SAXSdb — 2pke

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

Haloacid delahogenase-like family hydrolase

Xanthomonas campestris pv. campestris

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 CHLORIDE ION × 3 DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8P4B4_XANCP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–251； UniProt 1–250 Author chain B； PDBConstruct 2–251； UniProt 1–250

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	2pke
Deposition date deposition_date	2007-04-17
Structure title title	Crystal structure of haloacid delahogenase-like family hydrolase (NP_639141.1) from Xanthomonas campestris at 1.81 A resolution
Keywords keywords	;NP_639141.1, haloacid delahogenase-like family hydrolase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, 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.

2pke__assembly_1__model_1

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

Download this curve (.dat)

2pke__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pke__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.15 Å
Rg (electron density)	24.09 Å
Total Rg	24.78 Å
Atom count	3536
Residues	452
Excluded volume	62908 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pke__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Haloacid delahogenase-like family hydrolase
Molecular weight formula_weight	28040.7 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	3847

GMTPIAQRDGQAIQLVGFDGDDTLWKSEDYYRTAEADFEAILSGYLDLGDSRMQQHLLAVERRNLKIFGYGAKGMTLSMIETAIELTEARIEARDIQRIVEIGRATLQHPVEVIAGVREAVAAIAADYAVVLITKGDLFHQEQKIEQSGLSDLFPRIEVVSEKDPQTYARVLSEFDLPAERFVMIGNSLRSDVEPVLAIGGWGIYTPYAVTWAHEQDHGVAADEPRLREVPDPSGWPAAVRALDAQAGRQQ

Source Source

Source organism organism	Xanthomonas campestris pv. campestris
NCBI taxonomy ID ncbi_taxonomy_id	340
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	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	255

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2pkeA01
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	2pkeA02
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	2pkeB01
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	2pkeB02
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	34.160 Å
Unit-cell length b length_b	107.100 Å
Unit-cell length c length_c	62.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	29.386 Å
R factor r_factor	0.1810
R_work r_work	0.1780
R_free r_free	0.2290

Crystal structure of haloacid delahogenase-like family hydrolase (NP_639141.1) from Xanthomonas campestris at 1.81 A resolution

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

Haloacid delahogenase-like family 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

2pke__assembly_1__model_1

2pke__assembly_1__model_1 | I(q)

2pke__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of haloacid delahogenase-like family hydrolase (NP_639141.1) from Xanthomonas campestris at 1.81 A resolution

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

Haloacid delahogenase-like family 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

2pke__assembly_1__model_1

2pke__assembly_1__model_1 | I(q)

2pke__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)