2rd5

Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana

Method: X-RAY DIFFRACTION

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

Acetylglutamate kinase-like protein

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	PII protein × 6 （Q9ZST4） ARGININE × 6 ADENOSINE-5'-DIPHOSPHATE × 6 N-ACETYL-L-GLUTAMATE × 6 MAGNESIUM ION × 9 ADENOSINE-5'-TRIPHOSPHATE × 6 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9SCL7_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–298； UniProt 51–347 Author chain B； PDBConstruct 2–298； UniProt 51–347

PII protein

Arabidopsis thaliana

UniProt Q9ZST4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Acetylglutamate kinase-like protein × 6 （Q9SCL7） ARGININE × 6 ADENOSINE-5'-DIPHOSPHATE × 6 N-ACETYL-L-GLUTAMATE × 6 MAGNESIUM ION × 9 ADENOSINE-5'-TRIPHOSPHATE × 6 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9ZST4_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–135； UniProt 63–196 Author chain D； PDBConstruct 2–135； UniProt 63–196

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	2rd5
Deposition date deposition_date	2007-09-21
Structure title title	Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana
Keywords keywords	;protein-protein complex, regulation of arginine biosynthesis, nitrogen metabolism, Kinase, Transferase, Transcription, Transcription regulation, PROTEIN BINDING ;; PROTEIN BINDING
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.

2rd5__assembly_1__model_1

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

Download this curve (.dat)

2rd5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rd5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.01 Å
Rg (electron density)	40.98 Å
Total Rg	41.46 Å
Atom count	18792
Residues	2445
Excluded volume	336120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rd5__assembly_1__model_1`	dodecameric （12）	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 (8)

Entity 1 Entity 1 polymer

Description description	Acetylglutamate kinase-like protein
Molecular weight formula_weight	31254.2 kDa
EC 编号 ec_number	2.7.2.8
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	6328

MTVSTPPSIATGNAPSPDYRVEILSESLPFIQKFRGKTIVVKYGGAAMTSPELKSSVVSDLVLLACVGLRPILVHGGGPDINRYLKQLNIPAEFRDGLRVTDATTMEIVSMVLVGKVNKNLVSLINAAGATAVGLSGHDGRLLTARPVPNSAQLGFVGEVARVDPSVLRPLVDYGYIPVIASVAADDSGQAYNINADTVAGELAAALGAEKLILLTDVAGILENKEDPSSLIKEIDIKGVKKMIEDGKVAGGMIPKVKCCIRSLAQGVKTASIIDGRRQHSLLHEIMSDEGAGTMITG

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PII protein
Molecular weight formula_weight	14779.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MQISSDYIPDSKFYKVEAIVRPWRIQQVSSALLKIGIRGVTVSDVRGFGAQGGSTERHGGSEFSEDKFVAKVKMEIVVKKDQVESVINTIIEGARTGEIGDGKIFVLPVSDVIRVRTGERGEKAEKMTGDMLSPS

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ARGININE
Molecular weight formula_weight	175.2 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

Entity 5 Entity 5 non-polymer

Description description	N-ACETYL-L-GLUTAMATE
Molecular weight formula_weight	189.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2rd5a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.0 — automated matches

Domain ID domain_id	d2rd5b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.0 — automated matches

Domain ID domain_id	d2rd5c_
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	d2rd5d_
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

CATH v4.4 (4 domains)

Domain ID domain_id	2rd5A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	2rd5B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	2rd5C00
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	2rd5D00
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	171.133 Å
Unit-cell length b length_b	171.133 Å
Unit-cell length c length_c	171.133 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	24

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2026
R_work r_work	0.2012
R_free r_free	0.2293

Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana

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

Acetylglutamate kinase-like protein

State in the Current Structure

Other States of the Same Protein in the Database

PII protein

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

2rd5__assembly_1__model_1

2rd5__assembly_1__model_1 | I(q)

2rd5__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 (8)

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 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana

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

Acetylglutamate kinase-like protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PII protein

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

2rd5__assembly_1__model_1

2rd5__assembly_1__model_1 | I(q)

2rd5__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 (8)

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 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)