SAXSdb — 1o12

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

N-acetylglucosamine-6-phosphate deacetylase

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WZS1_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–376； UniProt 1–364 Author chain B； PDBConstruct 13–376； UniProt 1–364

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	1o12
Deposition date deposition_date	2002-10-15
Structure title title	Crystal structure of N-acetylglucosamine-6-phosphate deacetylase (TM0814) from Thermotoga maritima at 2.5 A resolution
Keywords keywords	;STRUCTURAL GENOMICS, TM0814, N-acetylglucosamine-6-phosphate deacetylase, JCSG, PSI, Protein Structure Initiative, Joint Center for Structural Genomics, 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.

1o12__assembly_1__model_1

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

Download this curve (.dat)

1o12__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1o12__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.90 Å
Rg (electron density)	30.04 Å
Total Rg	30.78 Å
Atom count	5622
Residues	710
Excluded volume	101510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1o12__assembly_1__model_1`	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 (3)

Entity 1 Entity 1 polymer

Description description	N-acetylglucosamine-6-phosphate deacetylase
Molecular weight formula_weight	42190.0 kDa
EC 编号 ec_number	3.5.1.25
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	5828

MGSDKIHHHHHHMIVEKVLIVDPIDGEFTGDVEIEEGKIVKVEKRECIPRGVLMPGFVDPHIHGVVGADTMNCDFSEMEEFLYSQGVTTFLATTVSTSLEKMKEILRKARDYILENPSTSLLGVHLEGPYISKEKKGAHSEKHIRPPSERELSEIDSPAKMLTFAPEIESSELLLRLVKRDIVLSAGHSIATFEEFMKFYKEGVKRITHFPNGLKPLHHREIGITGAGLLLDDVKLELICDGVHLSREMVKLVYKVKKANGIVLVTDSISAAGLKDGTTTLGDLVVKVKDGVPRLEDGTLAGSTLFFSQAVKNFRKFTGCSITELAKVSSYNSCVELGLDDRGRIAEGTRADLVLLDEDLNVVMTIKEGEVVFRSR

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	206

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1o12a1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.5 — N-acetylglucosamine-6-phosphate deacetylase, NagA

Domain ID domain_id	d1o12a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.10 — N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain

Domain ID domain_id	d1o12b1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.5 — N-acetylglucosamine-6-phosphate deacetylase, NagA

Domain ID domain_id	d1o12b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.10 — N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	1o12A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1o12A02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	1o12B01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1o12B02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

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Unit-cell length a length_a	85.070 Å
Unit-cell length b length_b	85.070 Å
Unit-cell length c length_c	206.010 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	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	42.530 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2510

Crystal structure of N-acetylglucosamine-6-phosphate deacetylase (TM0814) from Thermotoga maritima at 2.5 A resolution

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

N-acetylglucosamine-6-phosphate deacetylase

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

1o12__assembly_1__model_1

1o12__assembly_1__model_1 | I(q)

1o12__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of N-acetylglucosamine-6-phosphate deacetylase (TM0814) from Thermotoga maritima at 2.5 A resolution

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

N-acetylglucosamine-6-phosphate deacetylase

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

1o12__assembly_1__model_1

1o12__assembly_1__model_1 | I(q)

1o12__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)