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- PDB-6kv0: Ferredoxin I from C. reinhardtii, high X-ray dose -

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Basic information

Entry
Database: PDB / ID: 6kv0
TitleFerredoxin I from C. reinhardtii, high X-ray dose
ComponentsFerredoxin, chloroplastic
KeywordsELECTRON TRANSPORT / [2Fe2S] cluster
Function / homology
Function and homology information


iron-sulfur cluster binding / chloroplast / 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 3, 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)20,79910
Polymers19,9702
Non-polymers8298
Water3,585199
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 area4710 Å2
MethodPISA
2
B: Ferredoxin, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3976
Polymers9,9851
Non-polymers4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-17 kcal/mol
Surface area4790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.820, 32.300, 49.930
Angle α, β, γ (deg.)72.270, 78.090, 72.220
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, 207 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur 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 / Benzamidine


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


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


Mass: 35.453 Da / Num. of mol.: 1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 34.45 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5.6
Details: Ammonium sulfate Sodium citrate Sodium thiocyanate Benzamidine Hydrochloride
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: RAYONIX MX225HE / 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→29.71 Å / Num. obs: 54425 / % possible obs: 95.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 9.3 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.059 / Rrim(I) all: 0.117 / Net I/σ(I): 8.1
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
1.4-1.423.90.439534813680.8610.2560.5082.892.9
7.54-29.713.70.0666791850.9930.0390.07714.497.9

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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→28.718 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.22 / Phase error: 19.96
RfactorNum. reflection% reflection
Rfree0.1874 2708 4.98 %
Rwork0.1751 --
obs0.1757 54425 95.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.1 Å2 / Biso mean: 15.2566 Å2 / Biso min: 5.71 Å2
Refinement stepCycle: final / Resolution: 1.4→28.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 40 205 1605
Biso mean--15.73 26.25 -
Num. residues----189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081507
X-RAY DIFFRACTIONf_angle_d1.2342062
X-RAY DIFFRACTIONf_chiral_restr0.082236
X-RAY DIFFRACTIONf_plane_restr0.007279
X-RAY DIFFRACTIONf_dihedral_angle_d6.809923
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.42550.26331270.2471268493
1.4255-1.45290.25281490.2507262493
1.4529-1.48260.19731340.2352264193
1.4826-1.51480.24381500.2201273494
1.5148-1.550.22761640.2121257894
1.55-1.58880.23121380.2046271194
1.5888-1.63170.22271280.1997275795
1.6317-1.67980.21871440.1963266394
1.6798-1.7340.20371480.1815274095
1.734-1.79590.24761260.1809271195
1.7959-1.86780.20311270.1749273095
1.8678-1.95280.1911260.1666277296
1.9528-2.05570.17421400.1711276596
2.0557-2.18450.22981600.168273396
2.1845-2.35310.16581680.1623275297
2.3531-2.58980.19361520.1718275097
2.5898-2.96420.17031240.1692280297
2.9642-3.73330.1491810.1547276798
3.7333-28.7180.14221220.1501280397
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)
16.40221.52744.30263.04791.20828.87250.0481-0.3141-0.10720.09630.03230.15060.0919-0.0846-0.10810.0641-0.01580.0250.0846-0.00280.075-4.057-14.692-9.818
22.00110.7751-1.80411.91620.11082.2945-0.23470.24820.0162-0.41990.10640.28360.1606-0.19870.05520.1715-0.0383-0.04570.0943-0.00710.1302-5.519-17.872-14.406
34.32060.25180.96213.44740.35846.0740.02680.1432-0.178-0.1231-0.0158-0.16880.36170.3771-0.04480.09230.00860.0160.0812-0.00460.07694.338-14.769-15.058
43.51911.1753-1.47591.5067-0.56664.33860.08780.02610.2091-0.11980.092-0.0124-0.08730.2059-0.17060.1028-0.0040.00790.059-0.01180.06231.095-5.115-19.7
50.5088-0.4880.19024.4648-0.43482.26940.0045-0.00740.1537-0.0535-0.0276-0.0553-0.18070.130.01960.0734-0.021-0.00030.0844-0.01030.08031.5220.837-13.646
63.26591.44370.05682.8590.30273.7666-0.0215-0.04320.04410.06330.0769-0.02590.052-0.0469-0.00730.0606-0.00530.01030.0801-0.01770.0633-1.331-9.265-8.172
74.35451.6657-0.86691.36841.17773.84230.13830.32210.3258-0.1849-0.02710.1183-0.2725-0.1959-0.03660.12820.01990.00330.08680.02470.0981-6.34-4.178-22.39
84.22221.61182.01722.42121.52915.38590.1261-0.2009-0.24280.37790.1086-0.43860.21590.3793-0.26060.16950.0141-0.05720.1264-0.00810.131710.238-22.838-36.119
93.11810.8069-0.00371.18880.07154.8654-0.058-0.2335-0.02460.4245-0.02340.26620.2757-0.14180.06450.18220.01370.01790.09010.00280.08171.062-19.829-34.174
103.5056-1.0799-2.10181.27311.22593.31190.05530.00660.12210.047-0.0224-0.0225-0.1789-0.0374-0.05580.1341-0.0006-0.0030.0673-0.00260.063.874-9.267-34.993
110.91780.7351.17576.85821.09372.6637-0.09890.07670.1843-0.0909-0.02960.292-0.2732-0.0460.13770.11-0.012-0.00770.09790.00440.08834.657-6.886-45.147
122.442-0.3876-0.08931.8001-0.1011.9203-0.003-0.03860.16610.1641-0.0138-0.1593-0.20230.20530.01510.1122-0.0264-0.00230.09380.00530.06698.236-11.963-38.603
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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