SAXSdb — 2evr

▼

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

COG0791: Cell wall-associated hydrolases (invasion-associated proteins)

Nostoc punctiforme

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 2 SODIUM ION × 2 1,2-ETHANEDIOL × 10 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2J9B4_NOSP7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–246； UniProt 1–234

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	2evr
Deposition date deposition_date	2005-10-31
Structure title title	CRYSTAL STRUCTURE OF A PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE (NPUN_R0659) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.60 A RESOLUTION
Keywords keywords	;PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, HYDROLASE ;; HYDROLASE
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.

2evr__assembly_1__model_1

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

Download this curve (.dat)

2evr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2evr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.77 Å
Rg (electron density)	25.25 Å
Total Rg	25.82 Å
Atom count	3472
Residues	440
Excluded volume	61505 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2evr__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	COG0791: Cell wall-associated hydrolases (invasion-associated proteins)
Molecular weight formula_weight	27591.1 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	2148

MGSDKIHHHHHHMVRLSEAEVQNPKLGEYQCLADLNLFDSPECTRLATQSASGRHLWVTSNHQNLAVEVYLCEDDYPGWLSLSDFDSLQPATVPYQAATFSESEIKKLLAEVIAFTQKAMQQSNYYLWGGTVGPNYDCSGLMQAAFASVGIWLPRDAYQQEGFTQPITIAELVAGDLVFFGTSQKATHVGLYLADGYYIHSSGKDQGRDGIGIDILSEQGDAVSLSYYQQLRGAGRVFKSYEPQRR

Source Source

Source organism organism	Nostoc punctiforme
NCBI taxonomy ID ncbi_taxonomy_id	63737
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	290

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2evra1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.11 — Prokaryotic SH3-related domain
Family Family family	b.34.11.3 — Spr N-terminal domain-like

Domain ID domain_id	d2evra2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.16 — NlpC/P60

CATH v4.4 (2 domains)

Domain ID domain_id	2evrA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	2evrA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1720 — endopeptidase fold (from Nostoc punctiforme)
Homologous superfamily homologous superfamily	10 — endopeptidase domain like (from Nostoc punctiforme)

▶

Unit-cell length a length_a	90.470 Å
Unit-cell length b length_b	90.470 Å
Unit-cell length c length_c	93.810 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 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	28.710 Å
R factor r_factor	—
R_work r_work	0.1590
R_free r_free	0.1760

CRYSTAL STRUCTURE OF A PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE (NPUN_R0659) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.60 A RESOLUTION

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

COG0791: Cell wall-associated hydrolases (invasion-associated proteins)

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

2evr__assembly_1__model_1

2evr__assembly_1__model_1 | I(q)

2evr__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE (NPUN_R0659) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.60 A RESOLUTION

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

COG0791: Cell wall-associated hydrolases (invasion-associated proteins)

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

2evr__assembly_1__model_1

2evr__assembly_1__model_1 | I(q)

2evr__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)