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9sqj

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

Method: X-RAY DIFFRACTION D_max: 125.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sqj
deposition_date	2025-09-22
last_revision	2025-10-08
title	Crystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes with bound AMPPNP
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	37.66 Å
rg_electron	37.46 Å
i0	313994000.00
molecular_weight	145210.0 kDa
excluded_volume	181980 Å³
envelope_volume	231070 Å³
shell_volume	51710 Å³
envelope_diameter	134.4 Å
shell_rg	43.20 Å
envelope_rg	37.28 Å
shape_rg	37.44 Å
total_rg	37.87 Å
total_atoms	10231
n_residues	1308
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	125.1 Å
rg_real	37.74 Å
rg_real_error	1.11 Å
i0_real	3.1400e+08
i0_real_error	5.2570e+06
rg_reciprocal	37.70 Å
i0_reciprocal	314000000.0000
total_estimate	0.8874
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.7 Å
skewness	0.378
kurtosis	-0.424
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	53970000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.909

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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	AAA,BBB
atom_count	11032

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	CCC,DDD

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	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	719

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6. Citations (1)

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length_a	88.289 Å
length_b	101.210 Å
length_c	177.296 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	—

resolution	1.981 Å
resolution_low	49.112 Å
r_factor	—
r_work	0.1803
r_free	0.2173

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

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

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)