4lrl

Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dTTP

Method: X-RAY DIFFRACTION

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

HD domain 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 4	NICKEL (II) ION × 4 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 4 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 THYMIDINE-5'-TRIPHOSPHATE × 2 MALONATE ION × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	NICKEL (II) ION × 2 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 THYMIDINE-5'-TRIPHOSPHATE × 1 MALONATE ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	NICKEL (II) ION × 2 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 2 THYMIDINE-5'-TRIPHOSPHATE × 1 MALONATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q836G9_ENTFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–480； UniProt 1–456 Author chain B； PDBConstruct 25–480； UniProt 1–456 Author chain C； PDBConstruct 25–480； UniProt 1–456 Author chain D； PDBConstruct 25–480； UniProt 1–456

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	4lrl
Deposition date deposition_date	2013-07-19
Structure title title	Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dTTP
Keywords keywords	;Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, HD Domain, Phosphohydrolase, dNTPase, Allosteric Regulation, METAL BINDING PROTEIN, 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.

4lrl__assembly_2__model_1

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

Download this curve (.dat)

4lrl__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4lrl__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.96 Å
Rg (electron density)	29.02 Å
Total Rg	29.87 Å
Atom count	7485
Residues	896
Excluded volume	132690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4lrl__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4lrl__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4lrl__assembly_3__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 (7)

Entity 1 Entity 1 polymer

Description description	HD domain protein
Molecular weight formula_weight	55886.0 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	15805

MHHHHHHSSGVDLGTENLYFQSNAMTIPYKEQRLPIEKVFRDPVHNYIHVQHQVILDLINSAEVQRLRRIKQLGTSSFTFHGAEHSRFSHSLGVYEITRRICEIFQRNYSVERLGENGWNDDERLITLCAALLHDVGHGPYSHTFEHIFDTNHEAITVQIITSPETEVYQILNRVSADFPEKVASVITKQYPNPQVVQMISSQIDADRMDYLLRDAYFTGTEYGTFDLTRILRVIRPYKGGIAFAMNGMHAVEDYIVSRYQMYVQVYFHPVSRGMEVILDHLLHRAKELFENPEFDYDLQASLLVPFFKGDFTLQEYLKLDDGVLSTYFTQWMDVPDSILGDLAKRFLMRKPLKSATFTNEKESAATIAYLRELIEKVGFNPKYYTAINSSYDLPYDFYRPNKDRHRTQIELMQKDGSLVELATVSPLVAALAGQSQGDERFYFPKEMLDQGNKKHYDLFDETYREFSSYIHNGALVLKK

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	THYMIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	482.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	734

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d4lrla1
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

Domain ID domain_id	d4lrla2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4lrlb_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

Domain ID domain_id	d4lrlc_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

Domain ID domain_id	d4lrld_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

CATH v4.4 (8 domains)

Domain ID domain_id	4lrlA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	4lrlA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4lrlB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	4lrlB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4lrlC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	4lrlC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4lrlD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	4lrlD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	91.541 Å
Unit-cell length b length_b	144.625 Å
Unit-cell length c length_c	155.560 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	29.860 Å
R factor r_factor	0.1869
R_work r_work	0.1844
R_free r_free	0.2346

Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dTTP

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

HD domain 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

4lrl__assembly_2__model_1

4lrl__assembly_2__model_1 | I(q)

4lrl__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dTTP

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

HD domain 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

4lrl__assembly_2__model_1

4lrl__assembly_2__model_1 | I(q)

4lrl__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

CATH v4.4 (8 domains)

7. Citations (1)