SAXSdb — 3gzg

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

Molybdate-binding periplasmic protein; permease

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	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

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 22–253； UniProt 26–257 Author chain B； PDBConstruct 22–253； UniProt 26–257 Author chain C； PDBConstruct 22–253； UniProt 26–257

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	3gzg
Deposition date deposition_date	2009-04-07
Structure title title	Crystal structure of the Xanthomonas axonopodis pv. citri molybdate-binding protein (ModA) mutant (K127S)
Keywords keywords	molybdate complex, mutant K127S, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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.

3gzg__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3gzg__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gzg__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	18.61 Å
Rg (electron density)	17.74 Å
Total Rg	18.58 Å
Atom count	1718
Residues	232
Excluded volume	30506 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gzg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gzg__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3gzg__assembly_3__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	Molybdate-binding periplasmic protein; permease
Molecular weight formula_weight	26542.1 kDa
Mutation mutation	K127S
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	6015

MGSSHHHHHHSSGLVPRGSHMTAPVTVFAAASLKESMDEAATAYEKATGTPVRVSYAASSALARQIEQGAPADVFLSADLEWMDYLQQHGLVLPAQRHNLLGNTLVLVAPASSKLRVDPRAPGAIAKALGENGRLAVGQTASVPAGSYAAAALRKLGQWDSVSNRLAESESVRAALMLVSRGEAPLGIVYGSDARADAKVRVVATFPDDSHDAIVYPVAALKNSNNPATAAFVSWLGSKPAKAIFARRGFSLK

Source Source

Source organism organism	Xanthomonas axonopodis pv. citri
Common name common_name	Citrus canker
NCBI taxonomy ID ncbi_taxonomy_id	92829
Host organism host_organism	Escherichia coli

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	3

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	850

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3gzga_
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	d3gzgb_
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	d3gzgc_
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	3gzgA01
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	3gzgA02
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	3gzgB01
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	3gzgB02
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	3gzgC01
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	3gzgC02
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	67.075 Å
Unit-cell length b length_b	171.648 Å
Unit-cell length c length_c	113.861 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	1.550 Å
Low-resolution limit resolution_low	25.740 Å
R factor r_factor	0.2027
R_work r_work	0.2016
R_free r_free	0.2349

Crystal structure of the Xanthomonas axonopodis pv. citri molybdate-binding protein (ModA) mutant (K127S)

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

Molybdate-binding periplasmic protein; permease

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

3gzg__assembly_3__model_1

3gzg__assembly_3__model_1 | I(q)

3gzg__assembly_3__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)

Crystal structure of the Xanthomonas axonopodis pv. citri molybdate-binding protein (ModA) mutant (K127S)

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

Molybdate-binding periplasmic protein; permease

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

3gzg__assembly_3__model_1

3gzg__assembly_3__model_1 | I(q)

3gzg__assembly_3__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)