SAXSdb — 7lkm

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

Pilus biogenesis protein

Xanthomonas axonopodis pv. citri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Type IV fimbriae assembly protein × 1 （Q8PND9） SULFATE ION × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Type IV fimbriae assembly protein × 1 （Q8PND9） SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8PHL2_XANAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–173； UniProt 12–163 Author chain B； PDBConstruct 22–173； UniProt 12–163

Type IV fimbriae assembly protein

Xanthomonas axonopodis pv. citri

UniProt Q8PND9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Pilus biogenesis protein × 1 （Q8PHL2） SULFATE ION × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Pilus biogenesis protein × 1 （Q8PHL2） SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8PND9_XANAC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–117； UniProt 1–117 Author chain D； PDBConstruct 1–117； UniProt 1–117

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	7lkm
Deposition date deposition_date	2021-02-02
Structure title title	The PilB(N-terminal_P70S mutant)-PilZ complex of the Type IV pilus from Xanthomonas citri
Keywords keywords	Type IV pilus, TRANSPORT PROTEIN; TRANSPORT 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.

7lkm__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7lkm__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7lkm__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.12 Å
Rg (electron density)	19.07 Å
Total Rg	20.06 Å
Atom count	1936
Residues	257
Excluded volume	34678 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7lkm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7lkm__assembly_2__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	Pilus biogenesis protein
Molecular weight formula_weight	18828.2 kDa
Mutation mutation	P70S
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	4417

MGSSHHHHHHSSGLVPRGSHMITGIARRLVQDGAVEEAVARSAMDQASAAKVPLPQWFAEKKLVTASQLAAANAVEFGMSLLDVSAFDASQNAVKLVSEELLQKHQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSALGDDE

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 polymer

Description description	Type IV fimbriae assembly protein
Molecular weight formula_weight	12443.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MSAMNARQGILSLALKDKPALYSAYMPFVKGGGIFVPTPKRYMLGDEVFLLLTLPDSSERLPVAGKVIWTTPAGAQGNRAAGIGVQFPDGPEGEAVRNKIETLLAGLTTSDKPTHTM

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 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	443

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7lkmC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	220 — predicted glycosyltransferase like domains

Domain ID domain_id	7lkmD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	220 — predicted glycosyltransferase like domains

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Unit-cell length a length_a	39.063 Å
Unit-cell length b length_b	122.408 Å
Unit-cell length c length_c	62.730 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.98 °
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	monoclinic

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	28.000 Å
R factor r_factor	0.1815
R_work r_work	0.1791
R_free r_free	0.2274

The PilB(N-terminal_P70S mutant)-PilZ complex of the Type IV pilus from Xanthomonas citri

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

Pilus biogenesis protein

State in the Current Structure

Other States of the Same Protein in the Database

Type IV fimbriae assembly 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

7lkm__assembly_2__model_1

7lkm__assembly_2__model_1 | I(q)

7lkm__assembly_2__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

The PilB(N-terminal_P70S mutant)-PilZ complex of the Type IV pilus from Xanthomonas citri

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

Pilus biogenesis 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

Type IV fimbriae assembly 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

7lkm__assembly_2__model_1

7lkm__assembly_2__model_1 | I(q)

7lkm__assembly_2__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)