SAXSdb — 2qr4

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

Peptidase M3B, oligoendopeptidase F

Enterococcus faecium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3XYC8_ENTFC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–579； UniProt 26–601 Author chain B； PDBConstruct 4–579； UniProt 26–601

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	2qr4
Deposition date deposition_date	2007-07-27
Structure title title	Crystal structure of oligoendopeptidase-F from Enterococcus faecium
Keywords keywords	;structural genomics, oligoendopeptidase F, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, 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.

2qr4__assembly_1__model_1

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

Download this curve (.dat)

2qr4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qr4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.80 Å
Rg (electron density)	34.38 Å
Total Rg	35.11 Å
Atom count	8308
Residues	1007
Excluded volume	147160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qr4__assembly_1__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	Peptidase M3B, oligoendopeptidase F
Molecular weight formula_weight	68498.3 kDa
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	8549

MSLSDQEFDEKYLELSEELKQSEKHKGTLDQGASQFLNAIEFVLRVYRQTEVIYVYAHLKNDQDTGNTDYQALYARASSLFSKVSEAVSWFEPEILQLSDDQIWQYFKEEPKLEVYRHYIQQIVDNRAHVLSAEQESLLAGAGEIFDASSDTFAVLNNADLVFPTIEGENGEIVQLSHGVYGQLLESTDRRVREAAFKGLYSVYEQFRNTFASTLGTHIKGHNFKAKVRNYSSAREASLSNNHIPESVYDTLVDVVNKHLPLLHRYMELRKRLLEVEKLHMYDLYTPVLGEAPITFTYEEAKEKALEALKPMGEEYMAIVEKAFSERWIDVVENKGKRSGAYSSGSYDTNPYILLNWHDTLDQLFTLVHEMGHSVHSYFTRSNQPYVYGDYSIFLAEIASTTNENILTEYLLETEKDPRVRAYVLNHYLDGFKGTVFRQTQFAEFEHFMHTEDEKGVPLTSEYLSDSYGKLNAKYYGPAVEEDPEIKFEWSRIPHFYYNYYVFQYSTGFSAASALAKKILNQEPEALENYLAYLKAGNSDYPVEVMKKAGVDMTQAAYIEDAMSMFEQRLNELEELIDREGHHHHHH

Source Source

Source organism organism	Enterococcus faecium
NCBI taxonomy ID ncbi_taxonomy_id	333849
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	188

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2qr4A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	70 — Oligopeptidase f, N-terminal domain

Domain ID domain_id	2qr4A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	830 — putative peptidase helix hairpin domain like

Domain ID domain_id	2qr4A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily	20 — Oligoendopeptidase f, C-terminal domain

Domain ID domain_id	2qr4B01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	70 — Oligopeptidase f, N-terminal domain

Domain ID domain_id	2qr4B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	830 — putative peptidase helix hairpin domain like

Domain ID domain_id	2qr4B03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily	20 — Oligoendopeptidase f, C-terminal domain

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Unit-cell length a length_a	133.142 Å
Unit-cell length b length_b	133.142 Å
Unit-cell length c length_c	171.619 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	39.040 Å
R factor r_factor	0.1910
R_work r_work	0.1880
R_free r_free	0.2440

Crystal structure of oligoendopeptidase-F from Enterococcus faecium

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

Peptidase M3B, oligoendopeptidase F

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

2qr4__assembly_1__model_1

2qr4__assembly_1__model_1 | I(q)

2qr4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of oligoendopeptidase-F from Enterococcus faecium

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

Peptidase M3B, oligoendopeptidase F

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

2qr4__assembly_1__model_1

2qr4__assembly_1__model_1 | I(q)

2qr4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)