1nl3

CRYSTAL STRUCTURE OF THE SECA PROTEIN TRANSLOCATION ATPASE FROM MYCOBACTERIUM TUBERCULOSIS in APO FORM

Method: X-RAY DIFFRACTION

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

PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECA1_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 32–922； UniProt 2–892 Author chain B； PDBConstruct 32–922； UniProt 2–892

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	1nl3
Deposition date deposition_date	2003-01-06
Structure title title	CRYSTAL STRUCTURE OF THE SECA PROTEIN TRANSLOCATION ATPASE FROM MYCOBACTERIUM TUBERCULOSIS in APO FORM
Keywords keywords	;PREPROTEIN TRANSLOCATION, ATPASE, TRANSMEMBRANE TRANSPORT, HELICASE-LIKE MOTOR DOMAIN, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, PROTEIN TRANSPORT ;; PROTEIN TRANSPORT
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.

1nl3__assembly_1__model_1

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

Download this curve (.dat)

1nl3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nl3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.59 Å
Rg (electron density)	46.40 Å
Total Rg	46.47 Å
Atom count	13279
Residues	1677
Excluded volume	235050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nl3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nl3__assembly_2__model_1`	tetrameric （4）	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 (2)

Entity 1 Entity 1 polymer

Description description	PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT
Molecular weight formula_weight	103463.9 kDa
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	14209

MKETAAAKFERQHMDSPDLGTLVPRGSMADILSKLLRLGEGRMVKRLKKVADYVGTLSDDVEKLTDAELRAKTDEFKRRLADQKNPETLDDLLPEAFAVAREAAWRVLDQRPFDVQVMGAAALHLGNVAEMKTGEGKTLTCVLPAYLNALAGNGVHIVTVNDYLAKRDSEWMGRVHRFLGLQVGVILATMTPDERRVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFSRDKDYIVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAELHEIYKLGVVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRGGVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDELMRRFNGAALETLLTRLNLPDDVPIEAKMVTRAIKSAQTQVEQQNFEVRKNVLKYDEVMNQQRKVIYAERRRILEGENLKDQALDMVRDVITAYVDGATGEGYAEDWDLDALWTALKTLYPVGITADSLTRKDHEFERDDLTREELLEALLKDAERAYAAREAELEEIAGEGAMRQLERNVLLNVIDRKWREHLYEMDYLKEGIGLRAMAQRDPLVEYQREGYDMFMAMLDGMKEESVGFLFNVTVEAVPAPPVAPAAEPAELAEFAAAAAAAAQQRSAVDGGARERAPSALRAKGVASESPA

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	930

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1nl3a1
Class class	a — All alpha proteins
Fold Fold fold	a.162 — Pre-protein crosslinking domain of SecA
Superfamily Superfamily superfamily	a.162.1 — Pre-protein crosslinking domain of SecA
Family Family family	a.162.1.1 — Pre-protein crosslinking domain of SecA

Domain ID domain_id	d1nl3a2
Class class	a — All alpha proteins
Fold Fold fold	a.172 — Helical scaffold and wing domains of SecA
Superfamily Superfamily superfamily	a.172.1 — Helical scaffold and wing domains of SecA
Family Family family	a.172.1.1 — Helical scaffold and wing domains of SecA

Domain ID domain_id	d1nl3a3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d1nl3a4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d1nl3a5
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	d1nl3b1
Class class	a — All alpha proteins
Fold Fold fold	a.162 — Pre-protein crosslinking domain of SecA
Superfamily Superfamily superfamily	a.162.1 — Pre-protein crosslinking domain of SecA
Family Family family	a.162.1.1 — Pre-protein crosslinking domain of SecA

Domain ID domain_id	d1nl3b2
Class class	a — All alpha proteins
Fold Fold fold	a.172 — Helical scaffold and wing domains of SecA
Superfamily Superfamily superfamily	a.172.1 — Helical scaffold and wing domains of SecA
Family Family family	a.172.1.1 — Helical scaffold and wing domains of SecA

Domain ID domain_id	d1nl3b3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d1nl3b4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d1nl3b5
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 (8 domains)

Domain ID domain_id	1nl3A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1nl3A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1440 — Pre-protein croslinking domain of SecA
Homologous superfamily homologous superfamily	10 — SecA, preprotein cross-linking domain

Domain ID domain_id	1nl3A03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1nl3A04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3060 — Helical scaffold and wing domains of SecA
Homologous superfamily homologous superfamily	10 — Helical scaffold and wing domains of SecA

Domain ID domain_id	1nl3B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1nl3B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1440 — Pre-protein croslinking domain of SecA
Homologous superfamily homologous superfamily	10 — SecA, preprotein cross-linking domain

Domain ID domain_id	1nl3B03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1nl3B04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3060 — Helical scaffold and wing domains of SecA
Homologous superfamily homologous superfamily	10 — Helical scaffold and wing domains of SecA

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Unit-cell length a length_a	206.196 Å
Unit-cell length b length_b	206.196 Å
Unit-cell length c length_c	295.412 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1959
R_work r_work	0.1925
R_free r_free	0.2588

CRYSTAL STRUCTURE OF THE SECA PROTEIN TRANSLOCATION ATPASE FROM MYCOBACTERIUM TUBERCULOSIS in APO FORM

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

PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT

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

1nl3__assembly_1__model_1

1nl3__assembly_1__model_1 | I(q)

1nl3__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF THE SECA PROTEIN TRANSLOCATION ATPASE FROM MYCOBACTERIUM TUBERCULOSIS in APO FORM

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

PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT

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

1nl3__assembly_1__model_1

1nl3__assembly_1__model_1 | I(q)

1nl3__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. Citations (1)