PDB-6za2: Crystal structure of dimeric latent PorU from Porphyromonas gingivalis

ID or keywords:

Entry

Database: PDB / ID: 6za2

Title

Crystal structure of dimeric latent PorU from Porphyromonas gingivalis

Components

Por secretion system protein porU

Keywords

HYDROLASE / sortase / transpeptidase / type-IX secretion system / periodontopathogen / virulence factor

Function / homology

Function and homology information

cysteine-type peptidase activity / proteolysis / metal ion binding
Similarity search - Function

Biological species

Porphyromonas gingivalis ATCC 33277 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.35 Å

Authors

Gomis-Ruth, F.X. / Goulas, T. / Guevara, T. / Rodriguez-Banqueri, A. / Potempa, J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Intermolecular latency regulates the essential C-terminal signal peptidase and sortase of the Porphyromonas gingivalis type-IX secretion system.
Authors: Mizgalska, D. / Goulas, T. / Rodriguez-Banqueri, A. / Veillard, F. / Madej, M. / Malecka, E. / Szczesniak, K. / Ksiazek, M. / Widziolek, M. / Guevara, T. / Eckhard, U. / Sola, M. / Potempa, J. / Gomis-Ruth, F.X.

History

Deposition	Jun 4, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 29, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 13, 2021	Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / struct Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title
Revision 1.2	Jun 19, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6za2.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb6za2.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	6za2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6za2_validation.pdf.gz	481.8 KB	Display	wwPDB validaton report
Full document	6za2_full_validation.pdf.gz	501.2 KB	Display
Data in XML	6za2_validation.xml.gz	69.5 KB	Display
Data in CIF	6za2_validation.cif.gz	95.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/za/6za2 ftp://data.pdbj.org/pub/pdb/validation_reports/za/6za2	HTTPS FTP

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Related structure data

Similar structure data	5bk3-d 5mvj-d 6smp-d 4657 7mlv-d 6en4-d 3hno-d 5bo5-d 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
Related items in Molecule of the Month	#56 - Aug 2004 Caspases similarity (1) #224 - Aug 2018 Legumain similarity (1)

Deposited unit

A: Por secretion system protein porU

B: Por secretion system protein porU

hetero molecules

257 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering, SEC-MALLS

Unit cell

Length a, b, c (Å)	171.700, 171.700, 440.400
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

#1: Protein	Por secretion system protein porU Mass: 128308.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria) Gene: porU, PGN_0022 / Production host: Escherichia coli (E. coli) / References: UniProt: B2RGP6
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.65 Å³/Da / Density % sol: 66.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: The best crystals of full-length native and selenomethionine-derivatized PorU were obtained at 20 degrees in drops with 1 microL of protein solution (at 5-10 mg per mL in 20 mM Tris-HCl, 150 ...Details: The best crystals of full-length native and selenomethionine-derivatized PorU were obtained at 20 degrees in drops with 1 microL of protein solution (at 5-10 mg per mL in 20 mM Tris-HCl, 150 mM NaCl, pH 7.5) and 1 microL of reservoir solution (100 mM HEPES, 200 mM calcium chloride, 28-32 per cent v/v PEG600, pH 7.5). Crystals were cryoprotected by rapid passage through drops containing increasing amounts of glycerol (5-to-20 per cent v/v).

Crystal

Density Matthews: 3.65 Å³/Da / Density % sol: 66.31 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The best crystals of full-length native and selenomethionine-derivatized PorU were obtained at 20 degrees in drops with 1 microL of protein solution (at 5-10 mg per mL in 20 mM Tris-HCl, 150 ...

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Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9817 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9817 Å / Relative weight: 1
Reflection	Resolution: 3.35→88.48 Å / Num. obs: 56055 / % possible obs: 100 % / Redundancy: 38.5 % / B_iso Wilson estimate: 107 Å² / CC_1/2: 1 / R_merge(I) obs: 0.152 / R_rim(I) all: 0.154 / Χ²: 1.021 / Net I/σ(I): 22.71
Reflection shell	Resolution: 3.35→3.55 Å / Redundancy: 39.626 % / R_merge(I) obs: 1.899 / Mean I/σ(I) obs: 3.12 / Num. unique obs: 8750 / CC_1/2: 0.844 / R_rim(I) all: 1.923 / % possible all: 100

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
BUSTER	2.10.3	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.35→88.48 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.927 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R_free Blow DPI: 0.432

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.243	836	1.49 %	RANDOM
R_work	0.202	-	-	-
obs	0.203	56054	100 %	-

Displacement parameters

B_iso max: 293.76 Å² / B_iso mean: 140.3 Å² / B_iso min: 62.19 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-7.7643 Å²	0 Å²	0 Å²
2-	-	-7.7643 Å²	0 Å²
3-	-	-	15.5285 Å²

Refine analyze

Luzzati coordinate error obs: 0.4 Å

Refinement step

Cycle: final / Resolution: 3.35→88.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16378	0	4	4	16386
B_iso mean	-	-	148.26	94.39	-
Num. residues	-	-	-	-	2164

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	8830	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes
X-RAY DIFFRACTION	t_gen_planes	5344	HARMONIC	5
X-RAY DIFFRACTION	t_it	32210	HARMONIC	20
X-RAY DIFFRACTION	t_nbd	0	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	2231	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance	26	HARMONIC	1
X-RAY DIFFRACTION	t_utility_angle	46	HARMONIC	1
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	36182	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	32210	HARMONIC	2	0.01
X-RAY DIFFRACTION	t_angle_deg	57897	HARMONIC	2	1.15
X-RAY DIFFRACTION	t_omega_torsion				3.65
X-RAY DIFFRACTION	t_other_torsion				3.29

LS refinement shell

Resolution: 3.35→3.44 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2768	76	1.87 %
R_work	0.2322	3983	-
all	0.2331	4059	-
obs	-	-	99.98 %

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	2.1177	-0.0412	-0.28	3.3949	2.2045	1.8068	-0.3545	-0.0968	-0.1376	0.7258	0.4472	-0.3377	0.1761	0.8948	-0.0927	-0.0509	0.0177	-0.2757	0.1135	-0.0913	-0.2165	-18.343	86.901	221.781
2	2.3422	0.0033	0.4525	3.7024	2.593	3.8701	-0.2849	-0.3174	0.3942	0.5091	0.2685	-0.2579	-0.1963	0.6143	0.0164	0.0266	-0.1152	-0.2744	0.1133	-0.0805	-0.2717	-18.8489	100.5581	230.915
3	3.9928	0.314	1.574	4.427	0.9139	4.4106	-0.2462	-0.1329	0.58	-0.0715	-0.2438	0.9276	-0.6314	-0.5509	0.4899	-0.1687	0.0531	-0.2072	-0.1578	-0.1855	0.0805	-46.0731	104.994	219.578
4	2.5961	0.21	0.0102	2.5746	1.8486	3.5412	-0.2984	0.3805	-0.0121	0.0904	0.3224	-0.1955	0.0549	0.4134	-0.024	-0.2178	-0.1557	-0.0681	0.155	-0.0364	-0.14	-26.9037	79.3896	198.635
5	0.82	0.8257	-0.0578	2.1622	0.0799	5.0454	-0.1377	0.9369	0.2173	-0.4514	0.1006	0.1639	-0.402	-0.0895	0.0371	-0.2301	-0.2733	-0.1361	0.3214	0.079	-0.2459	-34.2822	84.9899	183.27
6	1.3394	-0.1623	-2.2871	2.1051	-0.9344	2.9027	-0.1399	0.0976	0.0376	-0.4486	0.0059	0.1784	0.1258	-0.0273	0.1341	-0.086	-0.2033	0.0044	0.3473	-0.0829	-0.3332	-31.863	55.7361	162.796
7	1.4651	-1.4609	0.1335	5.805	-2.2216	6.8551	-0.1623	0.3561	-0.6026	-0.7005	-0.0184	-0.2348	0.3098	0.9853	0.1807	-0.0928	-0.0427	0.1695	0.1282	-0.0955	-0.2194	-23.4775	24.1763	170.017
8	3.4362	0.8754	-0.3794	7.365	-0.2277	0.5175	-0.1681	-0.0008	-0.4424	0.6248	0.061	0.0202	0.146	0.5545	0.1071	0.0031	-0.0294	0.0799	0.4294	-0.0174	-0.34	-26.3539	42.1395	184.698
9	1.7668	-0.7128	-0.1313	1.3757	-0.6245	1.3094	-0.1114	-0.2293	0.2781	0.5994	0.2094	0.5166	-0.0609	-0.5065	-0.0981	0.1358	-0.0818	0.1602	-0.1346	0.0491	0.0326	-71.4368	55.4925	221.513
10	1.9074	-0.0421	-0.2135	3.2366	-1.791	4.0094	-0.014	-0.2605	0.0197	0.7629	0.0842	0.3245	0.2785	-0.2387	-0.0702	0.2267	-0.1565	0.1236	-0.1016	-0.0223	-0.2659	-69.2638	41.0592	230.584
11	3.5686	0.833	-1.5789	4.3882	-0.8011	3.9603	-0.0392	0.0524	-0.1008	0.092	-0.0582	-0.7316	0.5826	0.6989	0.0974	0.0704	0.0161	-0.0738	-0.1079	0.0943	-0.1729	-42.8081	37.9903	217.06
12	2.7987	-0.3381	0.4193	1.9356	-1.5446	3.8759	-0.0878	0.2877	0.0795	0.1158	0.1937	0.4831	-0.1125	-0.1674	-0.1059	-0.1214	-0.1559	-0.0831	-0.1071	0.0519	0.0376	-63.8176	64.1084	198.915
13	2.8247	0.8214	-0.3119	1.4431	0.0114	4.9112	-0.1945	1.043	-0.0559	-0.3136	-0.0712	0.1478	0.2799	0.17	0.2657	-0.1575	-0.2222	-0.0786	0.1481	0.0337	-0.1223	-57.1705	59.6601	182.516
14	6.8398	1.4626	2.5784	3.7618	1.7379	1.4218	-0.1253	1.4979	0.8316	-0.5242	-0.0418	0.4355	-0.3149	0.6379	0.1672	-0.1261	-0.2182	-0.3586	0.4612	0.6099	-0.293	-61.4982	90.5723	164.71
15	1.4763	-1.7286	-0.9074	2.2215	0.6833	4.2669	-0.2912	0.4382	1.1984	-0.0853	-0.139	-0.1179	-1.4359	-0.3588	0.4302	0.7125	0.0208	-0.7742	-0.7201	0.3988	0.5876	-70.1844	120.8623	175.171
16	1.9256	-2.7738	0.8158	5.7432	1.3505	0.4401	-0.7965	0.3339	1.2281	0.9362	-0.0698	-0.172	-0.8403	-0.0815	0.8663	0.2066	-0.083	-0.6206	-0.3354	0.2567	0.3868	-66.0952	101.9732	187.809

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|24 - A\|149 }	A	24 - 149
2	X-RAY DIFFRACTION	2	{ A\|150 - A\|164 A\|302 - A\|404 }	A	150 - 164
3	X-RAY DIFFRACTION	2	{ A\|150 - A\|164 A\|302 - A\|404 }	A	302 - 404
4	X-RAY DIFFRACTION	3	{ A\|165 - A\|301 A\|2001 - A\|2001 A\|2101 - A\|2102 }	A	165 - 301
5	X-RAY DIFFRACTION	3	{ A\|165 - A\|301 A\|2001 - A\|2001 A\|2101 - A\|2102 }	A	2001
6	X-RAY DIFFRACTION	3	{ A\|165 - A\|301 A\|2001 - A\|2001 A\|2101 - A\|2102 }	A	2101 - 2102
7	X-RAY DIFFRACTION	4	{ A\|405 - A\|588 }	A	405 - 588
8	X-RAY DIFFRACTION	5	{ A\|614 - A\|789 }	A	614 - 789
9	X-RAY DIFFRACTION	6	{ A\|790 - A\|932 }	A	790 - 932
10	X-RAY DIFFRACTION	7	{ A\|933 - A\|1054 A\|2002 - A\|2002 }	A	933 - 1054
11	X-RAY DIFFRACTION	7	{ A\|933 - A\|1054 A\|2002 - A\|2002 }	A	2002
12	X-RAY DIFFRACTION	8	{ A\|1055 - A\|1158 }	A	1055 - 1158
13	X-RAY DIFFRACTION	9	{ B\|-6 - B\|149 }	B	-6 - 149
14	X-RAY DIFFRACTION	10	{ B\|150 - B\|164 B\|302 - B\|404 }	B	150 - 164
15	X-RAY DIFFRACTION	10	{ B\|150 - B\|164 B\|302 - B\|404 }	B	302 - 404
16	X-RAY DIFFRACTION	11	{ B\|165 - B\|301 B\|2001 - B\|2001 B\|2101 - B\|2102 }	B	165 - 301
17	X-RAY DIFFRACTION	11	{ B\|165 - B\|301 B\|2001 - B\|2001 B\|2101 - B\|2102 }	B	2001
18	X-RAY DIFFRACTION	11	{ B\|165 - B\|301 B\|2001 - B\|2001 B\|2101 - B\|2102 }	B	2101 - 2102
19	X-RAY DIFFRACTION	12	{ B\|405 - B\|585 }	B	405 - 585
20	X-RAY DIFFRACTION	13	{ B\|614 - B\|789 }	B	614 - 789
21	X-RAY DIFFRACTION	14	{ B\|790 - B\|932 }	B	790 - 932
22	X-RAY DIFFRACTION	15	{ B\|933 - B\|1054 B\|2002 - B\|2002 }	B	933 - 1054
23	X-RAY DIFFRACTION	15	{ B\|933 - B\|1054 B\|2002 - B\|2002 }	B	2002
24	X-RAY DIFFRACTION	16	{ B\|1055 - B\|1158 }	B	1055 - 1158

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