1t35

CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN YVDD- A PUTATIVE LYSINE DECARBOXYLASE

Method: X-RAY DIFFRACTION

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

HYPOTHETICAL PROTEIN YVDD, Putative Lysine Decarboxylase

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	SULFATE ION × 14 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O06986_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–191； UniProt 1–191 Author chain B； PDBConstruct 1–191； UniProt 1–191 Author chain C； PDBConstruct 1–191； UniProt 1–191 Author chain D； PDBConstruct 1–191； UniProt 1–191 Author chain E； PDBConstruct 1–191； UniProt 1–191 Author chain F； PDBConstruct 1–191； UniProt 1–191 Author chain G； PDBConstruct 1–191； UniProt 1–191 Author chain H； PDBConstruct 1–191； UniProt 1–191

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	1t35
Deposition date deposition_date	2004-04-23
Structure title title	CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN YVDD- A PUTATIVE LYSINE DECARBOXYLASE
Keywords keywords	;HYPOTHETICAL PROTEIN YVDD, PUTATIVE LYSINE DECARBOXYLASE, STRUCTURAL GENOMICS TARGET, T833, NYSGXRC, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, LYASE ;; LYASE
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.

1t35__assembly_1__model_1

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

Download this curve (.dat)

1t35__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1t35__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.84 Å
Rg (electron density)	35.08 Å
Total Rg	35.41 Å
Atom count	11088
Residues	1346
Excluded volume	198660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1t35__assembly_1__model_1`	octameric （8）	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	HYPOTHETICAL PROTEIN YVDD, Putative Lysine Decarboxylase
Molecular weight formula_weight	21636.9 kDa
EC 编号 ec_number	4.1.1.18
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	11133

MKTICVFAGSNPGGNEAYKRKAAELGVYMAEQGIGLVYGGSRVGLMGTIADAIMENGGTAIGVMPSGLFSGEVVHQNLTELIEVNGMHERKAKMSELADGFISMPGGFGTYEELFEVLCWAQIGIHQKPIGLYNVNGYFEPMMKMVKYSIQEGFSNESHLKLIHSSSRPDELIEQMQNYSYPILEKKWTEI

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
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	14

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1t35a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d1t35b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d1t35c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d1t35d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d1t35e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d1t35f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d1t35g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d1t35h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

CATH v4.4 (8 domains)

Domain ID domain_id	1t35A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	1t35B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	1t35C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	1t35D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	1t35E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	1t35F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	1t35G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	1t35H00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

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Unit-cell length a length_a	117.562 Å
Unit-cell length b length_b	170.773 Å
Unit-cell length c length_c	89.721 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	32

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.720 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2430
R_work r_work	0.2430
R_free r_free	0.2860

CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN YVDD- A PUTATIVE LYSINE DECARBOXYLASE

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

HYPOTHETICAL PROTEIN YVDD, Putative Lysine Decarboxylase

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

1t35__assembly_1__model_1

1t35__assembly_1__model_1 | I(q)

1t35__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN YVDD- A PUTATIVE LYSINE DECARBOXYLASE

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

HYPOTHETICAL PROTEIN YVDD, Putative Lysine Decarboxylase

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

1t35__assembly_1__model_1

1t35__assembly_1__model_1 | I(q)

1t35__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)