SAXSdb — 1kn9

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

Signal peptidase I

Escherichia coli K12

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 77–324	Fragment：Residues 76-323, plus initiating methionine	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.4；295 K；ammonium dihydrogen phosphate, sodium citrate, Triton X-100, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.278
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 77–324	Fragment：Residues 76-323, plus initiating methionine	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.4；295 K；ammonium dihydrogen phosphate, sodium citrate, Triton X-100, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.278
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 77–324	Fragment：Residues 76-323, plus initiating methionine	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.4；295 K；ammonium dihydrogen phosphate, sodium citrate, Triton X-100, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.278
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 77–324	Fragment：Residues 76-323, plus initiating methionine	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.4；295 K；ammonium dihydrogen phosphate, sodium citrate, Triton X-100, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.278

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 1KN9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B12 CRYSTAL STRUCTURE OF TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR Deposited 1999-11-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 77–324（248 aa） Fragment：CATALYTIC DOMAIN	Not recorded	1PN prop-2-en-1-yl (2S)-2-[(2S,3R)-3-(acetyloxy)-1-oxobutan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.95 Å R-free 0.246
1B12 CRYSTAL STRUCTURE OF TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR Deposited 1999-11-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 77–324（248 aa） Fragment：CATALYTIC DOMAIN	Not recorded	1PN prop-2-en-1-yl (2S)-2-[(2S,3R)-3-(acetyloxy)-1-oxobutan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylate × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.95 Å R-free 0.246
1B12 CRYSTAL STRUCTURE OF TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR Deposited 1999-11-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 77–324（248 aa） Fragment：CATALYTIC DOMAIN	Not recorded	1PN prop-2-en-1-yl (2S)-2-[(2S,3R)-3-(acetyloxy)-1-oxobutan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.95 Å R-free 0.246
1B12 CRYSTAL STRUCTURE OF TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR Deposited 1999-11-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 77–324（248 aa） Fragment：CATALYTIC DOMAIN	Not recorded	1PN prop-2-en-1-yl (2S)-2-[(2S,3R)-3-(acetyloxy)-1-oxobutan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.95 Å R-free 0.246
1T7D Crystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor Deposited 2004-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 76–324（249 aa） Fragment：RESIDUES 76-324	Not recorded	M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.5% TRITON X-100, 15% PEG 4000, 20% PROPANOL, 0.1 M SODIUM CITRATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K	Resolution 2.47 Å R-free 0.283
1T7D Crystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor Deposited 2004-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 76–324（249 aa） Fragment：RESIDUES 76-324	Not recorded	M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.5% TRITON X-100, 15% PEG 4000, 20% PROPANOL, 0.1 M SODIUM CITRATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K	Resolution 2.47 Å R-free 0.283
3IIQ Crystallographic analysis of bacterial signal peptidase in ternary complex with Arylomycin A2 and a beta-sultam inhibitor Deposited 2009-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 77–324（248 aa） Fragment：UNP RESIDUES 76-323, PERIPLASMIC DOMAIN	Not recorded	JZA 4-[(1,1-dioxido-1,2-thiazetidin-2-yl)carbonyl]morpholine × 1 TRT FRAGMENT OF TRITON X-100 × 1 M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2M NH4 FORMATE, 25% PEG 2000, 0.1M NA CACODYLATE PH 6.5, AND 5% TERTIARY-AMYL ALCOHOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K	Resolution 2.00 Å R-free 0.250
3IIQ Crystallographic analysis of bacterial signal peptidase in ternary complex with Arylomycin A2 and a beta-sultam inhibitor Deposited 2009-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 77–324（248 aa） Fragment：UNP RESIDUES 76-323, PERIPLASMIC DOMAIN	Not recorded	JZA 4-[(1,1-dioxido-1,2-thiazetidin-2-yl)carbonyl]morpholine × 1 TRT FRAGMENT OF TRITON X-100 × 1 GOL GLYCEROL × 4 CCN ACETONITRILE × 2 M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2M NH4 FORMATE, 25% PEG 2000, 0.1M NA CACODYLATE PH 6.5, AND 5% TERTIARY-AMYL ALCOHOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K	Resolution 2.00 Å R-free 0.250
3S04 Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic Deposited 2011-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 76–324（249 aa） Fragment：Periplasmic domain, UNP residues 76-323	Not recorded	02U 14-methylhexadec-9-enoic acid × 1 RAM alpha-L-rhamnopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；22% PEG 4000, 0.2M KCl, 0.025M n-dodecyl beta-D-maltoside (DDM), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.44 Å R-free 0.265
3S04 Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic Deposited 2011-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 76–324（249 aa） Fragment：Periplasmic domain, UNP residues 76-323	Not recorded	02U 14-methylhexadec-9-enoic acid × 1 RAM alpha-L-rhamnopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；22% PEG 4000, 0.2M KCl, 0.025M n-dodecyl beta-D-maltoside (DDM), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.44 Å R-free 0.265
3S04 Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic Deposited 2011-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 76–324（249 aa） Fragment：Periplasmic domain, UNP residues 76-323 Chain B 76–324（249 aa） Fragment：Periplasmic domain, UNP residues 76-323	Not recorded	02U 14-methylhexadec-9-enoic acid × 2 RAM alpha-L-rhamnopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；22% PEG 4000, 0.2M KCl, 0.025M n-dodecyl beta-D-maltoside (DDM), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.44 Å R-free 0.265
6B88 E. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2-(2-(4-(tert-butyl)phenyl)-4-methylpyrimidine-5-carboxamido)-N-methylbutanamido)-16,26-bis(2-aminoethoxy)-N-(2-iminoethyl)-7-methyl-6,9-dioxo-5,8-diaza-1,2(1,3)-dibenzenacyclodecaphane-4-carboxamide) Deposited 2017-10-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–324（247 aa）	Not recorded	CZD (8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；292 K；30% PEG 300, 0.1 M Sodium Acetate pH 4.5	Resolution 2.41 Å R-free 0.265
6B88 E. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2-(2-(4-(tert-butyl)phenyl)-4-methylpyrimidine-5-carboxamido)-N-methylbutanamido)-16,26-bis(2-aminoethoxy)-N-(2-iminoethyl)-7-methyl-6,9-dioxo-5,8-diaza-1,2(1,3)-dibenzenacyclodecaphane-4-carboxamide) Deposited 2017-10-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 78–324（247 aa）	Not recorded	CZD (8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide × 1 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；292 K；30% PEG 300, 0.1 M Sodium Acetate pH 4.5	Resolution 2.41 Å R-free 0.265
9NLO Escherichia coli Signal Peptidase I Delta 2-76 P84A in complex with lipopeptide inhibitor Deposited 2025-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 77–324（248 aa）	Mutation：P84A	EDO 1,2-ETHANEDIOL × 1 M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；294.15 K；25%v/v PEG 4000, 0.05M NH4OAC, 0.1M NaOAc pH 4.6, 0.033M L-proline	Resolution 2.32 Å R-free 0.234
9NLO Escherichia coli Signal Peptidase I Delta 2-76 P84A in complex with lipopeptide inhibitor Deposited 2025-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 77–324（248 aa）	Mutation：P84A	EDO 1,2-ETHANEDIOL × 1 M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；294.15 K；25%v/v PEG 4000, 0.05M NH4OAC, 0.1M NaOAc pH 4.6, 0.033M L-proline	Resolution 2.32 Å R-free 0.234

6 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LEP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–249； UniProt 77–324 Author chain B； PDBConstruct 2–249； UniProt 77–324 Author chain C； PDBConstruct 2–249； UniProt 77–324 Author chain D； PDBConstruct 2–249； UniProt 77–324

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	1kn9
Deposition date deposition_date	2001-12-18
Structure title title	CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM.
Keywords keywords	serine protease, Lysine general base, membrane protein, mostly beta-fold, HYDROLASE; HYDROLASE
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	39.36 Å
Radius of gyration Rg (electron density) rg_electron	39.24 Å
Forward intensity I(0) i0	145863000.00
Molecular weight molecular_weight	97681.0 kDa
Excluded volume excluded_volume	122080 Å³
Envelope volume envelope_volume	176880 Å³
Hydration-shell volume shell_volume	39154 Å³
Envelope diameter envelope_diameter	137.4 Å
Shell Rg shell_rg	43.19 Å
Envelope Rg envelope_rg	38.21 Å
Shape Rg shape_rg	39.27 Å
Total Rg total_rg	39.39 Å
Total atoms total_atoms	6898
Residues n_residues	904
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	128.9 Å
Rg (real space) rg_real	39.49 Å
Rg uncertainty (real space) rg_real_error	1.29 Å
I(0) (real space) i0_real	1.4590e+08
I(0) uncertainty (real space) i0_real_error	2.7700e+06
Rg (reciprocal space) rg_reciprocal	39.42 Å
I(0) (reciprocal space) i0_reciprocal	145900000.0000
Solution quality estimate total_estimate	0.8786
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.3 Å
Skewness Skewness skewness	0.245
Kurtosis Kurtosis kurtosis	-0.755
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13600000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.856; Smooth: 0.890

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1kn9a_
Class class	b — All beta proteins
Fold Fold fold	b.87 — LexA/Signal peptidase
Superfamily Superfamily superfamily	b.87.1 — LexA/Signal peptidase
Family Family family	b.87.1.2 — Type 1 signal peptidase

Domain ID domain_id	d1kn9b_
Class class	b — All beta proteins
Fold Fold fold	b.87 — LexA/Signal peptidase
Superfamily Superfamily superfamily	b.87.1 — LexA/Signal peptidase
Family Family family	b.87.1.2 — Type 1 signal peptidase

Domain ID domain_id	d1kn9c_
Class class	b — All beta proteins
Fold Fold fold	b.87 — LexA/Signal peptidase
Superfamily Superfamily superfamily	b.87.1 — LexA/Signal peptidase
Family Family family	b.87.1.2 — Type 1 signal peptidase

Domain ID domain_id	d1kn9d_
Class class	b — All beta proteins
Fold Fold fold	b.87 — LexA/Signal peptidase
Superfamily Superfamily superfamily	b.87.1 — LexA/Signal peptidase
Family Family family	b.87.1.2 — Type 1 signal peptidase

CATH v4.4 (8 domains)

Domain ID domain_id	1kn9A01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily	10 — Umud Fragment, subunit A

Domain ID domain_id	1kn9A02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	230 — Signal Peptidase I; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1kn9B01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily	10 — Umud Fragment, subunit A

Domain ID domain_id	1kn9B02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	230 — Signal Peptidase I; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1kn9C01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily	10 — Umud Fragment, subunit A

Domain ID domain_id	1kn9C02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	230 — Signal Peptidase I; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1kn9D01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily	10 — Umud Fragment, subunit A

Domain ID domain_id	1kn9D02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	230 — Signal Peptidase I; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (2)

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Unit-cell length a length_a	112.441 Å
Unit-cell length b length_b	112.441 Å
Unit-cell length c length_c	198.675 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	40.050 Å
R factor r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.2780

Description description	Signal peptidase I
Molecular weight formula_weight	27966.7 kDa
EC 编号 ec_number	3.4.21.89
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7154

CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM.

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

Signal peptidase I

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli K12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	256

fit	/app/data/saxs_computation/kn/1kn9/1kn9.fit
pddf	/app/data/pr_computation/kn/1kn9/1kn9.pr.out
profile	/app/data/saxs_computation/kn/1kn9/1kn9.dat