SAXSdb — 3dza

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

uncharacterized putative membrane protein

Klebsiella pneumoniae subsp. pneumoniae MGH 78578

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 10 1,2-ETHANEDIOL × 24 ACETATE ION × 5 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A6TE93_KLEP7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–191； UniProt 31–220 Author chain B； PDBConstruct 2–191； UniProt 31–220 Author chain C； PDBConstruct 2–191； UniProt 31–220 Author chain D； PDBConstruct 2–191； UniProt 31–220

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	3dza
Deposition date deposition_date	2008-07-29
Structure title title	Crystal structure of a putative membrane protein of unknown function (yfdx) from klebsiella pneumoniae subsp. at 1.65 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function; UNKNOWN FUNCTION
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.

3dza__assembly_1__model_1

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

Download this curve (.dat)

3dza__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dza__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.54 Å
Rg (electron density)	24.43 Å
Total Rg	25.21 Å
Atom count	5440
Residues	695
Excluded volume	97813 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dza__assembly_1__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	uncharacterized putative membrane protein
Molecular weight formula_weight	20300.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6799

GATDSATAAPAAAATTQVQKEAADVLQVAVQGANAMRDIQFARLALFHGQPDSAKKLTDDAAALLAADDASWAKFVKTDAKAKMIADRYVIINASIALSEDYVATPEKESAIQSANEKLAKGDQKGAIDTLRLAGIGVIENQYLMPLNQTRKAVAQSQELLKAGKYYEANLVLKGAEEGIVVDSEMLVAGN

Source Source

Source organism organism	Klebsiella pneumoniae subsp. pneumoniae MGH 78578
NCBI taxonomy ID ncbi_taxonomy_id	272620
Host organism host_organism	Escherichia Coli

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	10

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1090

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3dzaA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1940 — YfdX protein domain

Domain ID domain_id	3dzaA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2140 —

Domain ID domain_id	3dzaB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1940 — YfdX protein domain

Domain ID domain_id	3dzaB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2140 —

Domain ID domain_id	3dzaC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1940 — YfdX protein domain

Domain ID domain_id	3dzaC02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2140 —

Domain ID domain_id	3dzaD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1940 — YfdX protein domain

Domain ID domain_id	3dzaD02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2140 —

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Unit-cell length a length_a	68.207 Å
Unit-cell length b length_b	79.016 Å
Unit-cell length c length_c	137.990 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	16

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

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	29.975 Å
R factor r_factor	0.1540
R_work r_work	0.1520
R_free r_free	0.1940

Crystal structure of a putative membrane protein of unknown function (yfdx) from klebsiella pneumoniae subsp. at 1.65 A resolution

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

uncharacterized putative membrane protein

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

3dza__assembly_1__model_1

3dza__assembly_1__model_1 | I(q)

3dza__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 (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) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of a putative membrane protein of unknown function (yfdx) from klebsiella pneumoniae subsp. at 1.65 A resolution

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

uncharacterized putative membrane protein

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

3dza__assembly_1__model_1

3dza__assembly_1__model_1 | I(q)

3dza__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 (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) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)