SAXSdb — 2h5y

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

Molybdate-binding periplasmic protein

Xanthomonas axonopodis pv. citri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 MOLYBDATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 MOLYBDATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 MOLYBDATE ION × 1 water × 1	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 6 MOLYBDATE ION × 4 water × 4	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 MOLYBDATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8PHA1_XANAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–254； UniProt 25–258 Author chain B； PDBConstruct 21–254； UniProt 25–258 Author chain C； PDBConstruct 21–254； UniProt 25–258

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	2h5y
Deposition date deposition_date	2006-05-29
Structure title title	Crystallographic structure of the Molybdate-Binding Protein of Xanthomonas citri at 1.7 Ang resolution bound to molybdate
Keywords keywords	Molybdate-binding protein, ModA, Xanthomonas axonopodis pv. citri, METAL TRANSPORT; METAL TRANSPORT
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.

2h5y__assembly_4__model_1

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

Download this curve (.dat)

2h5y__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2h5y__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	30.92 Å
Rg (electron density)	30.18 Å
Total Rg	30.71 Å
Atom count	6908
Residues	930
Excluded volume	122710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2h5y__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2h5y__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2h5y__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2h5y__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2h5y__assembly_5__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 (4)

Entity 1 Entity 1 polymer

Description description	Molybdate-binding periplasmic protein
Molecular weight formula_weight	26696.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6036

MGSSHHHHHHSSGLVPRGSHQTAPVTVFAAASLKESMDEAATAYEKATGTPVRVSYAASSALARQIEQGAPADVFLSADLEWMDYLQQHGLVLPAQRHNLLGNTLVLVAPASSKLRVDPRAPGAIAKALGENGRLAVGQTASVPAGKYAAAALRKLGQWDSVSNRLAESESVRAALMLVSRGEAPLGIVYGSDARADAKVRVVATFPDDSHDAIVYPVAALKNSNNPATAAFVSWLGSKPAKAIFARRGFSLKD

Source Source

Source organism organism	Xanthomonas axonopodis pv. citri
NCBI taxonomy ID ncbi_taxonomy_id	190486
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MOLYBDATE ION
Molecular weight formula_weight	159.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	829

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2h5ya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.0 — automated matches

Domain ID domain_id	d2h5yb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.0 — automated matches

Domain ID domain_id	d2h5yc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2h5yA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	2h5yA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	2h5yB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	2h5yB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	2h5yC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	2h5yC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

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Unit-cell length a length_a	68.153 Å
Unit-cell length b length_b	172.138 Å
Unit-cell length c length_c	112.036 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	30.070 Å
R factor r_factor	0.1683
R_work r_work	0.1673
R_free r_free	0.2024

Crystallographic structure of the Molybdate-Binding Protein of Xanthomonas citri at 1.7 Ang resolution bound to molybdate

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

Molybdate-binding periplasmic 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

2h5y__assembly_4__model_1

2h5y__assembly_4__model_1 | I(q)

2h5y__assembly_4__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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystallographic structure of the Molybdate-Binding Protein of Xanthomonas citri at 1.7 Ang resolution bound to molybdate

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

Molybdate-binding periplasmic 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

2h5y__assembly_4__model_1

2h5y__assembly_4__model_1 | I(q)

2h5y__assembly_4__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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)