2q42

Ensemble refinement of the protein crystal structure of glyoxalase II from Arabidopsis thaliana gene At2g31350

Method: X-RAY DIFFRACTION

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

Putative hydroxyacylglutathione hydrolase 2

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 FE (III) ION × 1 ACETIC ACID × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 FE (III) ION × 1 ACETIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLO2N_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–254； UniProt 72–324 Author chain B； PDBConstruct 2–254； UniProt 72–324

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	2q42
Deposition date deposition_date	2007-05-31
Structure title title	Ensemble refinement of the protein crystal structure of glyoxalase II from Arabidopsis thaliana gene At2g31350
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, AT2G31350, METALLO-HYDROLASE, ZINC/IRON BINUCLEAR CENTER, B-LACTAMASE FOLD, THIOESTER HYDROLASE, mitochondrial isozyme, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG, HYDROLASE ;; HYDROLASE
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.

2q42__assembly_2__model_4

Assembly 2 · Model 4 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2q42__assembly_2__model_4 | I(q)

100 plotted points; both axes use logarithmic scales.

2q42__assembly_2__model_4 | P(r) · Pending

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

Rg（Guinier）	19.05 Å
Rg (electron density)	18.11 Å
Total Rg	18.95 Å
Atom count	1984
Residues	254
Excluded volume	35250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q42__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2q42__assembly_1__model_2`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2q42__assembly_1__model_3`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2q42__assembly_1__model_4`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2q42__assembly_1__model_5`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2q42__assembly_1__model_6`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2q42__assembly_1__model_7`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2q42__assembly_1__model_8`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2q42__assembly_1__model_9`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2q42__assembly_1__model_10`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`2q42__assembly_1__model_11`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`2q42__assembly_1__model_12`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`2q42__assembly_1__model_13`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`2q42__assembly_1__model_14`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`2q42__assembly_1__model_15`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`2q42__assembly_1__model_16`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2q42__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	2	`2q42__assembly_2__model_2`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	3	`2q42__assembly_2__model_3`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	4	`2q42__assembly_2__model_4`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	5	`2q42__assembly_2__model_5`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	6	`2q42__assembly_2__model_6`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	7	`2q42__assembly_2__model_7`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	8	`2q42__assembly_2__model_8`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	9	`2q42__assembly_2__model_9`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	10	`2q42__assembly_2__model_10`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	11	`2q42__assembly_2__model_11`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	12	`2q42__assembly_2__model_12`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	13	`2q42__assembly_2__model_13`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	14	`2q42__assembly_2__model_14`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	15	`2q42__assembly_2__model_15`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	16	`2q42__assembly_2__model_16`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	Putative hydroxyacylglutathione hydrolase 2
Molecular weight formula_weight	28221.1 kDa
EC 编号 ec_number	3.1.2.6
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	72352

MQIELVPCLKDNYAYILHDEDTGTVGVVDPSEAEPIIDSLKRSGRNLTYILNTHHHYDHTGGNLELKDRYGAKVIGSAMDKDRIPGIDMALKDGDKWMFAGHEVHVMDTPGHTKGHISLYFPGSRAIFTGDTMFSLSCGKLFEGTPKQMLASLQKITSLPDDTSIYCGHEYTLSNSKFALSLEPNNEVLQSYAAHVAELRSKKLPTIPTTVKMEKACNPFLRSSNTDIRRALRIPEAADEAEALGIIRKAKDDF

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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	547

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2q42a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.2 — Glyoxalase II (hydroxyacylglutathione hydrolase)

Domain ID domain_id	d2q42a3
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	d2q42b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.2 — Glyoxalase II (hydroxyacylglutathione hydrolase)

Domain ID domain_id	d2q42b3
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 (2 domains)

Domain ID domain_id	2q42A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	2q42B00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

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Unit-cell length a length_a	68.494 Å
Unit-cell length b length_b	58.782 Å
Unit-cell length c length_c	69.049 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.742 Å
Low-resolution limit resolution_low	32.970 Å
R factor r_factor	0.1470
R_work r_work	0.1470
R_free r_free	0.1930

Ensemble refinement of the protein crystal structure of glyoxalase II from Arabidopsis thaliana gene At2g31350

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

Putative hydroxyacylglutathione hydrolase 2

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

2q42__assembly_2__model_4

2q42__assembly_2__model_4 | I(q)

2q42__assembly_2__model_4 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Ensemble refinement of the protein crystal structure of glyoxalase II from Arabidopsis thaliana gene At2g31350

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

Putative hydroxyacylglutathione hydrolase 2

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

2q42__assembly_2__model_4

2q42__assembly_2__model_4 | I(q)

2q42__assembly_2__model_4 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)