PDB-5dlh: SFX structure of thermolysin

ID or keywords:

Entry

Database: PDB / ID: 5dlh

Title

SFX structure of thermolysin

Components

Thermolysin

Keywords

HYDROLASE / thermolysin / SFX / ambient temperature

Function / homology

Function and homology information

thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function

Biological species

Geobacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

FREE ELECTRON LASER / Resolution: 2.2501 Å

Authors

DeMirci, H.D. / Sauter, N.K. / Brewster, A.S. / Kern, J.

Funding support

United States, 4items

Organization	Grant number	Country
Department of Energy (DOE, United States)	DE-AC02-05CH11231	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM055302	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM102520	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM095887	United States

Citation

Journal: To Be Published
Title: Serial Femtosecond Crystallography of Ribosome-Antibiotic and Photosystem II Complexes at Ambient Temperature using a Concentric Electrospinning Injector.
Authors: DeMirci, H.D.

History

Deposition	Sep 4, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Feb 14, 2018	Group: Data collection / Category: diffrn_source Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Sep 19, 2018	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5dlh.cif.gz	187.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5dlh.ent.gz	153.6 KB	Display	PDB format
PDBx/mmJSON format	5dlh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5dlh_validation.pdf.gz	423.5 KB	Display	wwPDB validaton report
Full document	5dlh_full_validation.pdf.gz	424.3 KB	Display
Data in XML	5dlh_validation.xml.gz	13.6 KB	Display
Data in CIF	5dlh_validation.cif.gz	18.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dl/5dlh ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dlh	HTTPS FTP

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Related structure data

Similar structure data	1fjv-d 4tli-d 5tmn-d 1tli-d 1lne-d 1lnf-d 2a7g-d 5hqd-d 4m65-d 1fjo-d 3ms3-d 5t9q-d 1esp-d 3p7u-d 5tac-d 4tnl-d 4ow3-d 3n21-d 1kl6-d 1fj3-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

Deposited unit

A: Thermolysin

hetero molecules

34.6 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)	93.794, 93.794, 132.243
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

#1: Protein	Thermolysin / Neutral protease Mass: 34360.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: nprS, nprM / Production host: Escherichia coli (E. coli) / References: UniProt: P43133, thermolysin
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.66 %
Crystal grow	Temperature: 298 K / Method: batch mode / Details: 40% PEG 2000, 100 mM MES pH 6.5, 5 mM CaCl2

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Data collection

Diffraction	Mean temperature: 298 K
Diffraction source	Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.27 Å
Detector	Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 17, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.27 Å / Relative weight: 1
Reflection	Resolution: 2.25→81.23 Å / Num. obs: 16903 / % possible obs: 99.9 % / Redundancy: 347.6 % / Net I/σ(I): 64.9

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Processing

Software

Name	Version	Classification
PHENIX	dev_1938	refinement
cctbx.xfel		data reduction
PHASER		phasing

Refinement

Resolution: 2.2501→44.2 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2271	1688	9.99 %
R_work	0.1789	-	-
obs	0.1836	16903	99.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.2501→44.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2424	0	5	89	2518

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2497
X-RAY DIFFRACTION	f_angle_d	0.945	3404
X-RAY DIFFRACTION	f_dihedral_angle_d	12.508	856
X-RAY DIFFRACTION	f_chiral_restr	0.046	361
X-RAY DIFFRACTION	f_plane_restr	0.004	450

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 (%)
2.2501-2.3163	0.3806	134	0.3396	1208	X-RAY DIFFRACTION	99
2.3163-2.391	0.3477	136	0.3189	1240	X-RAY DIFFRACTION	100
2.391-2.4765	0.2748	137	0.2638	1230	X-RAY DIFFRACTION	100
2.4765-2.5756	0.2807	138	0.2283	1249	X-RAY DIFFRACTION	100
2.5756-2.6928	0.264	138	0.1953	1241	X-RAY DIFFRACTION	100
2.6928-2.8348	0.2355	139	0.1865	1257	X-RAY DIFFRACTION	100
2.8348-3.0124	0.2387	139	0.1888	1255	X-RAY DIFFRACTION	100
3.0124-3.2449	0.22	141	0.1814	1262	X-RAY DIFFRACTION	100
3.2449-3.5713	0.2389	141	0.1587	1266	X-RAY DIFFRACTION	100
3.5713-4.0878	0.1948	143	0.1446	1290	X-RAY DIFFRACTION	100
4.0878-5.1489	0.1825	144	0.1279	1300	X-RAY DIFFRACTION	100
5.1489-44.2083	0.2167	158	0.1938	1417	X-RAY DIFFRACTION	100

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	8.1823	-6.2224	-1.807	7.0381	3.5942	5.6491	-0.0602	-0.4617	0.4717	0.2744	0.2645	-0.0098	-0.1229	0.03	-0.0078	0.2937	-0.0372	-0.0035	0.2212	0.0902	0.3528	26.8387	28.9234	78.3284
2	5.2719	1.8886	3.319	4.8847	0.8619	2.1114	-0.1787	0.099	-0.5624	-0.1483	0.2178	-0.3705	-0.259	0.2155	0.0042	0.3753	0.0177	0.0255	0.4087	0.0417	0.3844	32.3723	26.9207	72.5365
3	3.2247	-3.3463	1.2127	9.6317	2.0469	2.2243	-0.0059	0.3047	0.1814	-0.0784	-0.2761	-0.3867	0.054	0.1442	0.2042	0.3714	0.0041	0.0018	0.4171	0.0656	0.4143	28.8903	40.4203	65.8918
4	6.818	0.4266	0.717	2.415	2.3214	3.0073	0.0297	-0.1911	0.044	0.1205	0.0927	0.1881	0.0603	0.0827	-0.0643	0.3789	-0.0005	0.0449	0.3354	0.0042	0.3523	26.8127	34.1889	76.8502
5	5.1155	5.8754	4.3951	8.3886	4.3588	4.0651	0.3863	-0.5425	-0.7683	0.1593	-0.1007	-0.3885	0.3712	0.0513	-0.278	0.4615	0.0511	0.0165	0.3475	0.0384	0.4251	16.4982	19.709	63.9372
6	1.2458	1.4231	1.1624	2.8259	2.8496	3.331	0.1353	-0.0131	-0.0263	0.1254	-0.221	0.4312	0.0037	-0.2178	-0.1801	0.3767	0.0352	0.0309	0.4355	0.0156	0.3962	23.2947	31.8747	61.489
7	4.2081	-4.0982	-2.8866	7.5133	5.197	9.5104	0.1654	0.1134	0.1555	-0.1233	-0.0431	0.2054	0.1537	-0.5055	0.0173	0.3498	-0.0732	-0.0154	0.3849	0.0168	0.3587	18.5117	40.678	63.4649
8	2.8763	1.7964	0.7057	3.3384	-3.5188	7.7528	-0.2455	-0.3382	-0.0178	0.3238	-0.038	0.1406	0.2771	-0.0751	0.2793	0.2574	0.0585	-0.0341	0.4754	-0.03	0.2859	12.3517	39.9624	71.9842
9	3.8236	2.8053	4.0193	2.5838	3.2383	4.5935	0.1606	0.1575	0.5813	0.5011	-0.3844	-1.4076	0.5682	0.6847	0.1385	0.33	-0.0016	-0.0026	0.2948	0.0268	0.2779	14.0902	32.1634	62.8467
10	8.7989	-3.4912	0.6969	4.9297	2.323	4.8988	0.3311	0.2209	-0.0617	0.1845	-0.3592	-0.0954	-0.4261	0.3964	0.07	0.4805	0.0051	-0.0021	0.4789	0.0086	0.4484	14.1669	29.7437	51.8952
11	8.9283	5.8577	-5.6591	4.5364	-1.8846	8.4032	0.0976	1.2444	1.4358	-0.6851	-0.1224	-0.0389	0.8852	-0.3059	-1.6191	0.3164	0.1247	0.1162	0.2751	0.1187	0.5547	6.934	38.251	49.1356
12	3.9158	-1.7511	0.3288	3.1339	-2.9292	7.013	-0.0348	0.2828	0.6409	-0.3998	-0.0153	-0.2192	0.0103	0.6555	-0.14	0.4146	0.0003	0.0611	0.4252	-0.0006	0.4094	6.2717	31.2494	56.5938
13	2.6082	-0.928	-0.3948	3.2796	0.9294	1.4711	0.1758	-0.3268	-0.1006	0.2645	-0.2575	0.3603	0.2066	-0.2706	0.0053	0.4453	-0.01	0.0277	0.4724	0.0142	0.3677	3.9132	32.9101	71.1011
14	3.92	3.2843	1.5867	3.3724	2.0371	2.4059	-0.4495	0.0611	0.36	-0.0599	-0.3076	0.3857	-0.7208	-0.7899	0.5324	0.4762	-0.0095	0.0083	0.4483	-0.0622	0.4771	-6.4186	37.9555	59.8693
15	7.8936	3.4712	-0.1205	2.7703	-2.1371	3.5894	0.3194	1.5638	1.5764	-0.7112	-0.0127	1.1009	-0.4388	0.2922	-0.7671	0.6646	0.1259	-0.0708	0.6021	0.0268	0.6515	-4.2126	43.7064	51.3026
16	1.4716	1.7488	-1.2242	3.3922	-0.9627	1.6479	-0.0453	0.1042	0.2376	-0.0775	-0.0227	0.1611	-0.2544	0.1108	0.1484	0.3802	-0.009	0.0067	0.4236	-0.0488	0.4314	-4.6205	31.4285	58.9929
17	8.6984	1.3309	-7.858	2.4858	-0.4753	9.9138	0.4054	0.1964	-0.2432	-0.0597	-0.1842	-0.1987	-0.2641	0.5393	-0.1902	0.3342	-0.0228	-0.0212	0.2801	0.0234	0.36	2.6129	18.6949	58.3513
18	8.4683	4.9818	-2.2391	4.4606	-2.0637	7.7837	-0.0253	0.0934	-0.3505	-0.4712	-0.1336	0.0987	0.2254	-0.2505	0.0874	0.3426	0.0468	0.0003	0.3322	-0.0213	0.3164	2.0967	24.4311	46.611
19	6.0102	-1.4	-2.9093	5.7681	1.6107	4.413	0.0831	0.2538	-0.3185	-0.469	-0.1037	0.3686	0.5973	-0.3557	-0.0917	0.4684	-0.0215	-0.0222	0.4347	-0.0288	0.5314	-4.4179	13.2876	53.4003
20	8.1853	-4.9379	-2.3751	3.1603	2.4704	9.9718	-0.1812	0.8795	0.0368	0.1753	0.3064	0.0699	0.8705	-0.8553	-0.3208	0.3334	-0.0263	-0.09	0.5076	-0.003	0.479	-9.4343	26.3078	52.9608

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:17)
2	X-RAY DIFFRACTION	2	(chain A and resid 18:37)
3	X-RAY DIFFRACTION	3	(chain A and resid 38:53)
4	X-RAY DIFFRACTION	4	(chain A and resid 54:76)
5	X-RAY DIFFRACTION	5	(chain A and resid 77:89)
6	X-RAY DIFFRACTION	6	(chain A and resid 90:109)
7	X-RAY DIFFRACTION	7	(chain A and resid 110:126)
8	X-RAY DIFFRACTION	8	(chain A and resid 127:139)
9	X-RAY DIFFRACTION	9	(chain A and resid 140:144)
10	X-RAY DIFFRACTION	10	(chain A and resid 145:156)
11	X-RAY DIFFRACTION	11	(chain A and resid 157:160)
12	X-RAY DIFFRACTION	12	(chain A and resid 161:172)
13	X-RAY DIFFRACTION	13	(chain A and resid 173:209)
14	X-RAY DIFFRACTION	14	(chain A and resid 210:217)
15	X-RAY DIFFRACTION	15	(chain A and resid 218:225)
16	X-RAY DIFFRACTION	16	(chain A and resid 226:254)
17	X-RAY DIFFRACTION	17	(chain A and resid 255:272)
18	X-RAY DIFFRACTION	18	(chain A and resid 273:291)
19	X-RAY DIFFRACTION	19	(chain A and resid 292:307)
20	X-RAY DIFFRACTION	20	(chain A and resid 308:316)

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