SAXSdb — 1yv9

▼

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

hydrolase, haloacid dehalogenase family

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	PHOSPHATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q836C7_ENTFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–256； UniProt 4–256 Author chain B； PDBConstruct 4–256； UniProt 4–256

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	1yv9
Deposition date deposition_date	2005-02-15
Structure title title	Crystal structure of a HAD-like phosphatase from Enterococcus faecalis V583
Keywords keywords	;Hypothetical protein, hydrolase haloacid dehalogenase, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, 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.

1yv9__assembly_1__model_1

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

Download this curve (.dat)

1yv9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yv9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.73 Å
Rg (electron density)	23.69 Å
Total Rg	24.52 Å
Atom count	3984
Residues	514
Excluded volume	71502 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yv9__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 (3)

Entity 1 Entity 1 polymer

Description description	hydrolase, haloacid dehalogenase family
Molecular weight formula_weight	29067.9 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	4156

MSLDYQGYLIDLDGTIYLGKEPIPAGKRFVERLQEKDLPFLFVTNNTTKSPETVAQRLANEFDIHVPASLVYTATLATIDYMKEANRGKKVFVIGEAGLIDLILEAGFEWDETNPDYVVVGLDTELSYEKVVLATLAIQKGALFIGTNPDKNIPTERGLLPGAGSVVTFVETATQTKPVYIGKPKAIIMERAIAHLGVEKEQVIMVGDNYETDIQSGIQNGIDSLLVTSGFTPKSAVPTLPTPPTYVVDSLDEWTFEGHHHHHH

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	PHOSPHATE ION
Molecular weight formula_weight	95.0 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	172

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1yv9a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.14 — NagD-like

Domain ID domain_id	d1yv9a2
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	d1yv9a3
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	d1yv9b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.14 — NagD-like

Domain ID domain_id	d1yv9b3
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	d1yv9b4
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

CATH v4.4 (4 domains)

Domain ID domain_id	1yv9A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1yv9A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1yv9B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1yv9B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

▶

Unit-cell length a length_a	117.628 Å
Unit-cell length b length_b	126.114 Å
Unit-cell length c length_c	112.634 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	47.120 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2800

Crystal structure of a HAD-like phosphatase from Enterococcus faecalis V583

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

hydrolase, haloacid dehalogenase family

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

1yv9__assembly_1__model_1

1yv9__assembly_1__model_1 | I(q)

1yv9__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 (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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a HAD-like phosphatase from Enterococcus faecalis V583

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

hydrolase, haloacid dehalogenase family

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

1yv9__assembly_1__model_1

1yv9__assembly_1__model_1 | I(q)

1yv9__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 (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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)