1z7m

ATP Phosphoribosyl transferase (HisZG ATP-PRTase) from Lactococcus lactis

Method: X-RAY DIFFRACTION

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

ATP phosphoribosyltransferase regulatory subunit

Lactococcus lactis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	ATP phosphoribosyltransferase × 4 （Q02129） TUNGSTATE(VI)ION × 2 PHOSPHATE ION × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	ATP phosphoribosyltransferase × 2 （Q02129） TUNGSTATE(VI)ION × 1 PHOSPHATE ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	ATP phosphoribosyltransferase × 2 （Q02129） TUNGSTATE(VI)ION × 1 PHOSPHATE ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HISZ_LACLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–344； UniProt 1–328 Author chain B； PDBConstruct 17–344； UniProt 1–328 Author chain C； PDBConstruct 17–344； UniProt 1–328 Author chain D； PDBConstruct 17–344； UniProt 1–328

ATP phosphoribosyltransferase

Lactococcus lactis

UniProt Q02129

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	ATP phosphoribosyltransferase regulatory subunit × 4 （Q02147） TUNGSTATE(VI)ION × 2 PHOSPHATE ION × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	ATP phosphoribosyltransferase regulatory subunit × 2 （Q02147） TUNGSTATE(VI)ION × 1 PHOSPHATE ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	ATP phosphoribosyltransferase regulatory subunit × 2 （Q02147） TUNGSTATE(VI)ION × 1 PHOSPHATE ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIS1_LACLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–208； UniProt 1–208 Author chain F； PDBConstruct 1–208； UniProt 1–208 Author chain G； PDBConstruct 1–208； UniProt 1–208 Author chain H； PDBConstruct 1–208； UniProt 1–208

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	1z7m
Deposition date deposition_date	2005-03-25
Structure title title	ATP Phosphoribosyl transferase (HisZG ATP-PRTase) from Lactococcus lactis
Keywords keywords	ATP-PRT, histidine biosynthesis, transferase, HisZG, allosteric, evolution; TRANSFERASE
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.

1z7m__assembly_1__model_1

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

Download this curve (.dat)

1z7m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1z7m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.48 Å
Rg (electron density)	39.83 Å
Total Rg	40.40 Å
Atom count	16609
Residues	2048
Excluded volume	299380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1z7m__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1z7m__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1z7m__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	ATP phosphoribosyltransferase regulatory subunit
Molecular weight formula_weight	39848.4 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	16609

MRGSHHHHHHGSIEGRMEKINYLLPEESAEMTLNQVKSLRQIEGRLRKLFSLKNYQEVMPPSFEYTQLYTALESNGKTFNQEKMFQFIKHEGQSITLRYDFTLPLVRLYSQIKDSTSARYSYFGKIFRKEKRHKGRSTENYQIGIELFGESADKSELEILSLALQVIEQLGLNKTVFEIGSAKFFQRLCQLADGSTELLTELLLKKDLSGLNAFIEKNNFSKELRGLLKEIFITNELSRLENLVTNTKDDVLISSFDQLKEFSEKLSMIKPIIIDLGMVPKMDYYTDLMFKAYSSAANQPILSGGRYDQLLSNFQEEAFAIGFCCHMDTILKALERQELEEDND

Source Source

Source organism organism	Lactococcus lactis
NCBI taxonomy ID ncbi_taxonomy_id	1358
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ATP phosphoribosyltransferase
Molecular weight formula_weight	23708.3 kDa
EC 编号 ec_number	2.4.2.17
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

MIKIAITKGRIQKQVTKLLENADYDVEPILNLGRELQIKTKDDLQIIFGKPNDVITFLEHGIVDIGFVGKDTLDENDFDDYYELLYLKIGQCIFALASYPDFSNKNFQRHKRIASKYPRVTKKYFAQKQEDIEIIKLEGSVELGPVVGLADAIVDIVETGNTLSANGLEVIEKISDISTRMIVNKSSFKFKKDKIIEMVERLEDAQTN

Source Source

Source organism organism	Lactococcus lactis
NCBI taxonomy ID ncbi_taxonomy_id	1358
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	TUNGSTATE(VI)ION
Molecular weight formula_weight	247.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1z7ma1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Domain ID domain_id	d1z7mb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Domain ID domain_id	d1z7mc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Domain ID domain_id	d1z7md_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Domain ID domain_id	d1z7me1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d1z7mf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d1z7mg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d1z7mh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

CATH v4.4 (12 domains)

Domain ID domain_id	1z7mA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	1z7mB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	1z7mC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	1z7mD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	1z7mE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1z7mE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1z7mF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1z7mF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1z7mG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1z7mG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1z7mH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1z7mH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

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Unit-cell length a length_a	151.684 Å
Unit-cell length b length_b	222.936 Å
Unit-cell length c length_c	86.380 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2980
R_work r_work	0.2447
R_free r_free	0.2855

ATP Phosphoribosyl transferase (HisZG ATP-PRTase) from Lactococcus lactis

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

ATP phosphoribosyltransferase regulatory subunit

State in the Current Structure

Other States of the Same Protein in the Database

ATP phosphoribosyltransferase

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

1z7m__assembly_1__model_1

1z7m__assembly_1__model_1 | I(q)

1z7m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

ATP Phosphoribosyl transferase (HisZG ATP-PRTase) from Lactococcus lactis

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

ATP phosphoribosyltransferase regulatory subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP phosphoribosyltransferase

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

1z7m__assembly_1__model_1

1z7m__assembly_1__model_1 | I(q)

1z7m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)