4lrz

Crystal Structure of the E.coli DhaR(N)-DhaL complex

Method: X-RAY DIFFRACTION

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

PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL

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	PTS-dependent dihydroxyacetone kinase operon regulatory protein × 2 （P76016） ADENOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 4 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PTS-dependent dihydroxyacetone kinase operon regulatory protein × 2 （P76016） ADENOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHAL_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–211； UniProt 2–210 Author chain B； PDBConstruct 3–211； UniProt 2–210 Author chain C； PDBConstruct 3–211； UniProt 2–210 Author chain D； PDBConstruct 3–211； UniProt 2–210

PTS-dependent dihydroxyacetone kinase operon regulatory protein

Escherichia coli

UniProt P76016

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL × 2 （P76014） ADENOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 4 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL × 2 （P76014） ADENOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHAR_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–318； UniProt 1–318 Author chain F； PDBConstruct 1–318； UniProt 1–318 Author chain G； PDBConstruct 1–318； UniProt 1–318 Author chain H； PDBConstruct 1–318； UniProt 1–318

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	4lrz
Deposition date deposition_date	2013-07-21
Structure title title	Crystal Structure of the E.coli DhaR(N)-DhaL complex
Keywords keywords	coiled-coil, helix rotation, GAF, PAS, transcriptional regulation complex, Transferase-Transcription Regulator complex; Transferase/Transcription Regulator
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.

4lrz__assembly_1__model_1

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

Download this curve (.dat)

4lrz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4lrz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.15 Å
Rg (electron density)	30.33 Å
Total Rg	30.94 Å
Atom count	7729
Residues	1007
Excluded volume	137490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4lrz__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4lrz__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	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
Molecular weight formula_weight	22666.7 kDa
EC 编号 ec_number	2.7.-.-
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	15955

GSSLSRTQIVNWLTRCGDIFSTESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILKNTGMTLLSSVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPGDKTMCDVWVPVVESLRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRASYLGERSIGHQDPGATSVMFMMQMLALAAKE

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	PTS-dependent dihydroxyacetone kinase operon regulatory protein
Molecular weight formula_weight	34889.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

MSGAFNNDGRGISPLIATSWERCNKLMKRETWNVPHQAQGVTFASIYRRKKAMLTLGQAALEDAWEYMAPRECALFILDETACILSRNGDPQTLQQLSALGFNDGTYCAEGIIGTCALSLAAISGQAVKTMADQHFKQVLWNWAFCATPLFDSKGRLTGTIALACPVEQTTAADLPLTLAIAREVGNLLLTDSLLAETNRHLNQLNALLESMDDGVISWDEQGNLQFINAQAARVLRLDATASQGRAITELLTLPAVLQQAIKQAHPLKHVEATFESQHQFIDAVITLKPIIETQGTSFILLLHPVEQMRQLMTSQLG

Source Source

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

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	445

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4lrza1
Class class	a — All alpha proteins
Fold Fold fold	a.208 — DhaL-like
Superfamily Superfamily superfamily	a.208.1 — DhaL-like
Family Family family	a.208.1.0 — automated matches

Domain ID domain_id	d4lrza2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4lrzb1
Class class	a — All alpha proteins
Fold Fold fold	a.208 — DhaL-like
Superfamily Superfamily superfamily	a.208.1 — DhaL-like
Family Family family	a.208.1.0 — automated matches

Domain ID domain_id	d4lrzb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4lrzc1
Class class	a — All alpha proteins
Fold Fold fold	a.208 — DhaL-like
Superfamily Superfamily superfamily	a.208.1 — DhaL-like
Family Family family	a.208.1.0 — automated matches

Domain ID domain_id	d4lrzc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4lrzd1
Class class	a — All alpha proteins
Fold Fold fold	a.208 — DhaL-like
Superfamily Superfamily superfamily	a.208.1 — DhaL-like
Family Family family	a.208.1.0 — automated matches

Domain ID domain_id	d4lrzd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (12 domains)

Domain ID domain_id	4lrzA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	340 — DhaL domain

Domain ID domain_id	4lrzB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	340 — DhaL domain

Domain ID domain_id	4lrzC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	340 — DhaL domain

Domain ID domain_id	4lrzD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	340 — DhaL domain

Domain ID domain_id	4lrzE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	40 — GAF domain

Domain ID domain_id	4lrzE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	4lrzF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	40 — GAF domain

Domain ID domain_id	4lrzF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	4lrzG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	40 — GAF domain

Domain ID domain_id	4lrzG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	4lrzH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	40 — GAF domain

Domain ID domain_id	4lrzH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

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Unit-cell length a length_a	89.766 Å
Unit-cell length b length_b	91.500 Å
Unit-cell length c length_c	93.808 Å
Unit-cell angle α angle_alpha	84.15 °
Unit-cell angle β angle_beta	72.42 °
Unit-cell angle γ angle_gamma	90.01 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.320 Å
Low-resolution limit resolution_low	90.910 Å
R factor r_factor	0.2021
R_work r_work	0.1997
R_free r_free	0.2474

Crystal Structure of the E.coli DhaR(N)-DhaL complex

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

PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL

State in the Current Structure

Other States of the Same Protein in the Database

PTS-dependent dihydroxyacetone kinase operon regulatory 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

4lrz__assembly_1__model_1

4lrz__assembly_1__model_1 | I(q)

4lrz__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of the E.coli DhaR(N)-DhaL complex

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

PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PTS-dependent dihydroxyacetone kinase operon regulatory 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

4lrz__assembly_1__model_1

4lrz__assembly_1__model_1 | I(q)

4lrz__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)