PDB-7d6p: X-ray structure of the intermolecular complex of Clostridium perf...

ID or keywords:

Entry

Database: PDB / ID: 7d6p

Title

X-ray structure of the intermolecular complex of Clostridium perfringens sortase C with the C-terminal cell wall sorting signal motif.

Components

Sortase family protein

Keywords

TRANSFERASE / cysteine transpeptidase / complex

Function / homology

Sortase C / Sortase family / Sortase domain superfamily / Sortase domain / hydrolase activity / membrane / Sortase family protein

Function and homology information

Biological species

Clostridium perfringens (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.38 Å

Authors

Kamitori, S. / Tamai, E.

Funding support

Japan, 1items

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: X-ray structures of Clostridium perfringens sortase C with C-terminal cell wall sorting motif of LPST demonstrate role of subsite for substrate-binding and structural variations of catalytic site.
Authors: Tamai, E. / Sekiya, H. / Nariya, H. / Katayama, S. / Kamitori, S.

History

Deposition	Oct 1, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 2, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7d6p.cif.gz	57 KB	Display	PDBx/mmCIF format
PDB format	pdb7d6p.ent.gz	37.6 KB	Display	PDB format
PDBx/mmJSON format	7d6p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7d6p_validation.pdf.gz	455.5 KB	Display	wwPDB validaton report
Full document	7d6p_full_validation.pdf.gz	457.1 KB	Display
Data in XML	7d6p_validation.xml.gz	9.5 KB	Display
Data in CIF	7d6p_validation.cif.gz	11.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d6/7d6p ftp://data.pdbj.org/pub/pdb/validation_reports/d6/7d6p	HTTPS FTP

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Related structure data

Related structure data	7d6tC 6ixzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1deu-1 3dni-d 2yut-d 1q88-1 2k03-d 5v44-2 2qu8-d 5v47-1 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Sortase family protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	104.210, 104.210, 44.870
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Sortase family protein / sortase C Mass: 24830.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (strain SM101 / Type A) (bacteria) Gene: CPR_0146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SWL7
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.83 Å³/Da / Density % sol: 56.57 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% (w/v) PEG 3350, 200mM LiSO4, 100mM Tris-HCl, pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 26, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.38→18.8 Å / Num. obs: 11342 / % possible obs: 98.6 % / Redundancy: 10.5 % / CC_1/2: 0.997 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.38→2.44 Å / Num. unique obs: 825 / CC_1/2: 0.909

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6IXZ

6ixz

Resolution: 2.38→18.8 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.93 / SU B: 11.162 / SU ML: 0.252 / Cross valid method: FREE R-VALUE / ESU R: 0.353 / ESU R Free: 0.257
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2763	541	4.773 %
R_work	0.2445	10793	-
all	0.246	-	-
obs	-	11334	98.625 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 74.757 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.013 Å²	-0.006 Å²	0 Å²
2-	-	-0.013 Å²	0 Å²
3-	-	-	0.042 Å²

Refinement step

Cycle: LAST / Resolution: 2.38→18.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1555	0	11	14	1580

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	1592
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	1475
X-RAY DIFFRACTION	r_angle_refined_deg	1.5	1.64	2163
X-RAY DIFFRACTION	r_angle_other_deg	1.09	1.583	3446
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.088	5	197
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.156	25.6	75
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.824	15	278
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.431	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.051	0.2	213
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1759
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	282
X-RAY DIFFRACTION	r_nbd_refined	0.162	0.15	289
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.155	0.15	1321
X-RAY DIFFRACTION	r_nbtor_refined	0.274	0.15	1042
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.201	0.15	3064
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.15	96
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.134	0.15	7
X-RAY DIFFRACTION	r_nbd_other	0.16	0.15	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.196	0.15	13
X-RAY DIFFRACTION	r_mcbond_it	4.534	7.957	791
X-RAY DIFFRACTION	r_mcbond_other	4.508	7.945	790
X-RAY DIFFRACTION	r_mcangle_it	7.145	11.919	987
X-RAY DIFFRACTION	r_mcangle_other	7.147	11.931	988
X-RAY DIFFRACTION	r_scbond_it	4.346	8.215	801
X-RAY DIFFRACTION	r_scbond_other	4.344	8.214	802
X-RAY DIFFRACTION	r_scangle_it	6.791	12.181	1176
X-RAY DIFFRACTION	r_scangle_other	6.788	12.18	1177
X-RAY DIFFRACTION	r_lrange_it	10.661	99.072	1929
X-RAY DIFFRACTION	r_lrange_other	10.665	99.07	1928

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.38-2.441	0.414	43	0.395	768	0.396	813	0.67	0.632	99.754	0.365
2.441-2.507	0.328	44	0.349	781	0.348	827	0.702	0.732	99.7582	0.337
2.507-2.578	0.414	42	0.308	731	0.314	773	0.718	0.787	100	0.28
2.578-2.656	0.361	35	0.319	733	0.321	770	0.75	0.819	99.7403	0.282
2.656-2.741	0.369	41	0.296	680	0.3	726	0.832	0.849	99.3113	0.263
2.741-2.835	0.353	34	0.331	688	0.332	723	0.857	0.86	99.8617	0.301
2.835-2.94	0.278	37	0.298	639	0.297	680	0.892	0.868	99.4118	0.255
2.94-3.056	0.336	29	0.263	656	0.266	692	0.846	0.886	98.9884	0.245
3.056-3.189	0.321	22	0.288	599	0.289	632	0.869	0.857	98.2595	0.269
3.189-3.339	0.248	18	0.319	571	0.317	612	0.892	0.843	96.2418	0.297
3.339-3.514	0.315	31	0.296	535	0.297	587	0.842	0.868	96.4225	0.286
3.514-3.719	0.337	23	0.301	538	0.302	566	0.892	0.886	99.1166	0.3
3.719-3.965	0.232	30	0.247	458	0.246	511	0.912	0.905	95.499	0.258
3.965-4.266	0.31	27	0.255	466	0.257	503	0.885	0.909	98.0119	0.275
4.266-4.65	0.276	20	0.201	431	0.205	458	0.928	0.938	98.4716	0.232
4.65-5.159	0.235	23	0.187	403	0.189	430	0.93	0.944	99.0698	0.224
5.159-5.884	0.184	13	0.201	353	0.2	368	0.935	0.946	99.4565	0.245
5.884-7.036	0.3	14	0.225	317	0.228	331	0.924	0.93	100	0.286
7.036-9.319	0.093	8	0.175	264	0.172	272	0.985	0.961	100	0.228
9.319-18.8	0.289	7	0.179	180	0.183	187	0.948	0.968	100	0.225

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