3f4l

Crystal structure of a probable oxidoreductase yhhX in Triclinic form. Northeast Structural Genomics target ER647

Method: X-RAY DIFFRACTION

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

Putative oxidoreductase yhhX

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YHHX_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–345； UniProt 1–345 Author chain B； PDBConstruct 1–345； UniProt 1–345 Author chain C； PDBConstruct 1–345； UniProt 1–345 Author chain D； PDBConstruct 1–345； UniProt 1–345 Author chain E； PDBConstruct 1–345； UniProt 1–345 Author chain F； PDBConstruct 1–345； UniProt 1–345

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	3f4l
Deposition date deposition_date	2008-10-31
Structure title title	Crystal structure of a probable oxidoreductase yhhX in Triclinic form. Northeast Structural Genomics target ER647
Keywords keywords	;oxidoreductase yhhX, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, Oxidoreductase ;; OXIDOREDUCTASE
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.

3f4l__assembly_2__model_1

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

Download this curve (.dat)

3f4l__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f4l__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	30.74 Å
Rg (electron density)	30.44 Å
Total Rg	30.83 Å
Atom count	5462
Residues	680
Excluded volume	97286 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f4l__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3f4l__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3f4l__assembly_3__model_1`	dimeric （2）	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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3f4lA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3f4lA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3f4lB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3f4lB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3f4lC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3f4lC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3f4lD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3f4lD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3f4lE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3f4lE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3f4lF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3f4lF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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Unit-cell length a length_a	66.189 Å
Unit-cell length b length_b	100.785 Å
Unit-cell length c length_c	102.166 Å
Unit-cell angle α angle_alpha	114.40 °
Unit-cell angle β angle_beta	103.31 °
Unit-cell angle γ angle_gamma	101.62 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	42.600 Å
R factor r_factor	0.2310
R_work r_work	0.2310
R_free r_free	0.2640

Description description	Putative oxidoreductase yhhX
Molecular weight formula_weight	39053.4 kDa
EC 编号 ec_number	1.-.-.-
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	16970

Crystal structure of a probable oxidoreductase yhhX in Triclinic form. Northeast Structural Genomics target ER647

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

Putative oxidoreductase yhhX

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

3f4l__assembly_2__model_1

3f4l__assembly_2__model_1 | I(q)

3f4l__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (0)

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	584

Crystal structure of a probable oxidoreductase yhhX in Triclinic form. Northeast Structural Genomics target ER647

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

Putative oxidoreductase yhhX

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

3f4l__assembly_2__model_1

3f4l__assembly_2__model_1 | I(q)

3f4l__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (0)