3cc1

CRYSTAL STRUCTURE OF A PUTATIVE ALPHA-N-ACETYLGALACTOSAMINIDASE (BH1870) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

Method: X-RAY DIFFRACTION

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

Putative alpha-N-acetylgalactosaminidase

Bacillus halodurans C-125

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 12 IMIDAZOLE × 2 TRIETHYLENE GLYCOL × 10 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 2 GLYCEROL × 10 DI(HYDROXYETHYL)ETHER × 12 TETRAETHYLENE GLYCOL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KBQ5_BACHD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–433； UniProt 1–432 Author chain B； PDBConstruct 2–433； UniProt 1–432

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	3cc1
Deposition date deposition_date	2008-02-23
Structure title title	CRYSTAL STRUCTURE OF A PUTATIVE ALPHA-N-ACETYLGALACTOSAMINIDASE (BH1870) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION
Keywords keywords	;PUTATIVE ALPHA-N-ACETYLGALACTOSAMINIDASE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, 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.

3cc1__assembly_1__model_1

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

Download this curve (.dat)

3cc1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cc1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.22 Å
Rg (electron density)	37.69 Å
Total Rg	38.03 Å
Atom count	13854
Residues	1630
Excluded volume	247090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cc1__assembly_1__model_1`	tetrameric （4）	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 (9)

Entity 1 Entity 1 polymer

Description description	Putative alpha-N-acetylgalactosaminidase
Molecular weight formula_weight	50381.1 kDa
EC 编号 ec_number	3.2.1.49
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	7763

GMEVNRLSALTPPMGWNSWDCYGASVTEEEVLGNAEYMANHLKKYGWEYIVVDIQWYEPTANSSAYNPFAPLCMDEYGRLLPATNRFPSAKNGAGFKPLSDAIHDLGLKFGIHIMRGIPRQAVYENSPVLGSTKTAREIAHTNSICPWNTDMYGVDPTKEGAQSYYNSLFELYAQWGVDFVKVDDIAASRLYDTHLEEIKMIQRAIQACGRPMVLSLSPGPAPIKYAHHFKTNANMWRITDDFWDDWSLLYQMFERCEVWEKHIGTGHWPDCGMLPLGHIGIRSVDGPGGDRWTRFTKDEQLTMMNLWAICHSPLMFGGELRDNDEWTLSLLTNEGILSINQKSVLNRFVYREEDKVAWAANGRNGEAYVALFNLHDQQKTLQFRLDMVGIMETVQLFNVWDRSFLQSLAPSESFQIELKPHQSMMLKLSPDR

Source Source

Source organism organism	Bacillus halodurans C-125
NCBI taxonomy ID ncbi_taxonomy_id	272558
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
Molecular weight formula_weight	326.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	691

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3cc1A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3cc1A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	3cc1B01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3cc1B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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Unit-cell length a length_a	146.943 Å
Unit-cell length b length_b	146.943 Å
Unit-cell length c length_c	213.526 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	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	34.816 Å
R factor r_factor	0.1640
R_work r_work	0.1620
R_free r_free	0.1900

CRYSTAL STRUCTURE OF A PUTATIVE ALPHA-N-ACETYLGALACTOSAMINIDASE (BH1870) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

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

Putative alpha-N-acetylgalactosaminidase

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

3cc1__assembly_1__model_1

3cc1__assembly_1__model_1 | I(q)

3cc1__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 (9)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A PUTATIVE ALPHA-N-ACETYLGALACTOSAMINIDASE (BH1870) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

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

Putative alpha-N-acetylgalactosaminidase

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

3cc1__assembly_1__model_1

3cc1__assembly_1__model_1 | I(q)

3cc1__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 (9)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)