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- PDB-6xtf: Crystal structure a Thioredoxin Reductase from Gloeobacter violac... -

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Basic information

Entry
Database: PDB / ID: 6xtf
TitleCrystal structure a Thioredoxin Reductase from Gloeobacter violaceus bound to its electron donor
Components
  • Ferredoxin
  • Thioredoxin reductase
KeywordsFLAVOPROTEIN / Ferredoxin / Thioredoxin reductase / Deeply-rooted Thioredoxin redcutase (DTR) / Ferredoxin-dependent Flavin Thioredoxin Reductase (FFTR)
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain ...: / Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Ferredoxin / Thioredoxin reductase
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsBuey, R.M. / Gonzalez-Holgado, G. / Fernandez-Justel, D. / Balsera, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2016-80343-P Spain
CitationJournal: Plant Physiol. / Year: 2021
Title: Unexpected diversity of ferredoxin-dependent thioredoxin reductases in cyanobacteria.
Authors: Buey, R.M. / Fernandez-Justel, D. / Gonzalez-Holgado, G. / Martinez-Julvez, M. / Gonzalez-Lopez, A. / Velazquez-Campoy, A. / Medina, M. / Buchanan, B.B. / Balsera, M.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase
B: Thioredoxin reductase
C: Ferredoxin
D: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,29437
Polymers90,4624
Non-polymers4,83233
Water4,612256
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13440 Å2
ΔGint-6 kcal/mol
Surface area35760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.741, 181.312, 80.369
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-245-

HOH

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Thioredoxin reductase


Mass: 34502.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Gene: glr0719 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NMP6
#2: Protein Ferredoxin


Mass: 10728.890 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Gene: petF / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NFA3

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Non-polymers , 7 types, 289 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 40% PEG-300 100 mM Sodium cacodylate-HCl, pH 6.5 200 mM Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 2.23→83.4 Å / Num. obs: 40062 / % possible obs: 92.7 % / Redundancy: 13.1 % / Biso Wilson estimate: 27.98 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.298 / Rpim(I) all: 0.085 / Rrim(I) all: 0.31 / Net I/σ(I): 9.3
Reflection shellResolution: 2.23→2.47 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.673 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2004 / CC1/2: 0.584 / Rpim(I) all: 0.549 / Rrim(I) all: 1.763 / % possible all: 64.5

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Processing

Software
NameVersionClassification
PHENIXdev_3689refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J60

5j60


Resolution: 2.23→83.37 Å / SU ML: 0.2306 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2315 2035 5.08 %
Rwork0.2005 38019 -
obs0.2021 40054 66.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.21 Å2
Refinement stepCycle: LAST / Resolution: 2.23→83.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6156 0 308 256 6720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00686589
X-RAY DIFFRACTIONf_angle_d1.17288907
X-RAY DIFFRACTIONf_chiral_restr0.0653986
X-RAY DIFFRACTIONf_plane_restr0.00671138
X-RAY DIFFRACTIONf_dihedral_angle_d19.05582344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.280.424470.2992124X-RAY DIFFRACTION3.36
2.28-2.340.2507260.2692327X-RAY DIFFRACTION9.02
2.34-2.40.3334350.2597595X-RAY DIFFRACTION16.02
2.4-2.470.2718370.2883874X-RAY DIFFRACTION23.2
2.47-2.550.313840.2661449X-RAY DIFFRACTION38.88
2.55-2.640.2967860.25941977X-RAY DIFFRACTION52.4
2.64-2.750.26931240.23852562X-RAY DIFFRACTION67.73
2.75-2.870.30751970.24453359X-RAY DIFFRACTION89.37
2.87-3.020.25822100.24193745X-RAY DIFFRACTION99.87
3.02-3.210.28042120.22713766X-RAY DIFFRACTION99.97
3.21-3.460.23541840.20073785X-RAY DIFFRACTION99.97
3.46-3.810.21342090.17793810X-RAY DIFFRACTION99.95
3.81-4.360.18522010.15093801X-RAY DIFFRACTION100
4.36-5.490.18942110.15553851X-RAY DIFFRACTION99.98
5.49-83.370.22012120.22243994X-RAY DIFFRACTION99.72
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)
10.109208445551-0.0003181621973570.1333871358440.3239202007280.07367140643410.139666203431-0.05309682777840.03937967110060.3599851101810.06678306742220.02794143038580.00628112246846-0.1214418429280.05330740174220.1333026204970.157673989483-0.009265612488620.01206149119350.165870808180.05151597073380.210016955121-14.2266673208-7.044492955255.10952508199
20.103708992370.03356437513450.01045419913510.2586795439660.1800799373890.1135896577960.130649452484-0.40511244697-0.06654208656890.62958706464-0.06440316690430.008763438433560.4308145867570.0129724973650.01494653025850.306612887539-0.056693881489-0.009217812182750.3202895167730.02848424168190.253736410417-17.1068659454-12.149640352114.3177790734
30.033435593103-0.1174059113070.05146225042140.41377024592-0.1972961660610.0978035152810.078058657019-0.05468953141210.117297368979-0.2083798780870.121671874432-0.08913646705770.02326626374590.2160929694530.02517494332810.471822159432-0.2950926719910.001563133857230.8451239093190.1396528105670.512843327905-11.733290515-36.4043566264-44.7335909888
40.1658686677720.00102906133264-0.07628654515710.10062000998-0.1236249751440.3734142627340.06531702023450.171318758930.8394542000860.2223419351660.2887719251990.651090197539-0.2943364555510.2751931175980.1292300675490.441224611589-0.0745152330406-0.07873649063070.4181787190640.1367423304510.808638419822-18.206617086-36.693268917-40.9398452864
50.0602777328907-0.1030796335010.08128187835920.343107821345-0.0954182120070.1175120947650.4110880988110.1715139095350.302215920877-0.258537556801-0.09318624396770.320956609881-0.145017307279-0.278951218341-0.004837736786190.2416616724650.02571684385490.06091609334410.4308264816210.0547507511680.297619382593-25.5085111398-46.6707041999-37.5320748837
60.151499094412-0.125809657953-0.09697622026620.1666915113440.03256350717710.1109285094920.3019920798940.318106153326-0.424344251010.0950207841657-0.0774613591799-0.29476401564-0.01330692535740.528087440310.1193895672260.314267851578-0.06409994680980.04340103133690.721573765017-0.02325389026120.374548136789-14.2270659099-50.5191876265-40.1733273072
70.3743271968170.2378774965410.1214000382640.1602841601540.1463020939090.645507032982-0.3084903405840.717518805878-0.156350585365-0.2859349981540.226868808298-0.00329953766822-0.01394933147390.330502748235-0.1539108910050.24687801498-0.1194683975540.02309277867950.612550568108-0.03169190452030.324967933107-14.2032236136-49.4387426412-44.3330988107
81.365321560290.69205965213-0.124506339980.5547690011930.1999046894440.2809695429740.007525795008570.195391970217-0.0784422539082-0.1158784485020.0177199399506-0.02822632913480.024320323508-0.0649859311588-0.04614808990250.1935670031690.0064345379488-0.02070820314660.203617757313-0.006869055224030.171562453135-34.3303775776-26.0690419213-11.8552495595
90.7426944370830.158566677077-0.5253007617080.4387236328370.09744133747680.484252712824-0.04977958885570.337082592922-0.252878330916-0.221424957962-0.0321178710747-0.04425784820790.140813669532-0.200465739297-0.1241313451140.2955260166020.008844382460430.03469950430940.2050054837740.008381461230830.206938843085-14.229271088-17.9376124968-19.3947111105
100.486819345629-0.205078887556-0.02268628863850.930726725727-0.1156847092231.18398504053-0.006245755051390.1700844321920.0971466174288-0.1746151432010.0237637425571-0.00361370988848-0.0558115134929-0.1082353108540.0338797546160.1911590488260.0344570099443-0.02505783743290.08985188744630.02725558826540.118295707992-29.2019918461-15.5808803119-10.8725620901
110.3750448681770.2706729354590.4919875819820.347987240479-0.003557379102140.7978883543410.086071955306-0.01296290201580.2130839875820.0839370910999-0.06980865001840.0242016528392-0.0497980301875-0.1881094365990.1260669016410.222102816588-0.0672905884990.003879313471570.211886713691-0.01226488734180.17790450257-40.0483177611-60.2824630754-21.3195776719
120.2722948643080.0785665943066-0.03007043994140.1093040418860.1665757284160.4229258329370.0847896246006-0.177964923805-0.1906753137250.161690480125-0.0350569748788-0.2866681748160.0663967245939-0.1407142234560.01840459533560.212033745410.00798184873095-0.1039959055080.2225452068590.00367722298430.246791359045-20.0554376202-56.4592321062-15.1176668585
130.137130936178-0.0411626141102-0.0244731724580.156326937153-0.1117595909180.0926533560820.01422366460760.06995637223570.4208055239190.05735941847270.132042210823-0.0538290330239-0.0458705080444-0.1681467795530.0006132832196830.235760399025-0.0386712014711-0.02374328402630.301440426827-0.02646184695720.240711476456-22.7689962182-45.1644411213-13.0409945565
140.3530999466460.3264579134390.2928336667220.481827845543-0.01100202603760.771724579122-0.0262417151725-0.0186672407933-0.009416670761060.2373313044640.0397155775127-0.271059876591-0.01680007053950.1779036259610.3833495277890.1868008835560.00507892369153-0.03381092315680.275475073994-0.0662350805560.267786065038-13.6151879121-42.5902779601-18.8605491936
150.3530721963490.2919575962370.07145884145750.4099525340760.1119156587820.05807726004520.1224496044870.0174673371479-0.2372980901920.145377711268-0.00264255979425-0.2365558605750.1482653804730.0813737907736-0.01851925313360.225572278382-0.00842509186108-0.03185032026210.218594129911-0.006344737219530.249178533972-33.152298935-68.2215259156-26.3025906936
160.46266202531-0.314866223285-0.1597682237990.8851869296780.9228028139291.584430343270.3084521391270.292745239442-0.2462786594040.2943603906580.27129896448-0.3785153019720.3530058496260.02022597358290.7009636353630.2812296711060.00183488295015-0.1206972827280.341930840890.05988262283310.379815114316-2.14893765659-13.844659132912.5997846898
170.1349070068960.2234512453190.2727255573991.022875425150.5090561010180.5419034952710.08927103660620.310326823402-0.4884942525570.02303337330690.219393859802-0.5321979728020.08970803692060.2723485788320.2099209800180.242245596240.0717847503532-0.1010114475060.2870358027860.01354864704270.357279094058-5.0704112174-18.73018285215.56639316759
180.08652173170920.198294604892-0.2523419320960.446196983153-0.5821366888740.776085147190.3042590378090.0320813898473-0.4977338878560.446041267151-0.02165273844860.0588974101749-0.4038729921930.1896618619010.09092954890390.1465528805590.0911848147086-0.1138316682130.260485572802-0.03172312092010.21317854423-17.7136275682-18.77380854324.1154412055
190.0926148711080.2318379609150.1198702013640.580525058840.2927060487040.146851948008-0.025006230656-0.0294968418290.04993604886020.06764181745170.03285832416770.13772867905-0.398263786810.0949029571235-0.1028026471910.325137844738-0.132833858121-0.07314138773150.1510316956840.04289529096380.223402965794-12.1143086137-7.5538405191813.682733173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 55 through 85 )
2X-RAY DIFFRACTION2chain 'C' and (resid 86 through 97 )
3X-RAY DIFFRACTION3chain 'D' and (resid 2 through 10 )
4X-RAY DIFFRACTION4chain 'D' and (resid 11 through 36 )
5X-RAY DIFFRACTION5chain 'D' and (resid 37 through 41 )
6X-RAY DIFFRACTION6chain 'D' and (resid 42 through 66 )
7X-RAY DIFFRACTION7chain 'D' and (resid 67 through 97 )
8X-RAY DIFFRACTION8chain 'A' and (resid 3 through 125 )
9X-RAY DIFFRACTION9chain 'A' and (resid 126 through 186 )
10X-RAY DIFFRACTION10chain 'A' and (resid 187 through 317 )
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 105 )
12X-RAY DIFFRACTION12chain 'B' and (resid 106 through 154 )
13X-RAY DIFFRACTION13chain 'B' and (resid 155 through 175 )
14X-RAY DIFFRACTION14chain 'B' and (resid 176 through 226 )
15X-RAY DIFFRACTION15chain 'B' and (resid 227 through 317 )
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 20 )
17X-RAY DIFFRACTION17chain 'C' and (resid 21 through 36 )
18X-RAY DIFFRACTION18chain 'C' and (resid 37 through 48 )
19X-RAY DIFFRACTION19chain 'C' and (resid 49 through 54 )

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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