SAXSdb — 1vly

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

Unknown protein from 2D-page

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ACETATE ION × 1 CALCIUM ION × 1 CHLORIDE ION × 1 1,2-ETHANEDIOL × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UP14_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–338； UniProt 1–325

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	1vly
Deposition date deposition_date	2004-08-20
Structure title title	Crystal structure of a putative aminomethyltransferase (ygfz) from escherichia coli at 1.30 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, 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.

1vly__assembly_1__model_1

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

Download this curve (.dat)

1vly__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vly__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.80 Å
Rg (electron density)	19.69 Å
Total Rg	20.65 Å
Atom count	2493
Residues	314
Excluded volume	44524 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vly__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	Unknown protein from 2D-page
Molecular weight formula_weight	38110.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3020

MGSDKIHHHHHHMAFTPFPPRQPTASARLPLTLMTLDDWALATITGADSEKYMQGQVTADVSQMAEDQHLLAAHCDAKGKMWSNLRLFRDGDGFAWIERRSVREPQLTELKKYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQVVKEGATTLLWFEHPAERFLIVTDEATANMLTDKLRGEAELNNSQQWLALNIEAGFPVIDAANSGQFIPQATNLQALGGISFKKGCYTGQEMVARAKFRGANKRALWLLAGSASRLPEAGEDLELKMGENWRRTGTVLAAVKLEDGQVVVQVVMNNDMEPDSIFRVRDDANTLHIEPLPYSLEE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	477

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1vlya1
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.2 — Aminomethyltransferase beta-barrel domain
Family Family family	b.44.2.1 — Aminomethyltransferase beta-barrel domain

Domain ID domain_id	d1vlya2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.250 — Folate-binding domain
Superfamily Superfamily superfamily	d.250.1 — Folate-binding domain
Family Family family	d.250.1.1 — Aminomethyltransferase folate-binding domain

CATH v4.4 (3 domains)

Domain ID domain_id	1vlyA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1630 —

Domain ID domain_id	1vlyA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1400 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	1vlyA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	160 —

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Unit-cell length a length_a	44.814 Å
Unit-cell length b length_b	50.080 Å
Unit-cell length c length_c	52.014 Å
Unit-cell angle α angle_alpha	94.68 °
Unit-cell angle β angle_beta	115.29 °
Unit-cell angle γ angle_gamma	116.46 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	26.450 Å
R factor r_factor	0.1357
R_work r_work	0.1340
R_free r_free	0.1678

Crystal structure of a putative aminomethyltransferase (ygfz) from escherichia coli at 1.30 A resolution

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

Unknown protein from 2D-page

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

1vly__assembly_1__model_1

1vly__assembly_1__model_1 | I(q)

1vly__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of a putative aminomethyltransferase (ygfz) from escherichia coli at 1.30 A resolution

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

Unknown protein from 2D-page

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

1vly__assembly_1__model_1

1vly__assembly_1__model_1 | I(q)

1vly__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)