SAXSdb — 1czu

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

FLAVODOXIN

Synechococcus elongatus

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 1–169	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；AMMONIUM SULFATE, POTASSIUM PHOSPHATE, POTASSIUM CHLORIDE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.184

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 1CZU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CZH COMPARISONS OF WILD TYPE AND MUTANT FLAVODOXINS FROM ANACYSTIS NIDULANS. STRUCTURAL DETERMINANTS OF THE REDOX POTENTIALS. Deposited 1999-09-03	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 1–169（169 aa）	Mutation：N58G	SO4 SULFATE ION × 1 FMN FLAVIN MONONUCLEOTIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；AMMONIUM SULPHATE, POTASSIUM PHOSPHATE, POTASSIUM CHLORIDE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.86 Å R-free 0.209
1CZK COMPARISONS OF WILD TYPE AND MUTANT FLAVODOXINS FROM ANACYSTIS NIDULANS. STRUCTURAL DETERMINANTS OF THE REDOX POTENTIALS. Deposited 1999-09-03	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Mutation：D100N	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；AMMONIUN SULPHATE, POTASSIUM PHOSPHATE, POTASSIUM CHLORIDE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.200
1CZL COMPARISONS OF WILD TYPE AND MUTANT FLAVODOXINS FROM ANACYSTIS NIDULANS. STRUCTURAL DETERMINANTS OF THE REDOX POTENTIALS. Deposited 1999-09-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；AMMONIUM SULPHATE, POTTASIUM PHOSPHATE, POTASSIUM CHLORIDE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.218
1CZN REFINED STRUCTURES OF OXIDIZED FLAVODOXIN FROM ANACYSTIS NIDULANS Deposited 1999-09-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；AMMONIUM SULFATE, POTASSIUM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.210
1CZO COMPARISONS OF WILD TYPE AND MUTANT FLAVODOXINS FROM ANACYSTIS NIDULANS. STRUCTURAL DETERMINANTS OF THE REDOX POTENTIALS. Deposited 1999-09-03	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 1–169（169 aa）	Mutation：N58G	SO4 SULFATE ION × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；AMMONIUM SULPHATE, POTSSIUM PHOSPHATE, POTASSIM CHLORIDE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.85 Å R-free 0.202
1CZR COMPARISONS OF WILD TYPE AND MUTANT FLAVODOXINS FROM ANACYSTIS NIDULANS. STRUCTURAL DETERMINANTS OF THE REDOX POTENTIALS. Deposited 1999-09-07	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Mutation：D90N	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；AMMONIUNM SULPHATE, POTASSIUM PHOSPHATE, POTASSIUM CHLORIDE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.193
1D03 REFINED STRUCTURES OF OXIDIZED FLAVODOXIN FROM ANACYSTIS NIDULANS Deposited 1999-09-08	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Mutation：N58G	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；AMMONIUM SULFATE, POTASSIUM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.85 Å R-free 0.172
1D04 COMPARISONS OF WILD TYPE AND MUTANT FLAVODOXINS FROM ANACYSTIS NIDULANS. STRUCTURAL DETERMINANTS OF THE REDOX POTENTIALS. Deposited 1999-09-08	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；AMMONIUM SULPHATE, POTASSIUM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.85 Å R-free 0.207
1OFV FLAVODOXIN FROM ANACYSTIS NIDULANS: REFINEMENT OF TWO FORMS OF THE OXIDIZED PROTEIN Deposited 1992-06-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
6KIF Structure of cyanobacterial photosystem I-IsiA-flavodoxin supercomplex Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric	Chain P 2–170（169 aa） Chain X 2–170（169 aa） Chain p 2–170（169 aa）	Not recorded	CLA CHLOROPHYLL A × 594 PQN PHYLLOQUINONE × 6 SF4 IRON/SULFUR CLUSTER × 9 BCR BETA-CAROTENE × 144 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 45 LMU DODECYL-ALPHA-D-MALTOSIDE × 12 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 24 FMN FLAVIN MONONUCLEOTIDE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8HGQ The apo-flavodoxin dimer from Synechococcus elongatus PCC 7942 Deposited 2022-11-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–170（169 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.4 M NaH2PO4/1.6 M K2HPO4; 0.1 M imidazole PH8.0; 0.2 M NaCl	Resolution 2.09 Å R-free 0.239
8HGR The apo-flavodoxin monomer from Synechococcus elongatus PCC 7942 Deposited 2022-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–170（169 aa）	Not recorded	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2 M Magnesium chloride; 0.1 M Tris-HCl pH8.5; 30% PEG4000	Resolution 1.84 Å R-free 0.201

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FLAV_SYNP7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–169； UniProt 1–169

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	1czu
Deposition date deposition_date	1999-09-07
Structure title title	REFINED STRUCTURES OF OXIDIZED FLAVODOXIN FROM ANACYSTIS NIDULANS
Keywords keywords	FLAVODOXIN, FMN BINDING, REDOX POTENTIAL, CRYSTAL PACKING, 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	16.05 Å
Radius of gyration Rg (electron density) rg_electron	14.57 Å
Forward intensity I(0) i0	7167990.00
Molecular weight molecular_weight	19086.0 kDa
Excluded volume excluded_volume	23595 Å³
Envelope volume envelope_volume	25657 Å³
Hydration-shell volume shell_volume	14513 Å³
Envelope diameter envelope_diameter	45.5 Å
Shell Rg shell_rg	20.81 Å
Envelope Rg envelope_rg	14.83 Å
Shape Rg shape_rg	14.56 Å
Total Rg total_rg	15.69 Å
Total atoms total_atoms	1349
Residues n_residues	169
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	47.8 Å
Rg (real space) rg_real	15.90 Å
Rg uncertainty (real space) rg_real_error	0.16 Å
I(0) (real space) i0_real	7.1680e+06
I(0) uncertainty (real space) i0_real_error	6.9840e+04
Rg (reciprocal space) rg_reciprocal	15.92 Å
I(0) (reciprocal space) i0_reciprocal	7168000.0000
Solution quality estimate total_estimate	0.9059
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.025
Kurtosis Kurtosis kurtosis	-0.499
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1285000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	FLAVODOXIN
Molecular weight formula_weight	18656.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1465

AKIGLFYGTQTGVTQTIAESIQQEFGGESIVDLNDIANADASDLNAYDYLIIGCPTWNVGELQSDWEGIYDDLDSVNFQGKKVAYFGAGDQVGYSDNFQDAMGILEEKISSLGSQTVGYWPIEGYDFNESKAVRNNQFVGLAIDEDNQPDLTKNRIKTWVSQLKSEFGL

来源 Source

来源生物 organism	Synechococcus elongatus
NCBI Class编号 ncbi_taxonomy_id	1140
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	116

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1czua_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.5 — Flavoproteins
Family Family family	c.23.5.1 — Flavodoxin-related

CATH v4.4 (1 domains)

Domain ID domain_id	1czuA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	360 — Flavodoxin domain

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8. Citations (1)

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Unit-cell length a length_a	60.050 Å
Unit-cell length b length_b	65.850 Å
Unit-cell length c length_c	51.360 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1470
R_work r_work	0.1470
R_free r_free	0.1840

fit	/app/data/saxs_computation/cz/1czu/1czu.fit
pddf	/app/data/pr_computation/cz/1czu/1czu.pr.out
profile	/app/data/saxs_computation/cz/1czu/1czu.dat

REFINED STRUCTURES OF OXIDIZED FLAVODOXIN FROM ANACYSTIS NIDULANS

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

FLAVODOXIN

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