1rdf

G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate

Method: X-RAY DIFFRACTION

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

phosphonoacetaldehyde hydrolase

Bacillus cereus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 ETHANESULFONIC ACID × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 ETHANESULFONIC ACID × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 ETHANESULFONIC ACID × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 ETHANESULFONIC ACID × 4 water × 4	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 ETHANESULFONIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O31156_BACCE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–267； UniProt 1–267 Author chain B； PDBConstruct 1–267； UniProt 1–267 Author chain C； PDBConstruct 1–267； UniProt 1–267 Author chain D； PDBConstruct 1–267； UniProt 1–267 Author chain E； PDBConstruct 1–267； UniProt 1–267 Author chain F； PDBConstruct 1–267； UniProt 1–267

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	1rdf
Deposition date deposition_date	2003-11-05
Structure title title	G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate
Keywords keywords	haloacid dehalogenase, specificity loop, phosphonatase, Schiff-base, 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.

1rdf__assembly_1__model_1

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

Download this curve (.dat)

1rdf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rdf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.50 Å
Rg (electron density)	31.41 Å
Total Rg	31.74 Å
Atom count	4215
Residues	526
Excluded volume	75459 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rdf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rdf__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1rdf__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1rdf__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1rdf__assembly_5__model_1`	tetrameric （4）	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	phosphonoacetaldehyde hydrolase
Molecular weight formula_weight	30550.2 kDa
Mutation mutation	G50P
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	12927

MDRMKIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMPLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIEKQELIIS

Source Source

Source organism organism	Bacillus cereus
NCBI taxonomy ID ncbi_taxonomy_id	1396
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	6

Entity 3 Entity 3 non-polymer

Description description	ETHANESULFONIC ACID
Molecular weight formula_weight	110.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	286

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1rdfa_
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.108.1.3 — Phosphonoacetaldehyde hydrolase-like

Domain ID domain_id	d1rdfb_
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.108.1.3 — Phosphonoacetaldehyde hydrolase-like

Domain ID domain_id	d1rdfc_
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.108.1.3 — Phosphonoacetaldehyde hydrolase-like

Domain ID domain_id	d1rdfd_
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.108.1.3 — Phosphonoacetaldehyde hydrolase-like

Domain ID domain_id	d1rdfe_
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.108.1.3 — Phosphonoacetaldehyde hydrolase-like

Domain ID domain_id	d1rdff_
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.108.1.3 — Phosphonoacetaldehyde hydrolase-like

CATH v4.4 (12 domains)

Domain ID domain_id	1rdfA01
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	1rdfA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	240 — Putative phosphatase; domain 2

Domain ID domain_id	1rdfB01
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	1rdfB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	240 — Putative phosphatase; domain 2

Domain ID domain_id	1rdfC01
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	1rdfC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	240 — Putative phosphatase; domain 2

Domain ID domain_id	1rdfD01
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	1rdfD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	240 — Putative phosphatase; domain 2

Domain ID domain_id	1rdfE01
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	1rdfE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	240 — Putative phosphatase; domain 2

Domain ID domain_id	1rdfF01
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	1rdfF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	240 — Putative phosphatase; domain 2

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Unit-cell length a length_a	181.714 Å
Unit-cell length b length_b	147.348 Å
Unit-cell length c length_c	131.308 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	125.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	34.090 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2600

G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate

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

phosphonoacetaldehyde hydrolase

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

1rdf__assembly_1__model_1

1rdf__assembly_1__model_1 | I(q)

1rdf__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 (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) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)

G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate

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

phosphonoacetaldehyde hydrolase

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

1rdf__assembly_1__model_1

1rdf__assembly_1__model_1 | I(q)

1rdf__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 (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) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)