SAXSdb — 2zzk

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

Leucine carboxyl methyltransferase 2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CITRIC ACID × 2 TETRAETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CITRIC ACID × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LCMT2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–695； UniProt 1–695 Author chain B； PDBConstruct 1–695； UniProt 1–695

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	2zzk
Deposition date deposition_date	2009-02-17
Structure title title	Crystal structure of tRNA wybutosine synthesizing enzyme TYW4
Keywords keywords	tRNA modification, TRANSFERASE; TRANSFERASE
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.

2zzk__assembly_1__model_1

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

Download this curve (.dat)

2zzk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zzk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.02 Å
Rg (electron density)	28.27 Å
Total Rg	29.09 Å
Atom count	5450
Residues	680
Excluded volume	97584 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zzk__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zzk__assembly_2__model_1`	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 (4)

Entity 1 Entity 1 polymer

Description description	Leucine carboxyl methyltransferase 2
Molecular weight formula_weight	79050.5 kDa
EC 编号 ec_number	2.1.1.-
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	10899

MKNLTTIKQTNKNVKQERRKKYADLAIQGTNNSSIASKRSVELLYLPKLSSANNFQMDKNNKLLEYFKFFVPKKIKRSPCINRGYWLRLFAIRSRLNSIIEQTPQDKKIVVVNLGCGYDPLPFQLLDTNNIQSQQYHDRVSFIDIDYSDLLKIKIELIKTIPELSKIIGLSEDKDYVDDSNVDFLTTPKYLARPCDLNDSKMFSTLLNECQLYDPNVVKVFVAEVSLAYMKPERSDSIIEATSKMENSHFIILEQLIPKGPFEPFSKQMLAHFKRNDSPLQSVLKYNTIESQVQRFNKLGFAYVNVGDMFQLWESADEATKKELLKVEPFDELEEFHLFCHHYVLCHATNYKEFAFTQGFLFDRSISEINLTVDEDYQLLECECPINRKFGDVDVAGNDVFYMGGSNPYRVNEILQLSIHYDKIDMKNIEVSSSEVPVARMCHTFTTISRNNQLLLIGGRKAPHQGLSDNWIFDMKTREWSMIKSLSHTRFRHSACSLPDGNVLILGGVTEGPAMLLYNVTEEIFKDVTPKDEFFQNSLVSAGLEFDPVSKQGIILGGGFMDQTTVSDKAIIFKYDAENATEPITVIKKLQHPLFQRYGSQIKYITPRKLLIVGGTSPSGLFDRTNSIISLDPLSETLTSIPISRRIWEDHSLMLAGFSLVSTSMGTIHIIGGGATCYGFGSVTNVGLKLIAIAK

Source Source

Source organism organism	Saccharomyces cerevisiae
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2zzkA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	2zzkA02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	80 — Kelch-type beta propeller

Domain ID domain_id	2zzkB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	2zzkB02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	80 — Kelch-type beta propeller

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Unit-cell length a length_a	78.834 Å
Unit-cell length b length_b	90.139 Å
Unit-cell length c length_c	251.376 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.706 Å
Low-resolution limit resolution_low	42.389 Å
R factor r_factor	0.2160
R_work r_work	0.2097
R_free r_free	0.2735

Crystal structure of tRNA wybutosine synthesizing enzyme TYW4

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

Leucine carboxyl methyltransferase 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

2zzk__assembly_1__model_1

2zzk__assembly_1__model_1 | I(q)

2zzk__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of tRNA wybutosine synthesizing enzyme TYW4

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

Leucine carboxyl methyltransferase 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

2zzk__assembly_1__model_1

2zzk__assembly_1__model_1 | I(q)

2zzk__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)