SAXSdb — 1kmk

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

SELENOCYSTEINE LYASE

Escherichia coli

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–406	Non-standard monomer：Yes (specific site not provided by mmCIF)	SEC SELENOCYSTEINE × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；4M NACL, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.20 Å R-free 0.239

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 1KMK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C0N CSDB PROTEIN, NIFS HOMOLOGUE Deposited 1999-07-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；sodium acetate, pottasium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.80 Å R-free 0.239
1JF9 Crystal Structure of selenocysteine lyase Deposited 2001-06-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；4M NACL, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.207
1KMJ E. coli NifS/CsdB protein at 2.0A with the cysteine persulfide intermediate (residue CSS). Deposited 2001-12-16	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；4M NACL, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.208
5DB5 Crystal structure of PLP-bound E. coli SufS (cysteine persulfide intermediate) in space group P21 Deposited 2015-08-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PLP PYRIDOXAL-5'-PHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 2 CYS CYSTEINE × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1:1 or 1:2 protein to reservoir solution (4% PEG3350, 200 mM ammonium citrate), crystals grown over 3 days, cryoprotectant: reservoir solution + 10% PEG400	Resolution 2.75 Å R-free 0.217
6MR2 E. coli cysteine desulfurase SufS with a cysteine persulfide intermediate Deposited 2018-10-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；4-4.5 M sodium chloride, 100 mM MES	Resolution 2.40 Å R-free 0.191
6MR6 E. coli cysteine desulfurase SufS H55A with a cysteine persulfide intermediate Deposited 2018-10-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Mutation：H55A Non-standard monomer：Yes (specific site not provided by mmCIF)	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；4-4.5 M sodium chloride, 100 mM MES	Resolution 2.02 Å R-free 0.202
6MRE E. coli cysteine desulfurase SufS R92A with a cysteine persulfide intermediate Deposited 2018-10-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Mutation：R92A Non-standard monomer：Yes (specific site not provided by mmCIF)	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；4-4.5 M sodium chloride, 100 mM MES	Resolution 2.50 Å R-free 0.199
6MRH E. coli cysteine desulfurase SufS E96A with a cysteine persulfide intermediate Deposited 2018-10-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Mutation：E96A Non-standard monomer：Yes (specific site not provided by mmCIF)	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；4-4.5 M sodium chloride, 100 mM MES	Resolution 2.02 Å R-free 0.212
6MRI E. coli cysteine desulfurase SufS E250A with a cysteine persulfide intermediate Deposited 2018-10-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Mutation：E250A Non-standard monomer：Yes (specific site not provided by mmCIF)	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；4-4.5 M sodium chloride, 100 mM MES	Resolution 2.62 Å R-free 0.220
6O10 E. coli cysteine desulfurase SufS Deposited 2019-02-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；4-4.5 M sodium chloride, 100 mM MES	Resolution 2.00 Å R-free 0.204
6O11 E. coli cysteine desulfurase SufS C364A with a Cys-aldimine intermediate Deposited 2019-02-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Mutation：C364A	CL CHLORIDE ION × 2 C6P N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20-30% w/v PEG3350, 0.1 M Tris-HCl, 0.2 M magnesium chloride	Resolution 1.84 Å R-free 0.216
6O12 E. coli cysteine desulfurase SufS H123A Deposited 2019-02-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Mutation：H123A	PLP PYRIDOXAL-5'-PHOSPHATE × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；4-4.5 M sodium chloride, 100 mM MES	Resolution 2.05 Å R-free 0.216
6O13 E. coli cysteine desulfurase SufS H123A with a Cys-ketimine intermediate Deposited 2019-02-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Mutation：H123A	CKT Cys-ketimine × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；4-4.5 M sodium chloride, 100 mM MES	Resolution 2.20 Å R-free 0.199
6UY5 E. coli cysteine desulfurase SufS with a spontaneously rotated beta-hairpin Deposited 2019-11-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2 M MgCl2, 0.1M Bis-Tris HCl pH 5.5, 23.3% w/v PEG3350	Resolution 1.50 Å R-free 0.221
8VBS E. coli cysteine desulfurase SufS bound to SufE C51A Deposited 2023-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；24.5-31.5% w/v PEG2000 MME, 0.1 M KSCN	Resolution 3.31 Å R-free 0.272
9D2D E. coli cysteine desulfurase SufS R359A Deposited 2024-08-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa）	Mutation：R359A Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；4-4.5 M NaCl, 100 mM MES pH 6.5	Resolution 2.70 Å R-free 0.245

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSDB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–406； UniProt 1–406

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	1kmk
Deposition date deposition_date	2001-12-16
Structure title title	E. coli NifS/CsdB protein at 2.20A with the cysteine perselenide intermediate (residue CSZ).
Keywords keywords	;nifs selenocysteine cysteine persulfide perselenide xray, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, LYASE ;; LYASE
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	23.00 Å
Radius of gyration Rg (electron density) rg_electron	22.04 Å
Forward intensity I(0) i0	34255800.00
Molecular weight molecular_weight	44752.0 kDa
Excluded volume excluded_volume	55762 Å³
Envelope volume envelope_volume	64159 Å³
Hydration-shell volume shell_volume	24203 Å³
Envelope diameter envelope_diameter	82.4 Å
Shell Rg shell_rg	29.09 Å
Envelope Rg envelope_rg	22.50 Å
Shape Rg shape_rg	22.07 Å
Total Rg total_rg	22.76 Å
Total atoms total_atoms	3141
Residues n_residues	404
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	83.7 Å
Rg (real space) rg_real	22.96 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	3.4260e+07
I(0) uncertainty (real space) i0_real_error	4.5350e+05
Rg (reciprocal space) rg_reciprocal	22.97 Å
I(0) (reciprocal space) i0_reciprocal	34260000.0000
Solution quality estimate total_estimate	0.7668
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.0 Å
Skewness Skewness skewness	0.315
Kurtosis Kurtosis kurtosis	-0.310
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7570000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.672; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; 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)

Entity 1 Entity 1 polymer

Description description	SELENOCYSTEINE LYASE
Molecular weight formula_weight	44559.6 kDa
EC 编号 ec_number	4.4.1.16
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	3626

MIFSVDKVRADFPVLSREVNGLPLAYLDSAASAQKPSQVIDAEAEFYRHGYAAVHRGIHTLSAQATEKMENVRKRASLFINARSAEELVFVRGTTEGINLVANSWGNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPLNPDGTLQLETLPTLFDEKTRLLAITHVSNVLGTENPLAEMITLAHQHGAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHKLYGPTGIGILYVKEALLQEMPPWEGGGSMIATVSLSEGTTWTKAPWRFEAGTPNTGGIIGLGAALEYVSALGLNNIAEYEQNLMHYALSQLESVPDLTLYGPQNRLGVIAFNLGKHHAYDVGSFLDNYGIAVRTGHHCAMPLMAYYNVPAMCRASLAMYNTHEEVDRLVTGLQRIHRLLG

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SELENOCYSTEINE
Molecular weight formula_weight	168.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	485

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1kmka_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.3 — Cystathionine synthase-like

CATH v4.4 (2 domains)

Domain ID domain_id	1kmkA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1kmkA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

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8. Citations (1)

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Unit-cell length a length_a	125.855 Å
Unit-cell length b length_b	125.855 Å
Unit-cell length c length_c	133.200 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1960
R_free r_free	0.2390

fit	/app/data/saxs_computation/km/1kmk/1kmk.fit
pddf	/app/data/pr_computation/km/1kmk/1kmk.pr.out
profile	/app/data/saxs_computation/km/1kmk/1kmk.dat

E. coli NifS/CsdB protein at 2.20A with the cysteine perselenide intermediate (residue CSZ).

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

SELENOCYSTEINE LYASE

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