3fvt

Crystal Structure of Acetyl Xylan Esterase from Bacillus pumilus, monoclinic crystal form II

Method: X-RAY DIFFRACTION

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

Acetyl xylan esterase

Bacillus pumilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	CHLORIDE ION × 12 GLYCEROL × 1 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	CHLORIDE ION × 12 GLYCEROL × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9K5F2_BACPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–320； UniProt 1–320 Author chain B； PDBConstruct 1–320； UniProt 1–320 Author chain C； PDBConstruct 1–320； UniProt 1–320 Author chain D； PDBConstruct 1–320； UniProt 1–320 Author chain E； PDBConstruct 1–320； UniProt 1–320 Author chain F； PDBConstruct 1–320； UniProt 1–320 Author chain G； PDBConstruct 1–320； UniProt 1–320 Author chain H； PDBConstruct 1–320； UniProt 1–320 Author chain I； PDBConstruct 1–320； UniProt 1–320 Author chain L； PDBConstruct 1–320； UniProt 1–320 Author chain M； PDBConstruct 1–320； UniProt 1–320 Author chain N； PDBConstruct 1–320； UniProt 1–320

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	3fvt
Deposition date deposition_date	2009-01-16
Structure title title	Crystal Structure of Acetyl Xylan Esterase from Bacillus pumilus, monoclinic crystal form II
Keywords keywords	alpha/beta hydrolase, carbohydrate esterase, CE7, Bacillus pumilus, 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.

3fvt__assembly_1__model_1

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

Download this curve (.dat)

3fvt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fvt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.19 Å
Rg (electron density)	37.16 Å
Total Rg	37.72 Å
Atom count	15248
Residues	1904
Excluded volume	272380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fvt__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fvt__assembly_2__model_1`	hexameric （6）	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	Acetyl xylan esterase
Molecular weight formula_weight	36114.8 kDa
EC 编号 ec_number	3.1.1.6
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,L,M,N
Atom count atom_count	33650

MQLFDLSLEELKKYKPKKTARPDFSDFWKKSLEELRQVEAEPTLESYDYPVKGVKVYRLTYQSFGHSKIEGFYAVPDQTGPHPALVRFHGYNASYDGGIHDIVNWALHGYATFGMLVRGQGGSEDTSVTPGGHALGWMTKGILSKDTYYYRGVYLDAVRALEVIQSFPEVDEHRIGVIGGSQGGALAIAAAALSDIPKVVVADYPYLSNFERAVDVALEQPYLEINSYFRRNSDPKVEEKAFETLSYFDLINLAGWVKQPTLMAIGLIDKITPPSTVFAAYNHLETDKDLKVYRYFGHEFIPAFQTEKLSFLQKHLLLST

Source Source

Source organism organism	Bacillus pumilus
NCBI taxonomy ID ncbi_taxonomy_id	1408
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3152

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3fvta_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvtb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvtc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvtd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvte_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvtf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvtg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvth_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvti_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvtl_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvtm_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

Domain ID domain_id	d3fvtn_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.25 — Acetyl xylan esterase-like

CATH v4.4 (12 domains)

Domain ID domain_id	3fvtA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtM00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3fvtN00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	144.039 Å
Unit-cell length b length_b	87.205 Å
Unit-cell length c length_c	184.825 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	29.740 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2640

Crystal Structure of Acetyl Xylan Esterase from Bacillus pumilus, monoclinic crystal form II

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

Acetyl xylan esterase

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

3fvt__assembly_1__model_1

3fvt__assembly_1__model_1 | I(q)

3fvt__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (4)

Crystal Structure of Acetyl Xylan Esterase from Bacillus pumilus, monoclinic crystal form II

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

Acetyl xylan esterase

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

3fvt__assembly_1__model_1

3fvt__assembly_1__model_1 | I(q)

3fvt__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (4)