SAXSdb — 6lk1

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferredoxin, chloroplastic

Chlamydomonas reinhardtii

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 32–126	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 32–126	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

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 6LK1	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–32（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 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） 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
2N0S HADDOCK model of ferredoxin and [FeFe] hydrogenase complex Deposited 2015-03-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 33–126（94 aa）	Not recorded	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
6KUM Ferredoxin I from C. reinhardtii, low X-ray dose Deposited 2019-09-02	Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
7AKT CrPetF variant - A39G_A41V Deposited 2020-10-02	Different construct Different mutation/modification Different ligand/ion 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 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FER_CHLRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 32–126 Author chain B； PDBConstruct 1–95； UniProt 32–126

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6lk1
Deposition date deposition_date	2019-12-17
Structure title title	Ultrahigh resolution X-ray structure of Ferredoxin I from C. reinhardtii
Keywords keywords	[2Fe2S] cluster, electron transport; ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.09 Å
Radius of gyration Rg (electron density) rg_electron	17.29 Å
Forward intensity I(0) i0	8651820.00
Molecular weight molecular_weight	20056.0 kDa
Excluded volume excluded_volume	24323 Å³
Envelope volume envelope_volume	30021 Å³
Hydration-shell volume shell_volume	14972 Å³
Envelope diameter envelope_diameter	60.4 Å
Shell Rg shell_rg	22.58 Å
Envelope Rg envelope_rg	17.55 Å
Shape Rg shape_rg	17.35 Å
Total Rg total_rg	17.98 Å
Total atoms total_atoms	1384
Residues n_residues	175
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	61.3 Å
Rg (real space) rg_real	18.08 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	8.6520e+06
I(0) uncertainty (real space) i0_real_error	1.0490e+05
Rg (reciprocal space) rg_reciprocal	18.08 Å
I(0) (reciprocal space) i0_reciprocal	8652000.0000
Solution quality estimate total_estimate	0.8700
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.9 Å
Skewness Skewness skewness	0.356
Kurtosis Kurtosis kurtosis	-0.342
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2197000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ferredoxin, chloroplastic
Molecular weight formula_weight	9985.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1717

AYKVTLKTPSGDKTIECPADTYILDAAEEAGLDLPYSCRAGACSSCAGKVAAGTVDQSDQSFLDDAQMGNGFVLTCVAYPTSDCTIQTHQEEALY

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI Class编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	BENZAMIDINE
Molecular weight formula_weight	120.2 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	157

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6lk1a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

Domain ID domain_id	d6lk1b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

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8. Citations (1)

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Unit-cell length a length_a	25.955 Å
Unit-cell length b length_b	60.090 Å
Unit-cell length c length_c	50.085 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	0.900 Å
Low-resolution limit resolution_low	37.960 Å
R factor r_factor	—
R_work r_work	0.1449
R_free r_free	0.1713

fit	/app/data/saxs_computation/lk/6lk1/6lk1.fit
pddf	/app/data/pr_computation/lk/6lk1/6lk1.pr.out
profile	/app/data/saxs_computation/lk/6lk1/6lk1.dat

Ultrahigh resolution X-ray structure of Ferredoxin I from C. reinhardtii

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferredoxin, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction