SAXSdb — 21dg

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

Poly-gamma-glutamate hydrolase

Bacillus phage PM1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	DI(HYDROXYETHYL)ETHER × 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	M4ZS88_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 37–236； UniProt 1–200

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	21dg
Deposition date deposition_date	2025-12-09
Last revision last_revision	2026-04-08
Structure title title	Crystal structure of poly-gamma-glutamate hydrolase from Bacillus phage PM1 in complex with a zinc ion
Keywords keywords	poly-gamma-glutamate hydrolase, Bacillus phage, metallo peptidase, zinc, 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.

21dg__assembly_1__model_1

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

Download this curve (.dat)

21dg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

21dg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.88 Å
Rg (electron density)	15.64 Å
Total Rg	16.69 Å
Atom count	1563
Residues	201
Excluded volume	27438 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`21dg__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Poly-gamma-glutamate hydrolase
Molecular weight formula_weight	27238.1 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	1770

MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLMADKYINYAALKAAETIGVDYRIQAAVQSDNFIIVAPHAGGIEVATTELTLATAGNDTSYYLFEGLNSSGNGDLHITSTHFDEPIALHMMQNHEFGLSYHGYADSENEMTIIGGLSDTLKEAVYKSLSSYGFNVAYATDRFTATDPNNIVNRAIRRGVQLELSTAQRKAFFEGGDWSKDNRMNRTDAFYNYVTAVRYALTLEHHHHHH

Source Source

Source organism organism	Bacillus phage PM1
NCBI taxonomy ID ncbi_taxonomy_id	547228
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
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	200

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Unit-cell length a length_a	70.210 Å
Unit-cell length b length_b	70.210 Å
Unit-cell length c length_c	123.280 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 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	tetragonal

Resolution resolution	1.380 Å
Low-resolution limit resolution_low	49.650 Å
R factor r_factor	0.1541
R_work r_work	0.1533
R_free r_free	0.1792

Crystal structure of poly-gamma-glutamate hydrolase from Bacillus phage PM1 in complex with a zinc ion

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

Poly-gamma-glutamate hydrolase

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

21dg__assembly_1__model_1

21dg__assembly_1__model_1 | I(q)

21dg__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of poly-gamma-glutamate hydrolase from Bacillus phage PM1 in complex with a zinc ion

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

Poly-gamma-glutamate hydrolase

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

21dg__assembly_1__model_1

21dg__assembly_1__model_1 | I(q)

21dg__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)