1rlo

Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12

Method: X-RAY DIFFRACTION

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

Phosphatase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YBIV_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–271； UniProt 1–271 Author chain B； PDBConstruct 1–271； UniProt 1–271 Author chain C； PDBConstruct 1–271； UniProt 1–271 Author chain D； PDBConstruct 1–271； UniProt 1–271

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	1rlo
Deposition date deposition_date	2003-11-26
Structure title title	Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12
Keywords keywords	beryllium trifluoride, HAD family, phospho-aspartate, 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.

1rlo__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1rlo__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rlo__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	19.32 Å
Rg (electron density)	18.35 Å
Total Rg	19.28 Å
Atom count	2140
Residues	267
Excluded volume	38267 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rlo__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rlo__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1rlo__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1rlo__assembly_4__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Phosphatase
Molecular weight formula_weight	30573.9 kDa
EC 编号 ec_number	3.1.3.-
Mutation mutation	S2A, S267Y
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	9003

MAVKVIVTDMDGTFLNDAKTYNQPRFMAQYQELKKRGIKFVVASGNQYYQLISFFPELKDEISFVAENGALVYEHGKQLFHGELTRHESRIVIGELLKDKQLNFVACGLQSAYVSENAPEAFVALMAKHYHRLKPVKDYQEIDDVLFKFSLNLPDEQIPLVIDKLHVALDGIMKPVTSGFGFIDLIIPGLHKANGISRLLKRWDLSPQNVVAIGDSGNDAEMLKMARYSFAMGNAAENIKQIARYATDDNNHEGALNVIQAVLDNTYPFNS

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	455

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1rloa_
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.108.1.10 — Predicted hydrolases Cof

Domain ID domain_id	d1rlob_
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.108.1.10 — Predicted hydrolases Cof

Domain ID domain_id	d1rloc_
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.108.1.10 — Predicted hydrolases Cof

Domain ID domain_id	d1rlod_
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.108.1.10 — Predicted hydrolases Cof

CATH v4.4 (8 domains)

Domain ID domain_id	1rloA01
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	1rloA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1240 — Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1rloB01
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	1rloB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1240 — Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1rloC01
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	1rloC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1240 — Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1rloD01
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	1rloD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1240 — Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	71.276 Å
Unit-cell length b length_b	91.195 Å
Unit-cell length c length_c	176.415 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	2.000 Å
Low-resolution limit resolution_low	19.850 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2510

Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12

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

Phosphatase

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

1rlo__assembly_4__model_1

1rlo__assembly_4__model_1 | I(q)

1rlo__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12

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

Phosphatase

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

1rlo__assembly_4__model_1

1rlo__assembly_4__model_1 | I(q)

1rlo__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)