4es4

Crystal structure of YdiV and FlhD complex

Method: X-RAY DIFFRACTION

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

Putative cyclic di-GMP regulator CdgR

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Flagellar transcriptional regulator FlhD × 2 （P0A8S9）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Flagellar transcriptional regulator FlhD × 2 （P0A8S9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDGR_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–237； UniProt 1–237 Author chain C； PDBConstruct 1–237； UniProt 1–237 Author chain E； PDBConstruct 1–237； UniProt 1–237 Author chain G； PDBConstruct 1–237； UniProt 1–237

Flagellar transcriptional regulator FlhD

Escherichia coli

UniProt P0A8S9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Putative cyclic di-GMP regulator CdgR × 2 （P76204）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Putative cyclic di-GMP regulator CdgR × 2 （P76204）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FLHD_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–116； UniProt 1–116 Author chain D； PDBConstruct 1–116； UniProt 1–116 Author chain F； PDBConstruct 1–116； UniProt 1–116 Author chain H； PDBConstruct 1–116； UniProt 1–116

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	4es4
Deposition date deposition_date	2012-04-22
Structure title title	Crystal structure of YdiV and FlhD complex
Keywords keywords	Flagellar regulation, TRANSCRIPTION; TRANSCRIPTION
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.

4es4__assembly_1__model_1

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

Download this curve (.dat)

4es4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4es4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.04 Å
Rg (electron density)	28.44 Å
Total Rg	28.97 Å
Atom count	4537
Residues	566
Excluded volume	81516 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4es4__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4es4__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 (2)

Entity 1 Entity 1 polymer

Description description	Putative cyclic di-GMP regulator CdgR
Molecular weight formula_weight	27070.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	9074

MKIFLENLYHSDCYFLPIRDNQQVLVGVELITHFSSEDGTVRIPTSRVIAQLTEEQHWQLFSEQLELLKSCQHFFIQHKLFAWLNLTPQVATLLLERDNYAGELLKYPFIELLINENYPHLNEGKDNRGLLSLSQVYPLVLGNLGAGNSTMKAVFDGLFTRVMLDKSFIQQQITHRSFEPFIRAIQAQISPCCNCIIAGGIDTAEILAQITPFDFHALQGCLWPAVPINQITTLVQR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Flagellar transcriptional regulator FlhD
Molecular weight formula_weight	13333.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MHTSELLKHIYDINLSYLLLAQRLIVQDKASAMFRLGINEEMATTLAALTLPQMVKLAETNQLVCHFRFDSHQTITQLTQDSRVDDLQQIHTGIMLSTRLLNDVNQPEEALRKKRA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4es4b_
Class class	a — All alpha proteins
Fold Fold fold	a.145 — Flagellar transcriptional activator FlhD
Superfamily Superfamily superfamily	a.145.1 — Flagellar transcriptional activator FlhD
Family Family family	a.145.1.1 — Flagellar transcriptional activator FlhD

Domain ID domain_id	d4es4d_
Class class	a — All alpha proteins
Fold Fold fold	a.145 — Flagellar transcriptional activator FlhD
Superfamily Superfamily superfamily	a.145.1 — Flagellar transcriptional activator FlhD
Family Family family	a.145.1.1 — Flagellar transcriptional activator FlhD

Domain ID domain_id	d4es4f_
Class class	a — All alpha proteins
Fold Fold fold	a.145 — Flagellar transcriptional activator FlhD
Superfamily Superfamily superfamily	a.145.1 — Flagellar transcriptional activator FlhD
Family Family family	a.145.1.1 — Flagellar transcriptional activator FlhD

Domain ID domain_id	d4es4h_
Class class	a — All alpha proteins
Fold Fold fold	a.145 — Flagellar transcriptional activator FlhD
Superfamily Superfamily superfamily	a.145.1 — Flagellar transcriptional activator FlhD
Family Family family	a.145.1.1 — Flagellar transcriptional activator FlhD

CATH v4.4 (8 domains)

Domain ID domain_id	4es4A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	450 — EAL domain

Domain ID domain_id	4es4B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4000 — Flagellar transcriptional activator fold
Homologous superfamily homologous superfamily	10 — Flagellar transcriptional activator FlhD

Domain ID domain_id	4es4C00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	450 — EAL domain

Domain ID domain_id	4es4D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4000 — Flagellar transcriptional activator fold
Homologous superfamily homologous superfamily	10 — Flagellar transcriptional activator FlhD

Domain ID domain_id	4es4E00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	450 — EAL domain

Domain ID domain_id	4es4F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4000 — Flagellar transcriptional activator fold
Homologous superfamily homologous superfamily	10 — Flagellar transcriptional activator FlhD

Domain ID domain_id	4es4G00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	450 — EAL domain

Domain ID domain_id	4es4H00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4000 — Flagellar transcriptional activator fold
Homologous superfamily homologous superfamily	10 — Flagellar transcriptional activator FlhD

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Unit-cell length a length_a	132.486 Å
Unit-cell length b length_b	132.486 Å
Unit-cell length c length_c	145.685 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	24

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	39.165 Å
R factor r_factor	0.2469
R_work r_work	0.2445
R_free r_free	0.2826

Crystal structure of YdiV and FlhD complex

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

Putative cyclic di-GMP regulator CdgR

State in the Current Structure

Other States of the Same Protein in the Database

Flagellar transcriptional regulator FlhD

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

4es4__assembly_1__model_1

4es4__assembly_1__model_1 | I(q)

4es4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of YdiV and FlhD complex

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

Putative cyclic di-GMP regulator CdgR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Flagellar transcriptional regulator FlhD

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

4es4__assembly_1__model_1

4es4__assembly_1__model_1 | I(q)

4es4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)