SAXSdb — 2q4d

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

Lysine decarboxylase-like protein At5g11950

Arabidopsis thaliana

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y5195_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–216； UniProt 2–216 Author chain B； PDBConstruct 2–216； UniProt 2–216

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	2q4d
Deposition date deposition_date	2007-05-31
Structure title title	Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, AT5G11950, LYSINE DECARBOXYLASE-LIKE PROTEIN, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2q4d__assembly_1__model_7

Assembly 1 · Model 7 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2q4d__assembly_1__model_7 | I(q)

100 plotted points; both axes use logarithmic scales.

2q4d__assembly_1__model_7 | P(r) · Pending

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

Rg（Guinier）	21.34 Å
Rg (electron density)	20.32 Å
Total Rg	21.01 Å
Atom count	2816
Residues	349
Excluded volume	50793 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q4d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2q4d__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2q4d__assembly_1__model_3`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2q4d__assembly_1__model_4`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2q4d__assembly_1__model_5`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2q4d__assembly_1__model_6`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2q4d__assembly_1__model_7`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2q4d__assembly_1__model_8`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2q4d__assembly_1__model_9`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2q4d__assembly_1__model_10`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`2q4d__assembly_1__model_11`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`2q4d__assembly_1__model_12`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`2q4d__assembly_1__model_13`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`2q4d__assembly_1__model_14`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`2q4d__assembly_1__model_15`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`2q4d__assembly_1__model_16`	dimeric （2）	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	Lysine decarboxylase-like protein At5g11950
Molecular weight formula_weight	24239.2 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	50160

SEDNQRSRFRKICVFCGSHSGHREVFSDAAIELGNELVKRKIDLVYGGGSVGLMGLISRRVYEGGLHVLGIIPKALMPIEISGETVGDVRVVADMHERKAAMAQEAEAFIALPGGYGTMEELLEMITWSQLGIHKKTVGLLNVDGYYNNLLALFDTGVEEGFIKPGARNIVVSAPTAKELMEKMEEYTPSHMHVASHESWKVEELGDYPGQENKPQ

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 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	319

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2q4da_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d2q4db_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

CATH v4.4 (2 domains)

Domain ID domain_id	2q4dA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	2q4dB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

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Unit-cell length a length_a	121.589 Å
Unit-cell length b length_b	80.427 Å
Unit-cell length c length_c	50.709 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.152 Å
Low-resolution limit resolution_low	34.350 Å
R factor r_factor	0.1520
R_work r_work	0.1520
R_free r_free	0.2070

Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950

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

Lysine decarboxylase-like protein At5g11950

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

2q4d__assembly_1__model_7

2q4d__assembly_1__model_7 | I(q)

2q4d__assembly_1__model_7 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950

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

Lysine decarboxylase-like protein At5g11950

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

2q4d__assembly_1__model_7

2q4d__assembly_1__model_7 | I(q)

2q4d__assembly_1__model_7 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)