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2n0s

HADDOCK model of ferredoxin and [FeFe] hydrogenase complex

Method: SOLUTION NMR Dmax: 75.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fe-hydrogenase

Chlamydomonas reinhardtii

UniProt Q9FYU1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 58–497 Not recorded Ferredoxin, chloroplastic × 1 （P07839） SF4 IRON/SULFUR CLUSTER × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure AMBIENT NMR sample composition：0.1-0.2 MM [U-100% 15N] PROTEIN_ 1, 1 MM PROTEIN_2, 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2N0S Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3LX4 Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG) Deposited 2010-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 57–497（441 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions capillary batch diffusion；pH 6.5；298 K；25.5% PEG 8000, 0.085 M sodium cacodylate, 0.17 M sodium acetate trihydrate, 1 mM dithionite, pH 6.5, capillary batch diffusion, temperature 298.0K
Resolution 1.97 Å R-free 0.216
3LX4 Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG) Deposited 2010-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 57–497（441 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions capillary batch diffusion；pH 6.5；298 K；25.5% PEG 8000, 0.085 M sodium cacodylate, 0.17 M sodium acetate trihydrate, 1 mM dithionite, pH 6.5, capillary batch diffusion, temperature 298.0K
Resolution 1.97 Å R-free 0.216
4R0V [FeFe]-hydrogenase Oxygen Inactivation is Initiated by the Modification and Degradation of the H cluster 2Fe Subcluster Deposited 2014-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–497（497 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SF4 IRON/SULFUR CLUSTER × 1 CL CHLORIDE ION × 2 ARS ARSENIC × 1 X-RAY DIFFRACTION
X-ray crystallization conditions SMALL TUBES；pH 6.5；298 K；25.5% Polyethylene Glycol 8,000, 0.085 M Sodium Cacodylate, 0.17 M Sodium Acetate Trihydrate, 1mM Sodium Dithionite, pH 6.5, SMALL TUBES, temperature 298K
Resolution 2.29 Å R-free 0.252
4R0V [FeFe]-hydrogenase Oxygen Inactivation is Initiated by the Modification and Degradation of the H cluster 2Fe Subcluster Deposited 2014-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–497（497 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SF4 IRON/SULFUR CLUSTER × 1 CL CHLORIDE ION × 2 ARS ARSENIC × 1 X-RAY DIFFRACTION
X-ray crystallization conditions SMALL TUBES；pH 6.5；298 K；25.5% Polyethylene Glycol 8,000, 0.085 M Sodium Cacodylate, 0.17 M Sodium Acetate Trihydrate, 1mM Sodium Dithionite, pH 6.5, SMALL TUBES, temperature 298K
Resolution 2.29 Å R-free 0.252
6GL6 apo [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii, variant C377H Deposited 2018-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 57–497（441 aa）
Mutation：C377H SF4 IRON/SULFUR CLUSTER × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2 SO3 SULFITE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES, 12% PEG 4000, 0.6 M NaCl
Resolution 1.80 Å R-free 0.197
6GM5 [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E141A Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 57–497（441 aa） Fragment：apo enzyme
Mutation：E141A SF4 IRON/SULFUR CLUSTER × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；11% PEG 4000, 0.5 M NaCl,0.1 M MES
Resolution 1.45 Å R-free 0.197
6GM6 [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E141Q Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 57–497（441 aa） Fragment：apo enzyme
Mutation：E141Q SF4 IRON/SULFUR CLUSTER × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；15% PEG 4000, 0.6 M NaCl,0.1 M MES
Resolution 1.61 Å R-free 0.199
6GM7 [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E144A Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 57–497（441 aa） Fragment：apo enzyme
Mutation：E144A SF4 IRON/SULFUR CLUSTER × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% PEG 4000, 0.4 M NaCl,0.1 M MES
Resolution 2.14 Å R-free 0.227

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9FYU1_CHLRE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–442； UniProt 58–497

Ferredoxin, chloroplastic

Chlamydomonas reinhardtii

UniProt P07839

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 33–126 Not recorded Fe-hydrogenase × 1 （Q9FYU1） SF4 IRON/SULFUR CLUSTER × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure AMBIENT NMR sample composition：0.1-0.2 MM [U-100% 15N] PROTEIN_ 1, 1 MM PROTEIN_2, 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2N0S Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1FCT NMR STRUCTURES OF FERREDOXIN CHLOROPLASTIC TRANSIT PEPTIDE FROM CHLAMYDOMONAS REINHARDTII PROMOTED BY TRIFLUOROETHANOL IN AQUEOUS SOLUTION Deposited 1994-03-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–32（32 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2MH7 Solution structure of oxidized [2Fe-2S] ferredoxin PetF from Chlamydomonas reinhardtii Deposited 2013-11-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 33–126（94 aa） Fragment：unp residues 33-126
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 50 mM potassium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6KUM Ferredoxin I from C. reinhardtii, low X-ray dose Deposited 2019-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–126（95 aa）
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 BEN BENZAMIDINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 5.6；298 K；Ammonium Sulfate, Sodium Citrate, Benzamidine Hydrochloride, Sodium Thiocyanate
Resolution 1.40 Å R-free 0.190
6KUM Ferredoxin I from C. reinhardtii, low X-ray dose Deposited 2019-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 32–126（95 aa）
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 BEN BENZAMIDINE × 1 SCN THIOCYANATE ION × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 5.6；298 K；Ammonium Sulfate, Sodium Citrate, Benzamidine Hydrochloride, Sodium Thiocyanate
Resolution 1.40 Å R-free 0.190
6KV0 Ferredoxin I from C. reinhardtii, high X-ray dose Deposited 2019-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–126（95 aa）
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 BEN BENZAMIDINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 5.6；293 K；Ammonium sulfate Sodium citrate Sodium thiocyanate Benzamidine Hydrochloride
Resolution 1.40 Å R-free 0.187
6KV0 Ferredoxin I from C. reinhardtii, high X-ray dose Deposited 2019-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 32–126（95 aa）
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 BEN BENZAMIDINE × 1 SCN THIOCYANATE ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 5.6；293 K；Ammonium sulfate Sodium citrate Sodium thiocyanate Benzamidine Hydrochloride
Resolution 1.40 Å R-free 0.187
6LK1 Ultrahigh resolution X-ray structure of Ferredoxin I from C. reinhardtii Deposited 2019-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–126（95 aa）
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 BEN BENZAMIDINE × 6 SCN THIOCYANATE ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；Ammonium sulfate Sodium citrate Sodium thiocyanate Benzamidine Hydrochloride
Resolution 0.90 Å R-free 0.171
6LK1 Ultrahigh resolution X-ray structure of Ferredoxin I from C. reinhardtii Deposited 2019-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 32–126（95 aa）
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；Ammonium sulfate Sodium citrate Sodium thiocyanate Benzamidine Hydrochloride
Resolution 0.90 Å R-free 0.171
7AKT CrPetF variant - A39G_A41V Deposited 2020-10-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 33–126（94 aa）
Mutation：A39G, A41V FES FE2/S2 (INORGANIC) CLUSTER × 1 BEN BENZAMIDINE × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；281.15 K；2 % (w/v) benzamidine hydrochloride, 1.8 M (NH4)2SO4 and 0.2 M NaSCN in 0.1 M sodium citrate buffer
Resolution 1.11 Å R-free 0.191
7WZN PSI-LHCI from Chlamydomonas reinhardtii with bound ferredoxin Deposited 2022-02-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain G 1–126（126 aa）
Not recorded CL0 CHLOROPHYLL A ISOMER × 1 CLA CHLOROPHYLL A × 188 PQN PHYLLOQUINONE × 2 SF4 IRON/SULFUR CLUSTER × 3 CHL CHLOROPHYLL B × 16 FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE；2.6 microliter of sample were applied to cryo-grids and blotted for 3.5 seconds using Whatman #1 before plunge freezing.
Resolution 4.90 Å

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FER_CHLRE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–94； UniProt 33–126

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2n0s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2n0s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2n0s
Deposition date deposition_date2015-03-13
Structure title titleHADDOCK model of ferredoxin and [FeFe] hydrogenase complex
Keywords keywordsOXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.53 Å
Radius of gyration Rg (electron density) rg_electron23.17 Å
Forward intensity I(0) i0715149000.00
Molecular weight molecular_weight217610.0 kDa
Excluded volume excluded_volume269720 ų
Envelope volume envelope_volume90083 ų
Hydration-shell volume shell_volume30868 ų
Envelope diameter envelope_diameter84.8 Å
Shell Rg shell_rg31.84 Å
Envelope Rg envelope_rg24.25 Å
Shape Rg shape_rg23.26 Å
Total Rg total_rg23.14 Å
Total atoms total_atoms30152
Residues n_residues2004
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax75.9 Å
Rg (real space) rg_real23.46 Å
Rg uncertainty (real space) rg_real_error0.55 Å
I(0) (real space) i0_real7.1510e+08
I(0) uncertainty (real space) i0_real_error1.0640e+07
Rg (reciprocal space) rg_reciprocal23.48 Å
I(0) (reciprocal space) i0_reciprocal715200000.0000
Solution quality estimate total_estimate0.8111
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary28.5 Å
Skewness Skewness skewness0.298
Kurtosis Kurtosis kurtosis-0.311
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11760000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.850; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id2n0sA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1780 —
Domain ID domain_id2n0sA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology950 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
Homologous superfamily homologous superfamily10 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
Domain ID domain_id2n0sB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily30 — Beta-grasp domain
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8. Citations (1)

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9. Files and Curves (10)