4h4l

Crystal Structure of ternary complex of HutP(HutP-L-His-Zn)

Method: X-RAY DIFFRACTION

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

Hut operon positive regulatory protein

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	HISTIDINE × 6 ZINC ION × 6 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	HISTIDINE × 6 ZINC ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HUTP_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–148； UniProt 1–148 Author chain B； PDBConstruct 1–148； UniProt 1–148 Author chain C； PDBConstruct 1–148； UniProt 1–148 Author chain D； PDBConstruct 1–148； UniProt 1–148 Author chain E； PDBConstruct 1–148； UniProt 1–148 Author chain F； PDBConstruct 1–148； UniProt 1–148 Author chain G； PDBConstruct 1–148； UniProt 1–148 Author chain H； PDBConstruct 1–148； UniProt 1–148 Author chain I； PDBConstruct 1–148； UniProt 1–148 Author chain J； PDBConstruct 1–148； UniProt 1–148 Author chain K； PDBConstruct 1–148； UniProt 1–148 Author chain L； PDBConstruct 1–148； UniProt 1–148

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	4h4l
Deposition date deposition_date	2012-09-17
Structure title title	Crystal Structure of ternary complex of HutP(HutP-L-His-Zn)
Keywords keywords	HUTP, ANTI-TERMINATION, HISTIDINE METABOLISM, TRANSCRIPTION, TRANSCRIPTION REGULATION, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

4h4l__assembly_1__model_1

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

Download this curve (.dat)

4h4l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4h4l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.45 Å
Rg (electron density)	26.22 Å
Total Rg	26.97 Å
Atom count	6472
Residues	852
Excluded volume	115080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4h4l__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4h4l__assembly_2__model_1`	hexameric （6）	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 (4)

Entity 1 Entity 1 polymer

Description description	Hut operon positive regulatory protein
Molecular weight formula_weight	16232.6 kDa
Mutation mutation	V51I
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	13047

MTLHKERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	HISTIDINE
Molecular weight formula_weight	156.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4h4la_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4lb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4lc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4ld_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4le_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4lf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4lg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4lh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4li_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4lj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4lk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

Domain ID domain_id	d4h4ll_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.275 — Hut operon positive regulatory protein HutP
Superfamily Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
Family Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

CATH v4.4 (12 domains)

Domain ID domain_id	4h4lA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lK00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

Domain ID domain_id	4h4lL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1510 — Hut operon positive regulatory protein HutP
Homologous superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

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Unit-cell length a length_a	129.530 Å
Unit-cell length b length_b	129.530 Å
Unit-cell length c length_c	76.670 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	36

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	36.280 Å
R factor r_factor	0.2233
R_work r_work	0.2193
R_free r_free	0.2978

Crystal Structure of ternary complex of HutP(HutP-L-His-Zn)

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

Hut operon positive 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

4h4l__assembly_1__model_1

4h4l__assembly_1__model_1 | I(q)

4h4l__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of ternary complex of HutP(HutP-L-His-Zn)

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

Hut operon positive 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

4h4l__assembly_1__model_1

4h4l__assembly_1__model_1 | I(q)

4h4l__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)