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9sq9

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

Method: X-RAY DIFFRACTION D_max: 124.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sq9
deposition_date	2025-09-19
last_revision	2025-10-08
title	Crystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes
keywords	Peptidoglycan, Amidotransferase, Complex, LIGASE; LIGASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	37.57 Å
rg_electron	37.30 Å
i0	306159000.00
molecular_weight	143740.0 kDa
excluded_volume	180240 Å³
envelope_volume	227230 Å³
shell_volume	51195 Å³
envelope_diameter	131.1 Å
shell_rg	43.07 Å
envelope_rg	37.12 Å
shape_rg	37.29 Å
total_rg	37.67 Å
total_atoms	10139
n_residues	1302
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	124.8 Å
rg_real	37.65 Å
rg_real_error	0.95 Å
i0_real	3.0620e+08
i0_real_error	5.1470e+06
rg_reciprocal	37.60 Å
i0_reciprocal	306100000.0000
total_estimate	0.8864
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.6 Å
skewness	0.376
kurtosis	-0.430
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	48820000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.892

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
formula_weight	49037.6 kDa
ec_number	6.3.5.13
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	10898

HHHHHHPMSDYDIPTTENLYFQGAMACDKDILKDLSKDYDIVVVTGTNGKTLTTALTVGILKEAFGEIITNPSGANMITGITSTFLAAKKGKSERQIAVLEIDEASLPRITTYLKPSLFVYTNIFRDQMDRYGEIYTTYQMIVDGARNAPKATILANGDSPIFSSKDIVNPVQYYGFDTAKHAPQLAHYNTEGILCPKCEHILQYRLNTYANLGDFVCLNCQFQRPTLDYQLTELTAITHQSSEFVIDGQNYKINVGGLYNIYNALAAVSVAEFFGVSPEKIKAGFNKSKAVFGRQETFTIGDKSCTLILIKNPVGASQALEMIQLADYPFSLSVLLNANYADGIDTSWIWDANFELITQMPITEINAGGVRHSEIARRLRVTGFDDTKIKQAEKLEQIIETIEKQEAKHAYILATYTAMLEFRSLLADRHVVEKEMI

Source

organism	Streptococcus pyogenes MGAS10270
ncbi_taxonomy_id	370552
host_organism	Escherichia coli

Entity 2 polymer

description	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
formula_weight	29610.0 kDa
ec_number	6.3.5.13,3.5.1.2
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MTYTSLKSPENQDYIYDLTIAHLYGNLMNTYGDNGNILMLKYVAEKLGARVTVDIVSINDTFEQDDYDIVFFGGGQDYEQSIVAKDLPSKKAALADYIANNKVVLAICGGFQLLGQYYVQANGVKIDGLGIMGHYTLNQHQNRFIGDIKIHNDEFNETYYGFENHQGRTFLSGDEKPLGRVVYGNGNNKEDQTEGVHYKNVYGSYFHGPILSRNVNLAYRLVTTALKKKYGSAISLSSYDDILKQEITEEYADLKSKASFNKV

Source

organism	Streptococcus pyogenes MGAS10270
ncbi_taxonomy_id	370552
host_organism	Escherichia coli

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CITRIC ACID
formula_weight	192.1 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	nat
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	707

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6. Citations (1)

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length_a	88.280 Å
length_b	101.650 Å
length_c	178.660 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.050 Å
resolution_low	44.140 Å
r_factor	0.1752
r_work	0.1743
r_free	0.2181

fit	/app/data/saxs_computation/sq/9sq9/9sq9.fit
pddf	/app/data/pr_computation/sq/9sq9/9sq9.pr.out
profile	/app/data/saxs_computation/sq/9sq9/9sq9.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)