PDB-6q3t: Structure of Protease1 from Pyrococcus horikoshii at room tempera...

ID or keywords:

Entry

Database: PDB / ID: 6q3t

Title

Structure of Protease1 from Pyrococcus horikoshii at room temperature in ChipX microfluidic device

Components

Deglycase PH1704

Keywords

HYDROLASE / ChipX / nucleation / Xo4 / Crystallophore / Room temperature / Counterdiffusion

Function / homology

Function and homology information

protein deglycase / protein deglycase activity / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / cytoplasm
Similarity search - Function

Biological species

Pyrococcus horikoshii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

de Wijn, R. / Engilberge, S. / Olieric, V. / Girard, E. / Sauter, C.

Funding support

France, 3items

Organization	Grant number	Country
French National Research Agency	ANR-10-LABX-0036_NETRNA	France
French National Research Agency	ANR-11-LABX-0057_MITOCROSS	France
French National Research Agency	ANR-13-BS07-0007-01	France

Citation

Journal: Iucrj / Year: 2019
Title: A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography.
Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. ...

History

Deposition	Dec 4, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 1, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jun 5, 2019	Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.3	Jan 24, 2024	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

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Download

PDBx/mmCIF format	6q3t.cif.gz	207.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6q3t.ent.gz	168.7 KB	Display	PDB format
PDBx/mmJSON format	6q3t.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6q3t_validation.pdf.gz	425.2 KB	Display	wwPDB validaton report
Full document	6q3t_full_validation.pdf.gz	426.1 KB	Display
Data in XML	6q3t_validation.xml.gz	18.9 KB	Display
Data in CIF	6q3t_validation.cif.gz	26.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q3/6q3t ftp://data.pdbj.org/pub/pdb/validation_reports/q3/6q3t	HTTPS FTP

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Related structure data

Related structure data	6gzpC 6hw1C 6ibpC 6ibqC 6q52C 1g2iS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1g2i-1 6f2f-1 6f2h-1 6hf6-1 6f2h-2 2h8l-d 4ijs-4 4jng-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Deglycase PH1704

B: Deglycase PH1704

C: Deglycase PH1704

55.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Deglycase PH1704

B: Deglycase PH1704

C: Deglycase PH1704

A: Deglycase PH1704

B: Deglycase PH1704

C: Deglycase PH1704

defined by author
Evidence: gel filtration
111 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.560, 125.560, 133.870
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Deglycase PH1704 / Intracellular protease PH1704 / Protease1 Mass: 18476.309 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1704 / Production host: Escherichia coli (E. coli) References: UniProt: O59413, protein deglycase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Deglycase PH1704 / Intracellular protease PH1704 / Protease1

Mass: 18476.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pyrococcus horikoshii (archaea) / Gene: PH1704 / Production host:

Escherichia coli (E. coli)
References: UniProt: O59413, protein deglycase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal grow	Temperature: 293 K / Method: counter-diffusion / Details: 2.0 to 3.4M Sodium Malonate pH 6.0, 10mM Xo4

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Data collection

Diffraction	Mean temperature: 293 K / Serial crystal experiment: Y
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.2 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 10, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2 Å / Relative weight: 1
Reflection	Resolution: 2.15→45.79 Å / Num. obs: 57690 / % possible obs: 98.7 % / Redundancy: 19 % / R_merge(I) obs: 0.169 / R_pim(I) all: 0.038 / Net I/σ(I): 12
Reflection shell	Resolution: 2.15→2.21 Å
Serial crystallography sample delivery	Method: fixed target

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1G2I

1g2i

Resolution: 2.15→45.79 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.98

	R_factor	Num. reflection	% reflection
R_free	0.1847	2912	5.05 %
R_work	0.1627	-	-
obs	0.1638	57659	98.24 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.15→45.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3906	0	0	96	4002

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	4014
X-RAY DIFFRACTION	f_angle_d	1.095	5438
X-RAY DIFFRACTION	f_dihedral_angle_d	20.411	1484
X-RAY DIFFRACTION	f_chiral_restr	0.063	597
X-RAY DIFFRACTION	f_plane_restr	0.008	698

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 (%)
2.15-2.1853	0.3285	117	0.3102	2647	X-RAY DIFFRACTION	99
2.1853-2.223	0.3136	129	0.2846	2611	X-RAY DIFFRACTION	100
2.223-2.2634	0.2754	143	0.2656	2571	X-RAY DIFFRACTION	99
2.2634-2.3069	0.2535	154	0.2492	2577	X-RAY DIFFRACTION	99
2.3069-2.354	0.2982	135	0.2438	2609	X-RAY DIFFRACTION	99
2.354-2.4052	0.2744	141	0.2323	2595	X-RAY DIFFRACTION	99
2.4052-2.4611	0.2953	146	0.2236	2592	X-RAY DIFFRACTION	99
2.4611-2.5227	0.2924	124	0.2099	2601	X-RAY DIFFRACTION	99
2.5227-2.5909	0.2016	150	0.1892	2598	X-RAY DIFFRACTION	99
2.5909-2.6671	0.2047	135	0.1875	2585	X-RAY DIFFRACTION	99
2.6671-2.7532	0.2035	145	0.1911	2598	X-RAY DIFFRACTION	99
2.7532-2.8516	0.2156	131	0.1882	2613	X-RAY DIFFRACTION	98
2.8516-2.9657	0.2192	132	0.1866	2596	X-RAY DIFFRACTION	98
2.9657-3.1007	0.1971	171	0.1834	2556	X-RAY DIFFRACTION	98
3.1007-3.2641	0.1838	125	0.1721	2606	X-RAY DIFFRACTION	98
3.2641-3.4685	0.1707	131	0.1554	2619	X-RAY DIFFRACTION	98
3.4685-3.7362	0.1698	141	0.1452	2602	X-RAY DIFFRACTION	98
3.7362-4.112	0.1514	127	0.1269	2618	X-RAY DIFFRACTION	97
4.112-4.7065	0.1421	148	0.111	2600	X-RAY DIFFRACTION	97
4.7065-5.9277	0.1254	127	0.1301	2650	X-RAY DIFFRACTION	96
5.9277-45.801	0.1772	160	0.1509	2703	X-RAY DIFFRACTION	94

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	0.2632	0.1551	-0.1374	0.6502	-0.161	0.0791	0.0578	0.0447	-0.059	0.2958	0.022	0.073	-0.0207	-0.1027	-0	0.5467	-0.0081	-0.023	0.372	-0.0017	0.3204	92.1477	86.0926	17.7843
2	0.3944	0.0613	-0.1957	0.5522	-0.4718	0.4263	-0.0018	0.0439	0.06	0.3045	0.0404	-0.001	-0.0864	-0.0999	-0	0.6079	-0.0019	-0.0708	0.3725	-0.0474	0.3897	94.996	98.3858	17.5986
3	0.0778	-0.0121	0.1313	0.0866	-0.2372	0.6773	-0.0546	0.2062	0.2172	0.0917	-0.074	-0.4606	-0.0075	0.25	-0.0007	0.4482	-0.0449	-0.0834	0.4151	0.0119	0.5061	105.942	95.585	7.0298
4	0.1929	0.1569	-0.1762	0.1101	-0.1321	0.1501	0.0047	0.0976	-0.0981	0.1644	-0.1349	-0.3986	0.0469	0.1599	-0	0.4887	-0.0251	-0.1439	0.3878	0.0019	0.4289	107.8873	85.7194	14.4365
5	0.0021	-0.0207	0.0342	0.3262	-0.1783	0.0862	0.0268	0.125	0.0675	-0.0039	-0.0783	-0.2162	0.0348	0.0052	0	0.4401	0.0011	-0.0496	0.3613	0.0063	0.3928	98.4796	68.7635	11.7071
6	0.1432	0.011	-0.1119	0.116	-0.0255	0.0845	-0.0483	0.164	0.1684	-0.2687	-0.0478	-0.3156	-0.01	0.1604	-0	0.5746	-0.0194	-0.0311	0.4871	0.0194	0.4842	100.3965	64.6426	5.0416
7	0.0355	0.0228	0.1059	0.1155	0.0415	0.3077	-0.1011	0.0809	-0.0598	-0.3129	0.0064	-0.2372	0.0281	0.0312	0	0.5142	0.0105	0.0217	0.4237	0.011	0.5203	98.3337	62.6197	4.3458
8	0.1889	0.1847	-0.2213	0.3094	-0.1002	0.3224	0.0114	-0.05	0.2518	0.0507	-0.0279	-0.065	-0.0243	0.0416	0	0.4747	0.0184	-0.0567	0.3833	0.0217	0.4865	92.2294	59.1821	11.1086
9	0.0422	-0.0131	0.0271	0.0015	-0.0083	0.0154	0.1132	0.1546	-0.274	0.1682	0.2056	-0.5113	0.3939	0.3914	-0	0.5583	0.0168	-0.0348	0.4123	0.0183	0.5708	98.0427	50.7177	13.6697
10	0.0744	-0.0396	-0.0466	0.183	-0.0935	0.0992	0.1246	-0.0228	0.0268	0.2591	-0.0438	0.1065	-0.0131	-0.0177	0	0.5039	0.0155	-0.0344	0.3873	0.0513	0.4003	89.5375	56.9447	21.8403
11	0.0427	0.0074	-0.0027	0.0068	0.0174	0.054	-0.0628	-0.4776	-0.0707	0.2646	0.0932	0.2065	-0.1604	0.0063	0	0.8	0.0048	0.0144	0.5324	0.0195	0.4398	88.3361	62.2362	29.7976
12	0.1373	0.1131	-0.1855	0.142	-0.2024	0.2722	0.0836	-0.1666	-0.2341	0.4264	-0.1062	-0.0834	-0.1771	0.1429	0	0.5908	-0.005	-0.1274	0.4132	0.035	0.3909	97.9731	66.8498	24.6164
13	0.1245	-0.0589	0.0817	0.0818	-0.0687	0.3634	0.1379	-0.0799	0.0142	0.1204	0.2754	0.2214	-0.162	-0.1359	0.0221	0.4644	0.052	-0.0058	0.5116	0.1514	0.7937	60.895	62.5814	8.8015
14	0.289	-0.0148	0.2795	0.0681	0.0309	0.2813	-0.0155	-0.0187	0.3092	0.0254	0.2861	0.3219	-0.3413	-0.35	0.0029	0.5114	0.1219	0.101	0.5743	0.1049	0.7906	60.072	68.0154	15.7254
15	0.8461	-0.396	0.6384	0.2515	-0.1809	0.6576	0.1348	-0.1902	-0.222	0.0389	0.199	0.2776	0.0018	-0.0993	0.0047	0.455	0.008	0.008	0.4315	0.1437	0.65	70.029	53.8192	17.6502
16	0.2219	0.0354	-0.1329	0.0942	0.05	0.5899	0.2622	-0.3445	-0.2753	-0.2606	0.0942	0.5956	0.1958	-0.0484	0.036	0.4997	-0.0297	-0.1503	0.4862	0.1811	0.9577	62.8439	49.7755	7.4733

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 50 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 91 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 92 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 166 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 25 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 26 through 41 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 42 through 61 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 62 through 79 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 80 through 91 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 92 through 130 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 131 through 139 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 140 through 166 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 25 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 26 through 61 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 62 through 139 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 140 through 166 )

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