PDB-9crn: Crystal structure of Streptococcus pyogenes TglA

ID or keywords:

Entry

Database: PDB / ID: 9crn

Title

Crystal structure of Streptococcus pyogenes TglA

Components

Transglutaminase-like domain-containing protein

Keywords

UNKNOWN FUNCTION

Function / homology

: / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Papain-like cysteine peptidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / cytoplasm / Transglutaminase-like domain-containing protein

Function and homology information

Biological species

Streptococcus pyogenes serotype M49 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Campbell, I.R. / Neiditch, M.B.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of Streptococcus pyogenes TglA
Authors: Campbell, I.R. / Neiditch, M.B.

History

Deposition	Jul 22, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 14, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9crn.cif.gz	274.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9crn.ent.gz	184 KB	Display	PDB format
PDBx/mmJSON format	9crn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cr/9crn ftp://data.pdbj.org/pub/pdb/validation_reports/cr/9crn	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (3) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Transglutaminase-like domain-containing protein

hetero molecules

44 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	51.272, 88.334, 94.092
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Transglutaminase-like domain-containing protein Mass: 43788.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M49 (strain NZ131) (bacteria) Strain: NZ131 / Gene: Spy49_0186c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3BXA0
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM Bis-Tris (pH 6.5), 200 mM sodium chloride, 15% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.96→50 Å / Num. obs: 31441 / % possible obs: 99.8 % / Redundancy: 6.2 % / B_iso Wilson estimate: 26.92 Å² / CC_1/2: 0.97 / Net I/σ(I): 10.58
Reflection shell	Resolution: 1.96→1.99 Å / Num. unique obs: 1508 / CC_1/2: 0.426

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.96→45.02 Å / SU ML: 0.183 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7558
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.214	2000	6.4 %
R_work	0.1889	29253	-
obs	0.1906	31253	99.13 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 33.62 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→45.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2960	0	13	213	3186

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3045
X-RAY DIFFRACTION	f_angle_d	0.6755	4136
X-RAY DIFFRACTION	f_chiral_restr	0.0431	445
X-RAY DIFFRACTION	f_plane_restr	0.0052	537
X-RAY DIFFRACTION	f_dihedral_angle_d	14.7175	1093

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.96-2.01	0.2915	133	0.2661	1961	X-RAY DIFFRACTION	95.1
2.01-2.06	0.313	130	0.2458	2067	X-RAY DIFFRACTION	99.05
2.06-2.12	0.2888	145	0.2263	2050	X-RAY DIFFRACTION	99.1
2.12-2.19	0.2457	144	0.2157	2059	X-RAY DIFFRACTION	99.1
2.19-2.27	0.2499	147	0.2033	2054	X-RAY DIFFRACTION	99.37
2.27-2.36	0.2412	143	0.1926	2061	X-RAY DIFFRACTION	99.15
2.36-2.47	0.2187	140	0.1866	2085	X-RAY DIFFRACTION	99.64
2.47-2.6	0.2246	141	0.1934	2076	X-RAY DIFFRACTION	99.6
2.6-2.76	0.233	142	0.1954	2111	X-RAY DIFFRACTION	99.73
2.76-2.97	0.2158	147	0.1941	2084	X-RAY DIFFRACTION	99.51
2.97-3.27	0.2059	143	0.1871	2107	X-RAY DIFFRACTION	99.78
3.27-3.74	0.1967	148	0.178	2137	X-RAY DIFFRACTION	99.74
3.74-4.71	0.1788	145	0.1526	2142	X-RAY DIFFRACTION	99.52
4.72-45.02	0.1887	152	0.1899	2259	X-RAY DIFFRACTION	99.42

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.28335768507	-4.81354415768	2.83918038902	6.51664473324	1.04138103928	7.67478865529	-0.223093100966	-0.384631346076	0.21852136631	0.317785454542	0.354415568936	-0.258232142943	-0.370487234955	0.293302168442	-0.134609407466	0.148906857509	0.0114291550098	0.00640082284809	0.216363703096	-0.0532248967712	0.216683143784	-33.9761121999	16.4727256498	10.8115896491
2	2.89125575747	0.876509931691	0.371366400159	4.1037335657	0.575805476858	4.11265784412	-0.00196865177848	-0.156647213742	-0.0254171725909	0.278358576538	-0.0169733785126	0.0982044984317	0.153113108305	-0.145235206646	0.014270891963	0.169788957121	0.0206787156539	0.0202375478731	0.201239773008	-0.00296564368336	0.209467799547	-31.2132984033	6.5375247551	4.57605315771
3	4.34801415015	3.12254854001	-3.41995554479	8.46328946392	-4.9077073273	8.18332268335	-0.203179177714	-0.230614136285	-0.564850868427	0.126796961335	0.0576837904054	-0.326896071917	0.418079663328	0.0974461393617	0.176410970354	0.182609070593	0.0347998830391	0.00772392825121	0.260758537048	0.0197217976735	0.291614628526	-22.9083080633	2.74153708331	5.89663079498
4	1.02745643448	2.24792262324	-1.52895263844	6.2574802976	-4.49740171857	3.98760567013	0.0548398667583	-0.0876310831682	-0.163142510864	0.265943458407	-0.156702438154	-0.432077227789	-0.184388638171	0.282139624447	0.0995120372299	0.199944884223	0.0102718418546	-0.0154692814697	0.242185112212	-0.0632329666722	0.243038677397	-17.3140271522	14.3818611855	3.17150222269
5	6.30890121269	-2.65309849961	0.920331222173	5.11726070701	-0.179714001751	4.10669184977	0.0923710392044	0.406208724369	-0.169076929267	-0.046312848324	-0.122909869051	-0.171172771802	0.156865293937	0.215172478655	0.0429259973617	0.167585705667	-0.0509400027383	-0.0024462049035	0.186415369684	-0.0116346483918	0.158689371767	-18.100785239	15.7106112895	-16.4811208196
6	1.3219762129	-0.382863440671	0.607924809854	2.99115711481	1.00821123621	2.23424053738	0.0411343698434	-0.00987078879459	-0.226387216494	0.0343091687712	-0.0162855931061	0.0284874259416	0.197415862573	0.0624007643307	-0.0201483358587	0.181080944619	-0.0126395294524	0.0160248741915	0.189201983708	0.0129274282397	0.215401532204	-21.9775188125	8.7967744649	-13.9668902245
7	7.46299103975	-3.50983883126	-0.860764102076	4.33365666746	1.43643062392	5.18784416993	0.0529986630275	0.146286366991	0.282994883023	-0.142827795754	0.0983172646491	-0.32669770403	0.109513342176	0.29724796522	-0.160595589398	0.173622736445	-0.031838973571	-0.0237338957991	0.149423085052	0.00899834637839	0.214365947586	-22.5038224885	11.0919068467	-23.4839883973
8	0.63731547273	0.372535611816	-0.836571354707	2.13862138575	-2.26111028458	4.39795069805	-0.0230119240436	0.0763065634681	-0.0326347434508	-0.209780864836	0.0554372382291	0.115142927061	0.265488676827	-0.131761363889	-0.0768872293264	0.167955481424	-0.0333278787457	-0.0306290140026	0.188312906551	-0.0399322176993	0.248154843693	-31.4443293632	5.74305335063	-21.2640484243
9	5.46167284533	2.6509081283	-2.52771317779	8.68994258926	-6.31923980982	5.86617018003	-0.00964099131288	0.210066902845	0.0063810079126	0.03525122132	-0.115507209245	-0.425883739555	-0.0828079810228	-0.00489487984019	0.0605004411903	0.202627394222	-0.00213900227679	-0.0231229100441	0.23424950596	-0.0122542251631	0.177417216138	-26.2807595998	12.7487707206	-42.1497030761
10	4.30104402153	0.805659849953	-3.60619009586	3.83922860076	-3.72076151798	8.42575192443	0.124424114297	0.370246330047	0.139208006317	-0.474977797209	-0.199371923252	-0.456278032207	0.0336872313318	0.226731803252	0.0681323611061	0.31421078879	0.0193864918193	0.0808709493698	0.246752561623	0.000368960300276	0.28370478873	-17.941262096	12.1812895754	-45.9112423147

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: B

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 32 through 48 )	32 - 48	2 - 18
2	2	chain 'A' and (resid 49 through 99 )	49 - 99	19 - 69
3	3	chain 'A' and (resid 100 through 118 )	100 - 118	70 - 88
4	4	chain 'A' and (resid 119 through 146 )	119 - 146	89 - 116
5	5	chain 'A' and (resid 147 through 191 )	147 - 191	117 - 152
6	6	chain 'A' and (resid 192 through 246 )	192 - 246	153 - 207
7	7	chain 'A' and (resid 247 through 275 )	247 - 275	208 - 231
8	8	chain 'A' and (resid 276 through 332 )	276 - 332	232 - 288
9	9	chain 'A' and (resid 333 through 368 )	333 - 368	289 - 324
10	10	chain 'A' and (resid 369 through 406 )	369 - 406	325 - 362

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