SAXSdb — 1y6h

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

Peptide deformylase

Leptospira interrogans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 FORMIC ACID × 8 GLYCINE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 FORMIC ACID × 16 GLYCINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEF_LEPIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–177； UniProt 2–178 Author chain B； PDBConstruct 1–177； UniProt 2–178

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	1y6h
Deposition date deposition_date	2004-12-06
Structure title title	Crystal structure of LIPDF
Keywords keywords	open and close conformation, PDF, 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.

1y6h__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1y6h__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y6h__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.04 Å
Rg (electron density)	30.40 Å
Total Rg	31.00 Å
Atom count	5668
Residues	708
Excluded volume	100860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y6h__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1y6h__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Peptide deformylase
Molecular weight formula_weight	20274.1 kDa
EC 编号 ec_number	3.5.1.88
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	3191

SVRKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDSSHNVLD

Source Source

Source organism organism	Leptospira interrogans
NCBI taxonomy ID ncbi_taxonomy_id	173
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	GLYCINE
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	357

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1y6ha_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.167 — Peptide deformylase
Superfamily Superfamily superfamily	d.167.1 — Peptide deformylase
Family Family family	d.167.1.1 — Peptide deformylase

Domain ID domain_id	d1y6hb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.167 — Peptide deformylase
Superfamily Superfamily superfamily	d.167.1 — Peptide deformylase
Family Family family	d.167.1.1 — Peptide deformylase

CATH v4.4 (2 domains)

Domain ID domain_id	1y6hA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	45 — Peptide Deformylase
Homologous superfamily homologous superfamily	10 — Peptide deformylase

Domain ID domain_id	1y6hB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	45 — Peptide Deformylase
Homologous superfamily homologous superfamily	10 — Peptide deformylase

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Unit-cell length a length_a	91.032 Å
Unit-cell length b length_b	91.032 Å
Unit-cell length c length_c	86.380 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	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	25.140 Å
R factor r_factor	0.1790
R_work r_work	0.1790
R_free r_free	0.2280

Crystal structure of LIPDF

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

Peptide deformylase

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

1y6h__assembly_2__model_1

1y6h__assembly_2__model_1 | I(q)

1y6h__assembly_2__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of LIPDF

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

Peptide deformylase

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

1y6h__assembly_2__model_1

1y6h__assembly_2__model_1 | I(q)

1y6h__assembly_2__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)