9sq9

Crystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes

Method: X-RAY DIFFRACTION

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

Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT

Streptococcus pyogenes MGAS10270

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD × 1 （A0A5S4TG60） ZINC ION × 1 CITRIC ACID × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD × 1 （A0A5S4TG60） ZINC ION × 1 CITRIC ACID × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 DI(HYDROXYETHYL)ETHER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8B6J667_STRPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 26–438； UniProt 33–445 Author chain B； PDBConstruct 26–438； UniProt 33–445

Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD

Streptococcus pyogenes MGAS10270

UniProt A0A5S4TG60

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT × 1 （A0A8B6J667） ZINC ION × 1 CITRIC ACID × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT × 1 （A0A8B6J667） ZINC ION × 1 CITRIC ACID × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 DI(HYDROXYETHYL)ETHER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A5S4TG60_STRPY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–263； UniProt 1–263 Author chain D； PDBConstruct 1–263； UniProt 1–263

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	9sq9
Deposition date deposition_date	2025-09-19
Last revision last_revision	2025-10-08
Structure title title	Crystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes
Keywords keywords	Peptidoglycan, Amidotransferase, Complex, LIGASE; LIGASE
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.

9sq9__assembly_2__model_1

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

Download this curve (.dat)

9sq9__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9sq9__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.24 Å
Rg (electron density)	26.34 Å
Total Rg	27.16 Å
Atom count	5139
Residues	656
Excluded volume	91449 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9sq9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9sq9__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
Molecular weight formula_weight	49037.6 kDa
EC 编号 ec_number	6.3.5.13
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	10898

HHHHHHPMSDYDIPTTENLYFQGAMACDKDILKDLSKDYDIVVVTGTNGKTLTTALTVGILKEAFGEIITNPSGANMITGITSTFLAAKKGKSERQIAVLEIDEASLPRITTYLKPSLFVYTNIFRDQMDRYGEIYTTYQMIVDGARNAPKATILANGDSPIFSSKDIVNPVQYYGFDTAKHAPQLAHYNTEGILCPKCEHILQYRLNTYANLGDFVCLNCQFQRPTLDYQLTELTAITHQSSEFVIDGQNYKINVGGLYNIYNALAAVSVAEFFGVSPEKIKAGFNKSKAVFGRQETFTIGDKSCTLILIKNPVGASQALEMIQLADYPFSLSVLLNANYADGIDTSWIWDANFELITQMPITEINAGGVRHSEIARRLRVTGFDDTKIKQAEKLEQIIETIEKQEAKHAYILATYTAMLEFRSLLADRHVVEKEMI

Source Source

Source organism organism	Streptococcus pyogenes MGAS10270
NCBI taxonomy ID ncbi_taxonomy_id	370552
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
Molecular weight formula_weight	29610.0 kDa
EC 编号 ec_number	6.3.5.13,3.5.1.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MTYTSLKSPENQDYIYDLTIAHLYGNLMNTYGDNGNILMLKYVAEKLGARVTVDIVSINDTFEQDDYDIVFFGGGQDYEQSIVAKDLPSKKAALADYIANNKVVLAICGGFQLLGQYYVQANGVKIDGLGIMGHYTLNQHQNRFIGDIKIHNDEFNETYYGFENHQGRTFLSGDEKPLGRVVYGNGNNKEDQTEGVHYKNVYGSYFHGPILSRNVNLAYRLVTTALKKKYGSAISLSSYDDILKQEITEEYADLKSKASFNKV

Source Source

Source organism organism	Streptococcus pyogenes MGAS10270
NCBI taxonomy ID ncbi_taxonomy_id	370552
Host organism host_organism	Escherichia coli

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	2

Entity 4 Entity 4 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	707

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Unit-cell length a length_a	88.280 Å
Unit-cell length b length_b	101.650 Å
Unit-cell length c length_c	178.660 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	44.140 Å
R factor r_factor	0.1752
R_work r_work	0.1743
R_free r_free	0.2181

Crystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes

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

Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT

State in the Current Structure

Other States of the Same Protein in the Database

Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD

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

9sq9__assembly_2__model_1

9sq9__assembly_2__model_1 | I(q)

9sq9__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes

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

Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD

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

9sq9__assembly_2__model_1

9sq9__assembly_2__model_1 | I(q)

9sq9__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)