1p3h

Crystal Structure of the Mycobacterium tuberculosis chaperonin 10 tetradecamer

Method: X-RAY DIFFRACTION

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

10 kDa chaperonin

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 7	CALCIUM ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 8 water × 7	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 7	(4S)-2-METHYL-2,4-PENTANEDIOL × 10 water × 5	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 14	CALCIUM ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 18 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CH10_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 1–99 Author chain B； PDBConstruct 1–99； UniProt 1–99 Author chain C； PDBConstruct 1–99； UniProt 1–99 Author chain D； PDBConstruct 1–99； UniProt 1–99 Author chain E； PDBConstruct 1–99； UniProt 1–99 Author chain F； PDBConstruct 1–99； UniProt 1–99 Author chain G； PDBConstruct 1–99； UniProt 1–99 Author chain H； PDBConstruct 1–99； UniProt 1–99 Author chain I； PDBConstruct 1–99； UniProt 1–99 Author chain J； PDBConstruct 1–99； UniProt 1–99 Author chain K； PDBConstruct 1–99； UniProt 1–99 Author chain L； PDBConstruct 1–99； UniProt 1–99 Author chain M； PDBConstruct 1–99； UniProt 1–99 Author chain N； PDBConstruct 1–99； UniProt 1–99

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	1p3h
Deposition date deposition_date	2003-04-17
Structure title title	Crystal Structure of the Mycobacterium tuberculosis chaperonin 10 tetradecamer
Keywords keywords	;BETA BARREL, ACIDIC CLUSTER, FLEXIBLE LOOP, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, CHAPERONE ;; CHAPERONE
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.

1p3h__assembly_2__model_1

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

Download this curve (.dat)

1p3h__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1p3h__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	30.90 Å
Rg (electron density)	30.04 Å
Total Rg	31.05 Å
Atom count	5316
Residues	689
Excluded volume	95394 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1p3h__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1p3h__assembly_2__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1p3h__assembly_3__model_1`	tetradecameric （14）	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	10 kDa chaperonin
Molecular weight formula_weight	10685.0 kDa
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
Atom count atom_count	10690

AKVNIKPLEDKILVQANEAETTTASGLVIPDTAKEKPQEGTVVAVGPGRWDEDGEKRIPLDVAEGDTVIYSKYGGTEIKYNGEEYLILSARDVLAVVSK

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	64

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d1p3ha_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hb_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hc_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hd_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3he_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hf_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hg_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hh_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hi_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hj_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hk_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hl_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hm_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

Domain ID domain_id	d1p3hn_
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.1 — GroES

CATH v4.4 (14 domains)

Domain ID domain_id	1p3hA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hF00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hG00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hH00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hI00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hJ00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hK00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hL00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hM00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	1p3hN00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

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Unit-cell length a length_a	76.460 Å
Unit-cell length b length_b	87.930 Å
Unit-cell length c length_c	124.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	28

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2600
R_work r_work	0.2590
R_free r_free	0.2800

Crystal Structure of the Mycobacterium tuberculosis chaperonin 10 tetradecamer

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

10 kDa chaperonin

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

1p3h__assembly_2__model_1

1p3h__assembly_2__model_1 | I(q)

1p3h__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

7. Citations (3)

Crystal Structure of the Mycobacterium tuberculosis chaperonin 10 tetradecamer

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

10 kDa chaperonin

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

1p3h__assembly_2__model_1

1p3h__assembly_2__model_1 | I(q)

1p3h__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

7. Citations (3)