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- PDB-6kum: Ferredoxin I from C. reinhardtii, low X-ray dose -

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Basic information

Entry
Database: PDB / ID: 6kum
TitleFerredoxin I from C. reinhardtii, low X-ray dose
ComponentsFerredoxin, chloroplastic
KeywordsELECTRON TRANSPORT / [2Fe2S] cluster
Function / homology
Function and homology information


iron-sulfur cluster binding / chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin, chloroplast transit peptide / Ferredoxin chloroplastic transit peptide / 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 / 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
Similarity search - Domain/homology
BENZAMIDINE / FE2/S2 (INORGANIC) CLUSTER / THIOCYANATE ION / Ferredoxin, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOnishi, Y. / Kurisu, G. / Tanaka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: J.Biochem. / Year: 2020
Title: X-ray dose-dependent structural changes of the [2Fe-2S] ferredoxin from Chlamydomonas reinhardtii.
Authors: Ohnishi, Y. / Muraki, N. / Kiyota, D. / Okumura, H. / Baba, S. / Kawano, Y. / Kumasaka, T. / Tanaka, H. / Kurisu, G.
History
DepositionSep 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ferredoxin, chloroplastic
B: Ferredoxin, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,83411
Polymers19,9702
Non-polymers8649
Water3,531196
1
A: Ferredoxin, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4014
Polymers9,9851
Non-polymers4163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-17 kcal/mol
Surface area4700 Å2
MethodPISA
2
B: Ferredoxin, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4337
Polymers9,9851
Non-polymers4486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-16 kcal/mol
Surface area4770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.878, 32.326, 49.915
Angle α, β, γ (deg.)72.380, 78.060, 72.390
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ferredoxin, chloroplastic


Mass: 9984.993 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PETF / Production host: Escherichia coli (E. coli) / References: UniProt: P07839

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Non-polymers , 6 types, 205 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.88 Å3/Da / Density % sol: 34.72 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 5.6
Details: Ammonium Sulfate, Sodium Citrate, Benzamidine Hydrochloride, Sodium Thiocyanate
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→28.74 Å / Num. obs: 54418 / % possible obs: 95.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 8.45 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.064 / Rrim(I) all: 0.126 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.423.80.302510813280.9170.1770.353.893
7.67-28.743.60.1136111700.9660.0680.13211.796.6

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→28.74 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0.19 / Phase error: 18.95
RfactorNum. reflection% reflection
Rfree0.1897 2688 4.94 %
Rwork0.1713 --
obs0.1722 54418 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 44.16 Å2 / Biso mean: 13.8497 Å2 / Biso min: 3.59 Å2
Refinement stepCycle: final / Resolution: 1.4→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 41 205 1597
Biso mean--14.59 24.36 -
Num. residues----189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111531
X-RAY DIFFRACTIONf_angle_d1.4352102
X-RAY DIFFRACTIONf_chiral_restr0.092238
X-RAY DIFFRACTIONf_plane_restr0.008290
X-RAY DIFFRACTIONf_dihedral_angle_d9.151906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.42550.18071450.2016265592
1.4255-1.45290.23051410.2134265793
1.4529-1.48250.23451430.195260292
1.4825-1.51480.21641380.1971276194
1.5148-1.550.23961590.1887259993
1.55-1.58880.23361770.1879266793
1.5888-1.63170.22731350.1925274894
1.6317-1.67970.2221320.1856269794
1.6797-1.73390.18471060.1714275294
1.7339-1.79590.21511350.172272295
1.7959-1.86780.2161490.1746271595
1.8678-1.95280.17251110.162274795
1.9528-2.05570.19741320.1688279195
2.0557-2.18450.19321420.1753274396
2.1845-2.35310.20691430.1674278197
2.3531-2.58970.1871360.1687277497
2.5897-2.96410.18361600.1636275797
2.9641-3.73320.14571350.1564281097
3.7332-28.740.15841690.1586275297
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)
15.9232.17622.65823.48042.12424.92640.1213-0.241-0.17310.03050.07340.07240.0874-0.2306-0.20490.0562-0.01430.01620.05910.0030.0661-4.107-14.722-9.835
22.11781.1518-1.15961.9603-0.12961.3677-0.19940.19040.0496-0.37720.13690.2930.1072-0.0886-0.0280.1465-0.0221-0.04520.06590.00050.1248-5.306-17.606-14.029
33.0910.41230.82322.66921.58014.321-0.01780.088-0.2162-0.16430.0713-0.2610.34830.3044-0.04440.11310.00540.01160.05450.00130.08334.944-14.72-14.924
42.64030.7519-1.78480.8418-0.68634.16980.11280.02070.2084-0.15560.0683-0.0117-0.11650.2399-0.16190.1167-0.0110.01010.0621-0.00920.05872.515-5.585-20.451
50.81290.2820.07113.8133-0.54242.1483-0.0069-0.0040.2032-0.0501-0.0126-0.0286-0.22330.11380.02320.0777-0.0132-0.00930.0584-0.00220.07821.2310.831-13.765
64.15031.14620.29862.85380.54772.8968-0.08490.00710.0751-0.03460.03370.0370.09610.0018-0.00730.0477-0.0047-0.00030.0435-0.00990.0485-2.238-9.183-9.023
75.16750.11570.86692.55740.16712.9786-0.01350.27040.2402-0.15020.07430.1906-0.2314-0.1463-0.06510.12560.01550.00340.06150.02120.057-6.383-4.2-22.402
83.35920.72470.74632.04940.9024.80910.1047-0.3334-0.25910.40950.0997-0.39370.2130.3178-0.18920.16760.0115-0.05840.12070.00170.128610.2-22.776-36.053
90.99590.02940.09590.04980.2222.7166-0.1415-0.2081-0.06930.61660.02150.47320.2814-0.12910.00470.26210.01580.02690.08630.01470.07741.076-19.806-34.166
103.0743-1.1679-1.8731.48141.27952.35150.0877-0.00270.13470.0977-0.0532-0.011-0.1714-0.0448-0.04550.14120.0032-0.010.04930.00480.05433.869-9.257-35
111.07310.08510.67717.73131.33522.8118-0.0540.13180.1561-0.0696-0.04640.2182-0.2867-0.02030.1030.0997-0.0122-0.01090.08010.0110.06965.092-6.712-45.022
121.6749-0.1014-0.29221.7937-0.02631.44660.0031-0.07210.16470.20130.0022-0.1054-0.2260.216-0.01120.1201-0.0263-0.01280.07510.00010.06548.453-11.82-38.429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:7 )A0 - 7
2X-RAY DIFFRACTION2( CHAIN A AND RESID 8:16 )A8 - 16
3X-RAY DIFFRACTION3( CHAIN A AND RESID 17:33 )A17 - 33
4X-RAY DIFFRACTION4( CHAIN A AND RESID 34:51 )A34 - 51
5X-RAY DIFFRACTION5( CHAIN A AND RESID 52:76 )A52 - 76
6X-RAY DIFFRACTION6( CHAIN A AND RESID 77:86 )A77 - 86
7X-RAY DIFFRACTION7( CHAIN A AND RESID 87:93 )A87 - 93
8X-RAY DIFFRACTION8( CHAIN B AND RESID 0:16 )B0 - 16
9X-RAY DIFFRACTION9( CHAIN B AND RESID 17:33 )B17 - 33
10X-RAY DIFFRACTION10( CHAIN B AND RESID 34:51 )B34 - 51
11X-RAY DIFFRACTION11( CHAIN B AND RESID 52:70 )B52 - 70
12X-RAY DIFFRACTION12( CHAIN B AND RESID 71:94 )B71 - 94

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