SAXSdb — 2yoc

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

PULLULANASE

KLEBSIELLA OXYTOCA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CALCIUM ION × 16 SULFATE ION × 28 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PULA_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–1070； UniProt 21–1089 Author chain B； PDBConstruct 2–1070； UniProt 21–1089

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	2yoc
Deposition date deposition_date	2012-10-23
Structure title title	Crystal structure of PulA from Klebsiella oxytoca
Keywords keywords	HYDROLASE, GLYCOSYL HYDROLASE, TYPE 2 SECRETION SYSTEMS; 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.

2yoc__assembly_1__model_1

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

Download this curve (.dat)

2yoc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yoc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	58.73 Å
Rg (electron density)	58.81 Å
Total Rg	59.00 Å
Atom count	32364
Residues	4124
Excluded volume	569450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yoc__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 (4)

Entity 1 Entity 1 polymer

Description description	PULLULANASE
Molecular weight formula_weight	118274.9 kDa
EC 编号 ec_number	3.2.1.41
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	16490

MDNGSSSSSSGNPDTPDNQDVVVRLPDVAVPGEAVTAVENQAVIHLVDIAGITSSSAADYSSKNLYLWNNETCDALSAPVADWNDVSTTPSGSDKYGPYWVIPLNKESGCINVIVRDGTDKLIDSDLRVAFGDFTDRTVSVIAGNSAVYDSRADAFRAAFGVALAEAHWVDKNTLLWPGGQDKPIVRLYYSHSSKVAADGEGKFTDRYLKLTPTTVSQQVSMRFPHLSSYAAFKLPDNANVDELLQGETVAIAAAEDGILISATQVQTAGVLDDAYAEAAEALSYGAQLADGGVTFRVWAPTAQQVDVVVYSADKKVIGSHPMTRDSASGAWSWQGGSDLKGAFYRYAMTVYHPQSRKVEQYEVTDPYAHSLSTNSEYSQVVDLNDSALKPDGWDNLTMPHAQKTKADLAKMTIHESHIRDLSAWDQTVPAELRGKYLALTAGDSNMVQHLKTLSASGVTHVELLPVFDLATVNEFSDKVADIQQPFSRLCEVNSAVKSSEFAGYCDSGSTVEEVLNQLKQSDSQDNPQVQALNTLVAQTDSYNWGYDPFHYTVPEGSYATDPEGTTRIKEFRTMIQAIKQDLGMNVIMDVVYNHTNAAGPTDRTSVLDKIVPWYYQRLNETTGSVESATCCSDSAPEHRMFAKLIADSLAVWTTDYKIDGFRFDLMGYHPKAQILSAWERIKALNPDIYFFGEGWDSNQSDRFEIASQINLKGTGIGTFSDRLRDSVRGGGPFDSGDALRQNQGIGSGAGVLPNELASLSDDQVRHLADLTRLGMAGNLADFVMIDKDGAAKKGSEIDYNGAPGGYAADPTEVVNYVSKHDNQTLWDMISYKASQEADLATRVRMQAVSLATVMLGQGIAFDQQGSELLRSKSFTRDSYDSGDWFNRVDYSLQDNNYNVGMPRISDDGSNYEVITRVKEMVATPGEAELKQMTAFYQELTELRKSSPLFTLGDGSAVMKRVDFRNTGSDQQAGLLVMTVDDGMKAGASLDSRLDGLVVAINAAPESRTLNEFAGETLQLSAIQQTAGENSLANGVQIAADGTVTLPAWSVAVLELPQGEAQGAGLPVSSYYHHHHHH

Source Source

Source organism organism	KLEBSIELLA OXYTOCA
NCBI taxonomy ID ncbi_taxonomy_id	571
Host organism host_organism	ESCHERICHIA COLI B

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	308

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	2yocA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1110 —

Domain ID domain_id	2yocA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1130 — Rab geranylgeranyltransferase alpha-subunit, insert domain

Domain ID domain_id	2yocA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2yocA04
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	2yocA05
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	2yocB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1110 —

Domain ID domain_id	2yocB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1130 — Rab geranylgeranyltransferase alpha-subunit, insert domain

Domain ID domain_id	2yocB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2yocB04
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	2yocB05
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	179.150 Å
Unit-cell length b length_b	179.150 Å
Unit-cell length c length_c	334.690 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 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.880 Å
Low-resolution limit resolution_low	42.170 Å
R factor r_factor	0.1733
R_work r_work	0.1711
R_free r_free	0.2131

Crystal structure of PulA from Klebsiella oxytoca

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

PULLULANASE

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

2yoc__assembly_1__model_1

2yoc__assembly_1__model_1 | I(q)

2yoc__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 (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) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of PulA from Klebsiella oxytoca

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

PULLULANASE

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

2yoc__assembly_1__model_1

2yoc__assembly_1__model_1 | I(q)

2yoc__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 (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) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)