SAXSdb — 3g9k

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

Capsule biosynthesis protein capD

Bacillus anthracis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLUTAMIC ACID × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAPD_BACAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain D； PDBConstruct 1–323； UniProt 29–351 Author chain L； PDBConstruct 1–323； UniProt 29–351 Author chain F； PDBConstruct 1–177； UniProt 352–528 Author chain S； PDBConstruct 1–177； UniProt 352–528

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	3g9k
Deposition date deposition_date	2009-02-13
Structure title title	Crystal structure of Bacillus anthracis transpeptidase enzyme CapD
Keywords keywords	;CapD protein, Bacillus anthracis, The Great Lakes Regional Center of Excellence, GLRCE, Capsule biogenesis/degradation, Virulence, 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.

3g9k__assembly_1__model_1

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

Download this curve (.dat)

3g9k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3g9k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.44 Å
Rg (electron density)	21.40 Å
Total Rg	22.35 Å
Atom count	3469
Residues	433
Excluded volume	62297 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3g9k__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3g9k__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	Capsule biosynthesis protein capD
Molecular weight formula_weight	36223.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,D
Atom count atom_count	7489

FNKIKDSVKQKIDSMGDKGTYGVSASHPLAVEEGMKVLKNGGSAVDAAIVVSYVLGVVELHASGIGGGGGMLIISKDKETFIDYRETTPYFTGNQKPHIGVPGFVAGMEYIHDNYGSLPMGELLQPAINYAEKGFKVDDSLTMRLDLAKPRIYSDKLSIFYPNGEPIETGETLIQTDLARTLKKIQKEGAKGFYEGGVARAISKTAKISLEDIKGYKVEVRKPVKGNYMGYDVYTAPPPFSGVTLLQMLKLAEKKEVYKDVDHTATYMSKMEEISRIAYQDRKKNLGDPNYVNMDPNKMVSDKYISTMKNENGDALSEAEHES

Source Source

Source organism organism	Bacillus anthracis
NCBI taxonomy ID ncbi_taxonomy_id	1392
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Capsule biosynthesis protein capD
Molecular weight formula_weight	19594.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S,F

TTHFVIIDRDGTVVSSTNTLSNFFGTGKYTAGFFLNNQLQNFGSEGFNSYEPGKRSRTFMAPTVLKKDGETIGIGSPGGNRIPQILTPILDKYTHGKGSLQDIINEYRFTFEKNTAYTEIQLSSEVKNELSRKGLNVKKKVSPAFFGGVQALIKDERDNVITGAGDGRRNGTWKSNK

Source Source

Source organism organism	Bacillus anthracis
NCBI taxonomy ID ncbi_taxonomy_id	1392
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLUTAMIC ACID
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	555

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3g9kD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	3g9kF01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	40 — Gamma-glutamyltranspeptidase, small (S) subunit

Domain ID domain_id	3g9kL02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	3g9kS01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	40 — Gamma-glutamyltranspeptidase, small (S) subunit

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Unit-cell length a length_a	52.668 Å
Unit-cell length b length_b	120.621 Å
Unit-cell length c length_c	77.375 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.87 °
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	1.790 Å
Low-resolution limit resolution_low	40.690 Å
R factor r_factor	0.1988
R_work r_work	0.1965
R_free r_free	0.2417

Crystal structure of Bacillus anthracis transpeptidase enzyme CapD

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

Capsule biosynthesis protein capD

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

3g9k__assembly_1__model_1

3g9k__assembly_1__model_1 | I(q)

3g9k__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Bacillus anthracis transpeptidase enzyme CapD

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

Capsule biosynthesis protein capD

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

3g9k__assembly_1__model_1

3g9k__assembly_1__model_1 | I(q)

3g9k__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)