2fge

Crystal structure of presequence protease PreP from Arabidopsis thaliana

Method: X-RAY DIFFRACTION

▼

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

zinc metalloprotease (insulinase family)

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	nonspecific peptide AALTRA × 1 ZINC ION × 1 CHLORIDE ION × 1 MAGNESIUM ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	nonspecific peptide AALTRA × 1 ZINC ION × 1 CHLORIDE ION × 1 MAGNESIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9LJL3_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–995； UniProt 58–1052 Author chain B； PDBConstruct 1–995； UniProt 58–1052

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2fge
Deposition date deposition_date	2005-12-21
Structure title title	Crystal structure of presequence protease PreP from Arabidopsis thaliana
Keywords keywords	PEPTIDASOME; PROTEASE-PEPTIDE COMPLEX, HYDROLASE, PLANT PROTEIN; HYDROLASE, PLANT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2fge__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2fge__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fge__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	29.83 Å
Rg (electron density)	28.64 Å
Total Rg	29.47 Å
Atom count	7776
Residues	965
Excluded volume	138770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fge__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2fge__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	zinc metalloprotease (insulinase family)
Molecular weight formula_weight	112536.4 kDa
Mutation mutation	E80Q
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	16500

VATQPAPLYPDVGQDEAEKLGFEKVSEEFISECKSKAILFKHKKTGCEVMSVSNEDENKVFGVVFRTPPKDSTGIPHILQHSVLCGSRKYPVKEPFVELLKGSLHTFLNAFTYPDRTCYPVASTNTKDFYNLVDVYLDAVFFPKCVDDAHTFQQEGWHYELNDPSEDISYKGVVFNEMKGVYSQPDNILGRIAQQALSPENTYGVDSGGDPKDIPNLTFEEFKEFHRQYYHPSNARIWFYGDDDPVHRLRVLSEYLDMFEASPSPNSSKIKFQKLFSEPVRLVEKYPAGRDGDLKKKHMLCVNWLLSEKPLDLQTQLALGFLDHLMLGTPASPLRKILLESGLGEALVSSGLSDELLQPQFGIGLKGVSEENVQKVEELIMDTLKKLAEEGFDNDAVEASMNTIEFSLRENNTGSFPRGLSLMLQSISKWIYDMDPFEPLKYTEPLKALKTRIAEEGSKAVFSPLIEKLILNNSHRVTIEMQPDPEKATQEEVEEKNILEKVKAAMTEEDLAELARATEELKLKQETPDPPEALRCVPSLNLGDIPKEPTYVPTEVGDINGVKVLRHDLFTNDIIYTEVVFDIGSLKHELLPLVPLFCQSLLEMGTKDLTFVQLNQLIGRKTGGISVYPLTSSVRGKDEPCSKIIVRGKSMAGRADDLFNLMNCLLQEVQFTDQQRFKQFVSQSRARMENRLRGSGHGIAAARMDAMLNIAGWMSEQMGGLSYLEFLHTLEKKVDEDWEGISSSLEEIRRSLLARNGCIVNMTADGKSLTNVEKSVAKFLDLLPENPSGGLVTWDGRLPLRNEAIVIPTQVNYVGKAGNIYSTGYELDGSAYVISKHISNTWLWDRVRVSGGAYGGFCDFDSHSGVFSYLSYRDPNLLKTLDIYDGTGDFLRGLDVDQETLTKAIIGTIGDVDSYQLPDAKGYSSLLRHLLGVTDEERQRKREEILTTSLKDFKDFAQAIDVVRDKGVAVAVASAEDIDAANNERSNFFEVKKAL

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	nonspecific peptide AALTRA
Molecular weight formula_weight	602.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

AALTRA

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	948

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2fgea1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2fgea2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2fgea3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2fgea4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2fgeb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2fgeb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2fgeb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2fgeb4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

CATH v4.4 (8 domains)

Domain ID domain_id	2fgeA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2fgeA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2fgeA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2fgeA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2fgeB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2fgeB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2fgeB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2fgeB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

▶

Unit-cell length a length_a	110.834 Å
Unit-cell length b length_b	114.332 Å
Unit-cell length c length_c	162.984 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	93.660 Å
R factor r_factor	0.2090
R_work r_work	0.2060
R_free r_free	0.2560

Crystal structure of presequence protease PreP from Arabidopsis thaliana

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

zinc metalloprotease (insulinase family)

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2fge__assembly_1__model_1

2fge__assembly_1__model_1 | I(q)

2fge__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (2)

Crystal structure of presequence protease PreP from Arabidopsis thaliana

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

zinc metalloprotease (insulinase family)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2fge__assembly_1__model_1

2fge__assembly_1__model_1 | I(q)

2fge__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (2)