2j9d

Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake

Method: X-RAY DIFFRACTION

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

HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059

METHANOCOCCUS JANNASCHII

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	ACETATE ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	ACETATE ION × 1 ADENOSINE MONOPHOSPHATE × 1 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	ACETATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 3	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	ACETATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 2 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y059_METJA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 3–114； UniProt 1–112 Author chain B； PDBConstruct 3–114； UniProt 1–112 Author chain C； PDBConstruct 3–114； UniProt 1–112 Author chain D； PDBConstruct 3–114； UniProt 1–112 Author chain F； PDBConstruct 3–114； UniProt 1–112 Author chain G； PDBConstruct 3–114； UniProt 1–112 Author chain H； PDBConstruct 3–114； UniProt 1–112 Author chain I； PDBConstruct 3–114； UniProt 1–112 Author chain J； PDBConstruct 3–114； UniProt 1–112 Author chain K； PDBConstruct 3–114； UniProt 1–112 Author chain L； PDBConstruct 3–114； UniProt 1–112 Author chain E； PDBConstruct 3–114； UniProt 1–112

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	2j9d
Deposition date deposition_date	2006-11-07
Structure title title	Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake
Keywords keywords	;EM SINGLE PARTICLE, NITROGEN METABOLISM, SIGNALLING, TRANSCRIPTION, MEMBRANE TRANSPORT, HYPOTHETICAL PROTEIN, TRANSCRIPTION REGULATION ;; MEMBRANE 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.

2j9d__assembly_1__model_1

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

Download this curve (.dat)

2j9d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2j9d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.86 Å
Rg (electron density)	19.37 Å
Total Rg	20.25 Å
Atom count	2499
Residues	321
Excluded volume	45150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2j9d__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2j9d__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2j9d__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2j9d__assembly_4__model_1`	trimeric （3）	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 (7)

Entity 1 Entity 1 polymer

Description description	HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
Molecular weight formula_weight	13311.5 kDa
Source method src_method	man
Copy count entity_count	11

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,F,G,H,I,J,K,L
Atom count atom_count	10840

GSMKKVEAIIRPEKLEIVKKALSDAGYVGMTVSEVKGRGVQGGIVERYRGREYIVDLIPKVKIELVVKEEDVDNVIDIICENARTGNPGDGKIFVIPVERVVRVRTKEEGKEALLEHHH

Source Source

Source organism organism	METHANOCOCCUS JANNASCHII
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
Molecular weight formula_weight	13327.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GSMKKVEAIIRPEKLEIVKKALSDAGYVGMTVSEVKGRGVQGGIVERYRGREYIVDLIPKVKIELVVKEEDVDNVIDIICENARTGNPGDGKIFVIPVERVVRVRTKEEGKEALEEHHH

Source Source

Source organism organism	METHANOCOCCUS JANNASCHII
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	694

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6. Fold Classification (SCOP + CATH) 34 domains

SCOP 2.08 (22 domains)

Domain ID domain_id	d2j9da1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9da2
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	d2j9db1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9db2
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	d2j9dc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9dc2
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	d2j9dd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9dd2
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	d2j9de_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9df1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9df2
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	d2j9dg1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9dg2
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	d2j9dh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9di1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9di2
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	d2j9dj1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9dj2
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	d2j9dk1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9dk2
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	d2j9dl1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.0 — automated matches

Domain ID domain_id	d2j9dl2
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 (12 domains)

Domain ID domain_id	2j9dA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2j9dL00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

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Unit-cell length a length_a	96.600 Å
Unit-cell length b length_b	107.030 Å
Unit-cell length c length_c	134.340 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	44

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	19.780 Å
R factor r_factor	0.2100
R_work r_work	0.2070
R_free r_free	0.2650

Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake

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

HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059

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

2j9d__assembly_1__model_1

2j9d__assembly_1__model_1 | I(q)

2j9d__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 34 domains

SCOP 2.08 (22 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake

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

HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059

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

2j9d__assembly_1__model_1

2j9d__assembly_1__model_1 | I(q)

2j9d__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 34 domains

SCOP 2.08 (22 domains)

CATH v4.4 (12 domains)

7. Citations (1)