PDB-3pv2: Structure of Legionella fallonii DegQ (wt)

ID or keywords:

Entry

Database: PDB / ID: 3pv2

Title

Structure of Legionella fallonii DegQ (wt)

Components

DegQ

Keywords

HYDROLASE / trypsin fold /

PDZ domain / chaperone protease

Function / homology

Function and homology information

peptidase Do /

periplasmic space / serine-type endopeptidase activity / identical protein binding
Similarity search - Function

Biological species

Legionella fallonii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Wrase, R. / Scott, H. / Hilgenfeld, R. / Hansen, G.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: The Legionella HtrA homologue DegQ is a self-compartmentizing protease that forms large 12-meric assemblies.
Authors: Wrase, R. / Scott, H. / Hilgenfeld, R. / Hansen, G.

History

Deposition	Dec 6, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 15, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3pv2.cif.gz	602.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3pv2.ent.gz	501.5 KB	Display	PDB format
PDBx/mmJSON format	3pv2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pv/3pv2 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/3pv2	HTTPS FTP

-
Related structure data

Related structure data	3pv3C 3pv4C 3pv5C 3cs0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3pv5-1 2w8r-1 2w8p-1 30134 2w8q-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#232 - Apr 2019 Proteins and Biominerals similarity (1)

Deposited unit

A: DegQ

B: DegQ

C: DegQ

D: DegQ

192 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DegQ

B: DegQ

C: DegQ

D: DegQ

A: DegQ

B: DegQ

C: DegQ

D: DegQ

A: DegQ

B: DegQ

C: DegQ

D: DegQ

defined by author&software
576 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	136.700, 136.700, 327.001
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	DegQ Mass: 48032.637 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella fallonii (bacteria) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 degP- / References: UniProt: F8W672*PLUS
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.81 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 29.5% (v/v) PEG 400, 100 mM MES pH 6.5, vapor diffusion, sitting drop, temperature 292K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.91841 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: May 27, 2009

Radiation

Monochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.91841 Å / Relative weight: 1

Reflection

Resolution: 2.15→111.32 Å / Num. all: 121567 / Num. obs: 121567 / % possible obs: 98.1 % / Redundancy: 2 % / R_sym value: 0.045 / Net I/σ(I): 10.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
2.15-2.27	1.9	0.424	1.7	0.424	1	99.7
2.27-2.4	1.9	0.288	2.5	0.288	1	99.6
2.4-2.57	1.9	0.191	3.9	0.191	1	99.4
2.57-2.78	2	0.117	6.3	0.117	1	99.1
2.78-3.04	2	0.072	10.1	0.072	1	98.7
3.04-3.4	2	0.044	15.7	0.044	1	98.2
3.4-3.93	2	0.032	20.1	0.032	1	97.3
3.93-4.81	2	0.029	17.9	0.029	1	95.9
4.81-6.8	2.1	0.026	21.4	0.026	1	94.1
6.8-37.105	2.1	0.018	18.7	0.018	1	86.6

-
Processing

Software

Name	Version	Classification
SCALA	3.3.9	data scaling
REFMAC	5.5.0110	refinement
PDB_EXTRACT	3.1	data extraction
MOSFLM		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CS0

3cs0

Resolution: 2.15→36.93 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.552 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25056	6107	5 %	RANDOM
R_work	0.21137	-	-	-
obs	0.21335	115449	98.07 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 43.277 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.9 Å²	0.95 Å²	0 Å²
2-	-	1.9 Å²	0 Å²
3-	-	-	-2.85 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→36.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11522	0	0	468	11990

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	11784
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	7859
X-RAY DIFFRACTION	r_angle_refined_deg	1.918	1.978	15973
X-RAY DIFFRACTION	r_angle_other_deg	2.334	3	19469
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.586	5	1544
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.443	25.888	445
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.683	15	2089
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.831	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.126	0.2	1939
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	12995
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	2010
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.483	1.5	7713
X-RAY DIFFRACTION	r_mcbond_other	0.083	1.5	3188
X-RAY DIFFRACTION	r_mcangle_it	2.717	2	12481
X-RAY DIFFRACTION	r_scbond_it	3.149	3	4071
X-RAY DIFFRACTION	r_scangle_it	5.41	4.5	3492
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.15→2.206 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.358	481	-
R_work	0.321	8741	-
obs	-	-	99.71 %

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	0.5531	0.0799	0.1834	2.0726	0.3582	0.1816	0.1803	-0.0421	-0.0592	-0.064	-0.0163	0.1819	0.0917	0.0427	-0.164	0.2286	-0.0002	-0.0605	0.168	0.0372	0.7254	-11.464	56.779	75.022
2	0.677	1.3645	1.0766	3.2099	0.4979	0.0315	0.035	-0.091	0.0675	-0.1254	0.0127	0.4272	-0.0646	0.1007	-0.0477	0.1787	0.0103	0.0042	0.1714	0.0184	0.835	-13.924	68.078	77.122
3	1.5118	1.6629	1.8851	3.3408	1.1727	1.4879	0.3593	-0.1504	-0.2878	0.404	-0.1703	-0.243	0.3192	-0.0041	-0.1891	0.3886	-0.008	0.0266	0.3329	0.0447	0.6979	-38.946	77.061	78.671
4	1.2765	0.1829	0.5033	2.2274	-1.9857	2.0953	-0.0909	0.0195	-0.1	-0.0797	0.1987	0.0336	0.0169	0.0003	-0.1078	0.2695	0.0156	0.052	0.2608	-0.0513	0.6095	-53.526	78.177	46.426
5	2.427	-1.6352	-0.196	1.1838	-0.2069	0.504	-0.187	-0.0514	-0.1746	-0.0177	-0.2233	0.0101	0.2484	0.2346	0.4103	0.349	0.1811	0.1384	0.2468	0.0961	0.5247	-12.164	33.801	14.754
6	1.5216	-1.3927	-0.8141	1.4719	-0.7865	-0.8826	-0.0479	0.1524	0.0272	-0.0279	-0.2271	0.0278	0.0259	0.0227	0.275	0.3389	0.1606	0.076	0.2912	0.0329	0.531	-19.358	41.146	9.186
7	2.9747	-0.9908	-0.027	2.1434	-0.3427	-0.3325	-0.1201	0.0994	-0.3004	0.0211	0.0148	0.1082	0.026	-0.0183	0.1054	0.3058	-0.0024	0.009	0.2745	-0.0156	0.652	-14.086	48.062	-16.864
8	1.885	-0.028	-0.4587	2.2917	-0.4506	0.5922	0.0366	-0.0239	0.0502	-0.0266	-0.0215	-0.0094	0.0706	-0.0386	-0.015	0.2524	0.0123	0.0042	0.2758	-0.0392	0.5765	14.176	68.966	-18.901
9	0.308	0.1244	-0.4833	0.5855	-0.3883	1.5585	0.0356	-0.0767	-0.1222	-0.1836	-0.0102	0.0058	-0.2935	-0.067	-0.0255	0.3565	0.073	0.0159	0.2821	-0.0178	0.5329	-35.208	68.355	0.786
10	0.2484	0.0044	-1.4244	3.3604	-2.1426	2.9743	0.0295	0.0308	-0.0589	0.1306	-0.0847	0.0559	-0.1258	0.0667	0.0552	0.2848	0.0588	0.0305	0.2875	-0.0078	0.5817	-36.482	58.836	14.084
11	0.879	-0.7496	-1.376	1.4618	1.9097	1.6369	0.0321	-0.0608	-0.1343	0.0466	-0.3524	0.1735	0.2024	-0.185	0.3203	0.2407	0.1042	-0.014	0.3565	-0.0795	0.6223	-52.179	71.83	19.534
12	0.0284	-0.52	0.8811	1.6256	0.4665	1.0171	-0.0643	0.1223	-0.0087	-0.0886	-0.0892	0.024	-0.3048	0.085	0.1535	0.2349	0.0228	0.0348	0.3367	-0.0201	0.6193	-51.982	96.951	31.786
13	0.8094	-0.9622	-0.2595	0.3955	0.1706	2.0126	-0.4025	-0.1589	-0.1368	0.1458	0.2637	0.0423	-0.0397	-0.2077	0.1388	0.3747	0.1325	0.1842	0.1895	0.0178	0.6104	-40.692	52.734	39.998
14	1.022	-0.8902	-0.4189	-0.8034	0.0244	4.0897	-0.2957	-0.0314	-0.1289	0.0249	0.1659	0.145	0.0772	0.1697	0.1297	0.4188	0.1058	0.2022	0.1248	0.057	0.6292	-34.665	45.83	34.916
15	3.0281	1.347	-0.3516	-0.1893	1.8627	1.8769	-0.087	0.4255	0.2489	0.2827	0.295	-0.0221	0.1006	-0.1127	-0.208	0.1979	-0.017	-0.0535	0.2898	0.0797	0.7088	-22.519	24.703	46.48
16	2.2041	-0.4605	-0.1607	0.2357	-0.3662	1.7718	-0.0883	-0.0943	0.0847	-0.0033	0.0369	0.011	-0.1815	0.0936	0.0515	0.3605	-0.0304	0.0064	0.2773	0.018	0.5834	4.674	35.059	65.76

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 137
2	X-RAY DIFFRACTION	2	A	138 - 245
3	X-RAY DIFFRACTION	3	A	246 - 346
4	X-RAY DIFFRACTION	4	A	347 - 439
5	X-RAY DIFFRACTION	5	B	7 - 136
6	X-RAY DIFFRACTION	6	B	137 - 245
7	X-RAY DIFFRACTION	7	B	246 - 346
8	X-RAY DIFFRACTION	8	B	347 - 439
9	X-RAY DIFFRACTION	9	C	6 - 136
10	X-RAY DIFFRACTION	10	C	137 - 192
11	X-RAY DIFFRACTION	11	C	193 - 296
12	X-RAY DIFFRACTION	12	C	297 - 439
13	X-RAY DIFFRACTION	13	D	6 - 142
14	X-RAY DIFFRACTION	14	D	143 - 243
15	X-RAY DIFFRACTION	15	D	244 - 346
16	X-RAY DIFFRACTION	16	D	347 - 439

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi