SAXSdb — 5a0p

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

ZINC METALLOPROTEASE ZMP1

CLOSTRIDIUM DIFFICILE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ZMP1_PEPD6
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–198； UniProt 27–220 Author chain B； PDBConstruct 5–198； UniProt 27–220

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	5a0p
Deposition date deposition_date	2015-04-22
Structure title title	Apo-structure of metalloprotease Zmp1 from Clostridium difficile
Keywords keywords	HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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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.

5a0p__assembly_1__model_1

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

Download this curve (.dat)

5a0p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5a0p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.46 Å
Rg (electron density)	16.21 Å
Total Rg	17.29 Å
Atom count	3043
Residues	195
Excluded volume	27246 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5a0p__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5a0p__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ZINC METALLOPROTEASE ZMP1
Molecular weight formula_weight	21983.7 kDa
EC 编号 ec_number	3.4.24.-
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	6714

GSHMDSTTIQQNKDTLSQIVVFPTGNYDKNEANAMVNRLANIDGKYLNALKQNNLKIKLLSGKLTDEKEYAYLKGVVPKGWEGTGKTWDDVPGLGGSTVALRIGFSNKGKGHDAINLELHETAHAIDHIVLNDISKSAQFKQIFAKEGRSLGNVNYLGVYPEEFFAESFAYYYLNQDTNSKLKSACPQTYSFLQNLAK

Source Source

Source organism organism	CLOSTRIDIUM DIFFICILE
NCBI taxonomy ID ncbi_taxonomy_id	272563
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	532

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Unit-cell length a length_a	43.169 Å
Unit-cell length b length_b	71.769 Å
Unit-cell length c length_c	117.798 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	1.398 Å
Low-resolution limit resolution_low	45.530 Å
R factor r_factor	0.1573
R_work r_work	0.1560
R_free r_free	0.1817

Apo-structure of metalloprotease Zmp1 from Clostridium difficile

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

ZINC METALLOPROTEASE ZMP1

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

5a0p__assembly_1__model_1

5a0p__assembly_1__model_1 | I(q)

5a0p__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

Apo-structure of metalloprotease Zmp1 from Clostridium difficile

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

ZINC METALLOPROTEASE ZMP1

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

5a0p__assembly_1__model_1

5a0p__assembly_1__model_1 | I(q)

5a0p__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)