SAXSdb — 1rwi

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

Serine/threonine-protein kinase pknD

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CADMIUM ION × 10 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CADMIUM ION × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PKND_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–262； UniProt 403–664 Author chain B； PDBConstruct 1–262； UniProt 403–664

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	1rwi
Deposition date deposition_date	2003-12-16
Structure title title	Extracellular domain of Mycobacterium tuberculosis PknD
Keywords keywords	beta propeller, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, TRANSFERASE; TRANSFERASE
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.

1rwi__assembly_1__model_1

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

Download this curve (.dat)

1rwi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rwi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.70 Å
Rg (electron density)	17.17 Å
Total Rg	18.52 Å
Atom count	1912
Residues	254
Excluded volume	33937 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rwi__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rwi__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Serine/threonine-protein kinase pknD
Molecular weight formula_weight	28519.5 kDa
EC 编号 ec_number	2.7.1.37
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	3992

RPSWSPTQASGQTVLPFTGIDFRLSPSGVAVDSAGNVYVTSEGMYGRVVKLATGSTGTTVLPFNGLYQPQGLAVDGAGTVYVTDFNNRVVTLAAGSNNQTVLPFDGLNYPEGLAVDTQGAVYVADRGNNRVVKLAAGSKTQTVLPFTGLNDPDGVAVDNSGNVYVTDTDNNRVVKLEAESNNQVVLPFTDITAPWGIAVDEAGTVYVTEHNTNQVVKLLAGSTTSTVLPFTGLNTPLAVAVDSDRTVYVADRGNDRVVKLTSLEHHHHHH

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1rwia1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.9 — NHL repeat
Family Family family	b.68.9.1 — NHL repeat

Domain ID domain_id	d1rwia2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1rwib1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.9 — NHL repeat
Family Family family	b.68.9.1 — NHL repeat

Domain ID domain_id	d1rwib2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1rwiA00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	1rwiB00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

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Unit-cell length a length_a	43.940 Å
Unit-cell length b length_b	94.580 Å
Unit-cell length c length_c	71.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.10 °
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	1.800 Å
Low-resolution limit resolution_low	15.400 Å
R factor r_factor	0.1930
R_work r_work	0.1900
R_free r_free	0.2200

Extracellular domain of Mycobacterium tuberculosis PknD

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

Serine/threonine-protein kinase pknD

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

1rwi__assembly_1__model_1

1rwi__assembly_1__model_1 | I(q)

1rwi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Extracellular domain of Mycobacterium tuberculosis PknD

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

Serine/threonine-protein kinase pknD

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

1rwi__assembly_1__model_1

1rwi__assembly_1__model_1 | I(q)

1rwi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)