

E: Thioredoxin reductase
F: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7097
Polymers87,0764
Non-polymers1,6333
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
Buried area8300 Å2
ΔGint-68 kcal/mol
Surface area32270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.230, 174.350, 114.304
Angle α, β, γ (deg.)90.00, 119.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thioredoxin reductase


Mass: 31691.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CYS131 has been replaced by SER. This is a covalent complex formed through a disulfide complex between CYS134 of FFTR and CYS30 of Trx.
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Gene: CA_C3082 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97EM8
#2: Protein
Thioredoxin


Mass: 11846.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CYS33 has been replaced by SER. This is a covalent complex formed through a disulfide complex between CYS134 of FFTR and CYS30 of Trx.
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Gene: CA_C3083 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97EM7
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.86 Å3/Da / Density % sol: 57 %
Description: Diffraction data has been truncated anisotropically by using the STARANISO software, as implemented in the autoPROC software package. The deposited structure factors are the ...Description: Diffraction data has been truncated anisotropically by using the STARANISO software, as implemented in the autoPROC software package. The deposited structure factors are the anisotropically-truncated date concatenated to the isotropically-truncated data.
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.02 M DL-glutamic acid monohydrate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine monohydrochloride, 0.02 M DL-serine, 0.1M imidazole/MES monohydrate pH 6.5, 20 % (v/v) ethylene glycol, 10% (w/v) PEG 8000

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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: 2.889→86.742 Å / Num. obs: 27743 / % possible obs: 92.7 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.076 / Net I/σ(I): 14.1
Reflection shellResolution: 2.889→3.178 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.058 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1371 / CC1/2: 0.609 / Rrim(I) all: 1.253 / % possible all: 75

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Processing

Software
NameVersionClassification
PHENIX(dev_3026: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GNA

6gna


Resolution: 2.889→86.742 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2785 1314 4.74 %
Rwork0.2353 --
obs0.2373 27732 63.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.889→86.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10367 0 220 68 10655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410861
X-RAY DIFFRACTIONf_angle_d0.66414839
X-RAY DIFFRACTIONf_dihedral_angle_d12.9336354
X-RAY DIFFRACTIONf_chiral_restr0.051723
X-RAY DIFFRACTIONf_plane_restr0.0051893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8888-3.00440.5902150.5532296X-RAY DIFFRACTION6
3.0044-3.14120.4341390.4163727X-RAY DIFFRACTION16
3.1412-3.30680.3392740.36131488X-RAY DIFFRACTION32
3.3068-3.5140.32221230.31582199X-RAY DIFFRACTION48
3.514-3.78530.33221770.28043446X-RAY DIFFRACTION74
3.7853-4.16620.26412420.24214277X-RAY DIFFRACTION93
4.1662-4.7690.23452300.20334627X-RAY DIFFRACTION100
4.769-6.00830.26952440.2294634X-RAY DIFFRACTION100
6.0083-86.78150.29191700.22064724X-RAY DIFFRACTION99
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)
12.11480.17470.20423.93750.54652.5570.30380.62490.0396-0.6277-0.0183-1.3431-0.14930.83930.10640.4024-0.17710.1710.3782-0.13020.3703124.241541.15240.4978
20.15020.39110.61820.97791.61212.5190.4497-0.5903-0.1678-0.2036-0.2637-0.55330.0349-1.00570.07310.7814-0.1053-0.01550.5015-0.05440.5609112.405622.102633.2862
32.7669-0.5887-0.20072.38941.4282.61520.06120.34-0.335-0.0773-0.14890.1027-0.0187-0.19250.14620.6095-0.1005-0.21660.3033-0.07030.4337107.836120.673817.7429
42.67341.255-1.73733.78391.03752.20480.27990.0788-0.1195-0.313-0.00930.61930.4367-0.29680.12460.5195-0.1015-0.18930.1445-0.03390.1883113.689435.130946.9949
51.0398-0.20150.390.14480.23411.0518-0.1655-0.3358-0.2047-0.0384-0.3499-0.68890.92780.3079-0.04871.917-0.2423-0.7460.77930.31431.3512109.7754-7.917843.4912
64.4351-1.30231.86430.7041-1.12823.08610.9113-0.4593-1.21520.0394-0.33470.18810.4666-0.43311.57841.6476-0.0925-0.69520.5015-0.0010.8492114.20074.494640.6499
74.3028-0.60412.1580.12360.05574.28640.54490.3695-1.73840.97930.3153-0.6416-0.10570.06530.53441.2249-0.1272-0.26740.80060.12240.7985119.763410.466845.728
80.28020.1375-0.17960.1970.68695.19211.333-0.67840.64350.96360.9904-0.86450.234-0.48350.30771.3986-0.38040.030.82920.03590.79113.8692.849549.7747
91.05370.37420.4420.9652-0.76351.20480.10230.1725-0.8815-0.14960.04350.4741.6492-0.41360.31641.6401-0.4044-0.16280.6582-0.21490.9104111.07282.746733.017
101.331-0.2678-3.3912.59041.21678.75620.42350.5539-0.1090.12480.410.54770.7947-3.21220.20780.9174-0.1509-0.21611.02360.34810.7035107.739210.191742.7625
110.05170.26750.59671.36623.05956.8459-0.7573-0.2225-0.19280.408-0.47611.37840.0776-2.2478-0.79830.37880.0485-0.01111.04530.13271.2021107.71512.960952.2573
120.8439-0.94330.12092.6066-0.70771.217-0.2141-0.6427-0.56510.6250.07190.3556-0.0683-0.635-0.07150.3351-0.1047-0.09840.58360.20280.4004150.73119.490133.6369
133.0586-0.6554-0.85492.20240.85460.7306-0.2208-0.4237-0.8190.04050.21080.32570.667-0.12980.15490.3583-0.2216-0.14180.35080.11620.7373146.4325-2.867324.594
141.3387-0.978-0.30624.3041-0.01063.1684-0.5739-0.44320.13750.4960.06120.6126-0.1665-0.6593-0.66280.35040.1582-0.13580.58810.26730.6424144.176810.055929.6878
151.3758-0.91710.37150.9605-0.05230.304-0.3435-0.00880.23310.2975-0.203-0.1445-0.35410.335-0.99630.553-0.0949-0.80070.42830.36940.5887145.744524.163314.042
163.684-1.41960.82132.83510.8852.02890.2143-0.0002-0.3785-0.1122-0.3048-0.5568-0.63190.1099-0.03770.5521-0.0622-0.29760.33090.25570.3833134.925724.75733.0481
178.7361-4.70041.8424.70070.31681.1842-0.30572.1698-0.128-0.7876-0.2665-0.1684-0.63180.8915-0.40850.4667-0.3243-0.17390.85760.1790.5433157.580215.932316.2349
181.9165-0.7784-0.48130.75380.00751.2985-0.2191-0.16120.20050.06660.0483-0.3531-0.39380.57660.02770.2069-0.1732-0.24590.55260.31520.6054158.65478.118424.8096
191.1491-0.4538-1.80270.17930.71592.84560.1591-0.33070.2830.0175-0.1617-0.2382-1.50190.56341.16561.5116-0.2806-0.82090.94680.19091.0811152.815741.472421.6898
201.81020.70261.51371.97722.54063.865-0.30310.6670.50640.18590.2543-0.4214-2.23870.44080.12231.3345-0.1787-0.37390.72330.4131.1593151.828743.441816.9224
211.37210.80750.27343.3357-1.06940.58620.02561.52230.1623-1.1349-0.6793-0.37640.34541.1468-0.26590.7636-0.3274-0.01790.92370.21080.9973160.230436.221215.6146
225.41630.326-0.35211.45930.08172.8575-0.65140.5753-1.21480.15880.38140.26260.84150.0323-0.06490.38160.01920.15230.59920.17170.5161112.4673.633524.5455
233.715-0.38461.04650.4402-0.07720.9281-0.13990.3778-0.1929-0.17120.308-0.27470.10270.52610.07950.006-0.30120.25580.98350.10660.427129.192578.183129.8416
240.9190.0651-1.76952.204-2.57946.1853-0.751.20250.1476-1.7350.6643-0.42611.34970.80960.2580.9783-0.39910.35471.72760.03971.5314141.016677.79187.8653
252.0140.31550.11391.47180.3990.1074-0.53360.2669-0.125-0.44510.4540.1890.2725-0.1188-3.92830.6446-0.28440.41461.22230.3751.026141.893482.32372.5539
260.1186-0.39210.01931.78610.34470.38070.037-0.34340.23630.3970.0587-0.6451-0.13940.3411-0.5820.2209-0.11810.28831.2027-0.00211.0368144.363581.028315.3462
276.12454.69236.54934.01554.93877.0188-1.02110.25432.6111-0.8525-0.47110.2898-1.37070.511-1.74910.764-0.34730.14821.2353-0.08691.6514134.20891.16518.3536
283.55751.2869-1.13310.5144-0.13372.02350.17780.04831.3368-0.02460.0015-0.0766-0.7836-0.7853-0.1280.59930.19880.10370.35180.00620.352102.897661.553153.1528
290.9447-0.7691-1.26130.83530.56162.70630.2017-0.12790.303-0.0394-0.1528-1.1145-0.91830.523-0.02550.4263-0.1844-0.08090.37860.06970.6724118.670759.098453.5385
303.51511.09721.23921.8941-1.38272.9502-0.29480.15941.35970.42490.1069-0.2667-1.6524-0.0309-0.14311.044-0.04790.11390.35010.18470.8004113.919665.849653.0774
312.67160.5330.83970.3806-0.52563.88230.0392-0.14310.97340.48880.24070.1745-1.4068-0.5554-0.07930.75280.3580.10640.64470.01120.3261100.034159.110765.4176
321.31920.3058-0.22952.02030.021.1944-0.3320.4287-0.32720.2956-0.03530.00030.0991-0.83171.27971.46280.29040.0220.6329-0.27390.408998.924254.170183.6362
330.524-0.0442-0.18520.08740.33581.59650.0614-0.31220.09280.24770.00070.03290.01790.03330.51552.01040.13490.35370.516-0.04570.1592106.69261.290.3103
343.585-0.3377-2.37644.57860.54043.2121-0.5023-0.585-0.43840.74140.3050.56440.0014-0.5213-0.14220.30970.1287-0.14490.31950.04320.3319105.219449.33959.019
353.52920.5512.46930.32780.04672.18020.1963-1.0172-0.54051.264-0.50510.70661.3956-0.92080.04051.3797-0.10420.70260.7426-0.10111.326880.787555.421578.5505
365.3392.15183.72632.1806-0.48825.61011.06880.2375-0.46731.70410.166-1.18281.326-0.02942.27051.1870.05320.25320.29240.00530.638187.513946.896375.6563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 142 )
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 217 )
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 283 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 15 )
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 30 )
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 46 )
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 57 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 74 )
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 93 )
11X-RAY DIFFRACTION11chain 'B' and (resid 94 through 105 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 25 )
13X-RAY DIFFRACTION13chain 'C' and (resid 26 through 57 )
14X-RAY DIFFRACTION14chain 'C' and (resid 58 through 98 )
15X-RAY DIFFRACTION15chain 'C' and (resid 99 through 142 )
16X-RAY DIFFRACTION16chain 'C' and (resid 143 through 222 )
17X-RAY DIFFRACTION17chain 'C' and (resid 223 through 241 )
18X-RAY DIFFRACTION18chain 'C' and (resid 242 through 281 )
19X-RAY DIFFRACTION19chain 'D' and (resid 7 through 46 )
20X-RAY DIFFRACTION20chain 'D' and (resid 47 through 74 )
21X-RAY DIFFRACTION21chain 'D' and (resid 75 through 105 )
22X-RAY DIFFRACTION22chain 'E' and (resid 2 through 131 )
23X-RAY DIFFRACTION23chain 'E' and (resid 132 through 283 )
24X-RAY DIFFRACTION24chain 'F' and (resid 7 through 47 )
25X-RAY DIFFRACTION25chain 'F' and (resid 48 through 57 )
26X-RAY DIFFRACTION26chain 'F' and (resid 58 through 93 )
27X-RAY DIFFRACTION27chain 'F' and (resid 94 through 105 )
28X-RAY DIFFRACTION28chain 'G' and (resid 0 through 24 )
29X-RAY DIFFRACTION29chain 'G' and (resid 25 through 57 )
30X-RAY DIFFRACTION30chain 'G' and (resid 58 through 82 )
31X-RAY DIFFRACTION31chain 'G' and (resid 83 through 117 )
32X-RAY DIFFRACTION32chain 'G' and (resid 118 through 135 )
33X-RAY DIFFRACTION33chain 'G' and (resid 136 through 217 )
34X-RAY DIFFRACTION34chain 'G' and (resid 218 through 284 )
35X-RAY DIFFRACTION35chain 'H' and (resid 8 through 68 )
36X-RAY DIFFRACTION36chain 'H' and (resid 69 through 105 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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