3clq

Crystal structure of a conserved protein of unknown function from Enterococcus faecalis V583

Method: X-RAY DIFFRACTION

▼

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

Uncharacterized protein

Enterococcus faecalis

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q82ZN9_ENTFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–421； UniProt 57–474 Author chain B； PDBConstruct 4–421； UniProt 57–474 Author chain C； PDBConstruct 4–421； UniProt 57–474 Author chain D； PDBConstruct 4–421； UniProt 57–474

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	3clq
Deposition date deposition_date	2008-03-19
Structure title title	Crystal structure of a conserved protein of unknown function from Enterococcus faecalis V583
Keywords keywords	;APC29596.3, conserved protein of unknown function, Enterococcus faecalis V583, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

3clq__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3clq__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3clq__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.84 Å
Rg (electron density)	29.27 Å
Total Rg	29.64 Å
Atom count	6298
Residues	800
Excluded volume	112980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3clq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3clq__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 (3)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein
Molecular weight formula_weight	45954.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12653

SNAPTLYEKIQQANEEAVTRIIQSKPILVGFDKAINVMPDMTETTILHAGPPITYENMCGPMKGAVQGALVFEGLAKDLADADRVARSGAITFSPCHEHDAVGSMAGVTSPNMYVHIIKNETYGNTAFTNLSEQLAKVLRFGANDQSVVDRLIWMRDVLGPLLHDAMTFCPEGIDLRLMLSQALHMGDECHNRNVAGSTLLVQALTPYMVQTDFSREQLKEVFEFLGSSDYFSGPTWMGAAKCALDAGHNVENSTIVTTMCRNGVEFGIRVSGIGGNHWFTGPAQRVIGPMFAGYTQEDAGLDMGDSAITETYGVGGFAMAAAPAIVPLVGGTVAEALNYSKEMLEITTKENPNVTIPVLDFMGIPTGIDVLKVLETGMLPVINTAIAHKEPGIGMIGAGLTNPPANVFNEALKALVATIN

Source Source

Source organism organism	Enterococcus faecalis
NCBI taxonomy ID ncbi_taxonomy_id	226185
Host organism host_organism	Escherichia coli BL21

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	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

▼

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	3clqA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	3clqA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1710 — Enterococcus faecalis V583 fold
Homologous superfamily homologous superfamily	10 — Enterococcus faecalis V583 domain

Domain ID domain_id	3clqA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	660 — conserved protein of unknown function from Enterococcus faecalis V583

Domain ID domain_id	3clqA04
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1700 — v583 fold
Homologous superfamily homologous superfamily	10 — v583 domain like

Domain ID domain_id	3clqB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	3clqB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1710 — Enterococcus faecalis V583 fold
Homologous superfamily homologous superfamily	10 — Enterococcus faecalis V583 domain

Domain ID domain_id	3clqB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	660 — conserved protein of unknown function from Enterococcus faecalis V583

Domain ID domain_id	3clqB04
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1700 — v583 fold
Homologous superfamily homologous superfamily	10 — v583 domain like

Domain ID domain_id	3clqC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	3clqC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1710 — Enterococcus faecalis V583 fold
Homologous superfamily homologous superfamily	10 — Enterococcus faecalis V583 domain

Domain ID domain_id	3clqC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	660 — conserved protein of unknown function from Enterococcus faecalis V583

Domain ID domain_id	3clqC04
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1700 — v583 fold
Homologous superfamily homologous superfamily	10 — v583 domain like

Domain ID domain_id	3clqD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	3clqD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1710 — Enterococcus faecalis V583 fold
Homologous superfamily homologous superfamily	10 — Enterococcus faecalis V583 domain

Domain ID domain_id	3clqD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	660 — conserved protein of unknown function from Enterococcus faecalis V583

Domain ID domain_id	3clqD04
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1700 — v583 fold
Homologous superfamily homologous superfamily	10 — v583 domain like

▶

Unit-cell length a length_a	104.159 Å
Unit-cell length b length_b	61.613 Å
Unit-cell length c length_c	164.544 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	43.030 Å
R factor r_factor	0.1860
R_work r_work	0.1832
R_free r_free	0.2397

Crystal structure of a conserved protein of unknown function from Enterococcus faecalis V583

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

Uncharacterized protein

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

3clq__assembly_2__model_1

3clq__assembly_2__model_1 | I(q)

3clq__assembly_2__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

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of a conserved protein of unknown function from Enterococcus faecalis V583

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

Uncharacterized protein

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

3clq__assembly_2__model_1

3clq__assembly_2__model_1 | I(q)

3clq__assembly_2__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

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)