PDB-5hl8: 1.93 Angstrom resolution crystal structure of a pullulanase-speci...

ID or keywords:

Entry

Database: PDB / ID: 5hl8

Title

1.93 Angstrom resolution crystal structure of a pullulanase-specific type II secretion system integral cytoplasmic membrane protein GspL (C-terminal fragment; residues 309-397) from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044

Components

Type II secretion system protein L

Keywords

PROTEIN TRANSPORT / pullulanase-specific type II secretion system / integral cytoplasmic membrane protein / structural genomics / CSGID / Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 / Center for Structural Genomics of Infectious Diseases

Function / homology

General secretion pathway protein M, EpsM / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta / :

Function and homology information

Biological species

Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.93 Å

Authors

Halavaty, A.S. / Minasov, G. / Kiryukhina, O. / Grimshaw, S. / Light, S. / Dubrovska, I. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.93 Angstrom resolution crystal structure of a pullulanase-specific type II secretion system integral cytoplasmic membrane protein GspL (C-terminal fragment; residues 309-397) from Klebsiella ...
Authors: Halavaty, A.S. / Minasov, G. / Kiryukhina, O. / Grimshaw, S. / Light, S. / Dubrovska, I. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 14, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hl8.cif.gz	142.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5hl8.ent.gz	113.5 KB	Display	PDB format
PDBx/mmJSON format	5hl8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5hl8_validation.pdf.gz	450.5 KB	Display	wwPDB validaton report
Full document	5hl8_full_validation.pdf.gz	456.5 KB	Display
Data in XML	5hl8_validation.xml.gz	15.8 KB	Display
Data in CIF	5hl8_validation.cif.gz	20.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hl/5hl8 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hl8	HTTPS FTP

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Related structure data

Similar structure data	1mx6-1 4qst-d 6epw-d 6hib-d 5r4f-d 6hid-d 6hi8-d 5r4w-d 5jx4-d 4qsp-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP95180

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Type II secretion system protein L

B: Type II secretion system protein L

C: Type II secretion system protein L

D: Type II secretion system protein L

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

1

A: Type II secretion system protein L

D: Type II secretion system protein L

defined by author&software
20.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Type II secretion system protein L

C: Type II secretion system protein L

defined by author&software
20.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	50.375, 51.284, 117.021
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	HIS	ASN	ASN	A	A	315 - 395	10 - 90
2	1	HIS	HIS	ASN	ASN	B	B	315 - 395	10 - 90
1	2	PRO	PRO	GLU	GLU	A	A	317 - 394	12 - 89
2	2	PRO	PRO	GLU	GLU	C	C	317 - 394	12 - 89
1	3	PRO	PRO	GLU	GLU	A	A	317 - 393	12 - 88
2	3	PRO	PRO	GLU	GLU	D	D	317 - 393	12 - 88
1	4	PRO	PRO	GLU	GLU	B	B	317 - 394	12 - 89
2	4	PRO	PRO	GLU	GLU	C	C	317 - 394	12 - 89
1	5	PRO	PRO	GLU	GLU	B	B	317 - 393	12 - 88
2	5	PRO	PRO	GLU	GLU	D	D	317 - 393	12 - 88
1	6	PRO	PRO	GLU	GLU	C	C	317 - 393	12 - 88
2	6	PRO	PRO	GLU	GLU	D	D	317 - 393	12 - 88

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Type II secretion system protein L / T2SS protein L / pullulanase-specific type II secretion system integral cytoplasmic membrane protein GspL Mass: 10192.266 Da / Num. of mol.: 4 / Fragment: UNP residues 316-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria) Strain: NTUH-K2044 / Gene: pulL, KpST82_0737 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: A0A060VDE2
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 1.87 Å³/Da / Density % sol: 34.13 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: protein: 9.7 mg/mL 10 mM Tris-HCl pH 8.3 crystallization: The Classics II Suite conditions E7 (#55): 0.05 M MgCl2, 0.1 M HEPES pH 7.5, 30 % (v/v) PEG 550 MME cryo: crystallization conditions

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2015 / Details: C(111)
Radiation	Monochromator: Be Lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.93→30 Å / Num. obs: 23407 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / B_iso Wilson estimate: 28.7 Å² / R_merge(I) obs: 0.069 / Net I/σ(I): 58.1
Reflection shell	Resolution: 1.93→1.96 Å / Redundancy: 14.7 % / R_merge(I) obs: 0.588 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.93→26.44 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.905 / SU B: 8.665 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.189 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28137	1203	5.2 %	RANDOM
R_work	0.22621	-	-	-
obs	0.22899	22151	99.77 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 45.834 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.18 Å²	-0 Å²	-0 Å²
2-	-	-0.52 Å²	0 Å²
3-	-	-	-2.66 Å²

Refinement step

Cycle: 1 / Resolution: 1.93→26.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2412	0	0	89	2501

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	2533
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	2509
X-RAY DIFFRACTION	r_angle_refined_deg	1.65	1.987	3440
X-RAY DIFFRACTION	r_angle_other_deg	1.302	3	5733
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.445	5	325
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.516	23.008	123
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.642	15	431
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.686	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	392
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	2948
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	596
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4273	0.16
1	2	B	4273	0.16
2	1	A	3461	0.22
2	2	C	3461	0.22
3	1	A	3537	0.18
3	2	D	3537	0.18
4	1	B	3430	0.22
4	2	C	3430	0.22
5	1	B	3479	0.19
5	2	D	3479	0.19
6	1	C	2998	0.23
6	2	D	2998	0.23

LS refinement shell

Resolution: 1.933→1.983 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	84	-
R_work	0.254	1569	-
obs	-	-	98.57 %

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	4.4649	-1.4603	-4.3725	5.5986	-0.1019	13.3737	-0.0878	-0.1465	-0.1593	-0.1647	-0.1174	-0.1268	0.1264	0.2339	0.2052	0.0203	0.0239	-0.0083	0.0762	0.0242	0.0714	-10.7873	-14.0265	26.4277
2	7.8206	-0.0388	-8.2383	0.7452	0.4091	10.09	-0.0942	-0.11	0.0343	0.0441	-0.023	0.0127	0.0482	-0.0067	0.1172	0.0108	-0.0019	-0.0039	0.0468	-0.0069	0.0685	-13.1266	-5.5386	22.1119
3	7.1461	8.5277	-5.7644	14.9959	-13.6498	14.3685	-0.4474	0.1669	-0.4946	-0.568	0.1176	-0.511	0.4911	-0.1417	0.3298	0.0634	-0.0499	0.0627	0.0689	-0.0407	0.1501	-13.2849	-14.8958	12.9006
4	5.418	-2.5509	-1.0378	21.6446	-10.2311	8.7195	-0.0278	0.127	0.0978	-0.052	0.5362	1.3901	-0.1115	-0.8246	-0.5084	0.0142	0.0107	-0.0137	0.1301	-0.0212	0.1673	-21.9199	-10.4831	18.7881
5	14.9476	-6.6538	-7.944	7.1765	1.8157	20.0735	0.2876	0.3788	0.2407	-0.247	-0.1055	-0.2375	-0.6563	0.2923	-0.1822	0.1345	0.005	-0.0188	0.0721	0.0639	0.177	-12.3407	-0.8696	5.7809
6	13.0327	5.4746	-7.8145	20.1984	-17.6431	19.7717	-0.0852	0.1588	0.1335	0.1207	0.1208	0.2734	-0.0443	0.0177	-0.0356	0.0082	-0.0017	-0.0037	0.1007	-0.0438	0.0623	-19.3246	-9.5901	20.9569
7	5.6084	-0.4503	1.2293	6.088	0.7109	13.7138	0.04	0.1859	0.1072	-0.2113	0.1414	0.3188	0.2971	-0.2345	-0.1814	0.0159	-0.0068	-0.0083	0.0468	0.0428	0.109	1.0644	4.4607	3.8008
8	3.1592	-0.0747	-2.4891	10.3966	4.9455	15.8886	-0.0933	-0.2351	-0.0999	-0.0118	-0.1118	0.0621	0.2121	0.324	0.2051	0.0176	0.0208	-0.0045	0.0672	0.0232	0.0644	10.4046	1.925	1.3698
9	8.1726	6.7856	5.8612	8.5239	5.653	9.69	0.1269	-0.4557	0.0868	0.1055	-0.0063	-0.0094	0.0027	0.0698	-0.1205	0.0198	-0.026	0.0127	0.1911	-0.0447	0.1262	4.7242	4.8676	16.9697
10	14.9785	2.2237	0.2471	4.1556	1.5499	3.7113	-0.2105	0.2125	-0.8641	-0.177	0.0262	-0.3615	0.4348	0.5667	0.1843	0.1763	0.0308	0.0419	0.1939	0.057	0.2346	4.6841	-4.9706	8.897
11	6.1955	0.5133	-1.88	21.334	23.4608	26.8894	0.3769	-0.1307	-0.1916	-0.3646	0.3219	-0.8642	-0.5495	0.6254	-0.6988	0.165	-0.0027	-0.0225	0.6296	0.1287	0.4581	17.4212	7.3066	15.9616
12	27.8977	14.211	3.729	16.7153	5.0955	5.8921	-0.1758	-0.006	-0.5638	0.0861	-0.1065	-0.1103	0.4887	0.2519	0.2823	0.1597	0.0552	0.0507	0.116	0.0266	0.0658	6.4044	-3.9555	6.0567
13	6.143	5.4589	1.5154	6.5078	3.8324	23.5505	-0.2033	-0.1716	0.2491	-0.0131	0.0114	0.6731	-0.3906	-0.475	0.1919	0.1015	0.1095	0.0526	0.1266	0.0604	0.1542	1.2896	12.1577	-1.9161
14	3.3503	0.4018	-0.1957	5.5644	3.3879	11.1344	0.0957	0.4401	0.0114	0.1713	-0.0538	0.2975	0.0077	-0.3069	-0.0419	0.0257	0.0034	-0.0037	0.0846	0.0343	0.0778	6.2951	3.684	-10.9855
15	1.0166	-0.296	1.1067	8.3264	3.5117	9.6508	0.1479	0.3824	0.2298	0.0332	0.0882	-0.2011	-0.254	0.458	-0.2361	0.1003	0.0052	0.054	0.2102	0.0758	0.1345	9.4739	8.4878	-14.3594
16	5.9957	-4.0923	-3.5125	18.5933	12.3099	12.17	0.3358	0.5814	0.5362	-0.1633	-0.3627	0.0992	-0.6363	-0.4111	0.0269	0.2518	0.046	-0.0589	0.2551	0.0466	0.2803	2.6133	13.2425	-16.8244
17	7.5416	-4.3365	-5.9073	13.3942	12.33	15.0251	-0.2401	0.5184	0.242	-0.8309	0.351	-0.7894	-0.6101	0.6883	-0.111	0.3258	-0.0392	0.0592	0.2901	0.0839	0.2594	13.7519	11.0874	-18.0952
18	3.3071	-5.1706	-4.5853	20.4788	12.5759	10.5746	0.096	0.3647	0.0567	0.2339	-0.2086	0.0011	-0.0567	-0.1048	0.1125	0.0857	-0.0368	0.0326	0.1263	0.0276	0.084	10.2506	12.4854	-13.0778
19	17.9466	-3.1511	-4.0393	4.5856	5.9352	36.8944	0.4513	-0.1291	-1.1617	0.1915	-0.6569	-0.0917	-1.0227	0.1097	0.2056	0.3628	-0.1439	-0.0303	0.2319	0.0636	0.6169	-5.4912	-6.2163	37.1149
20	5.796	-1.4604	-8.3395	4.0294	3.3923	26.1129	0.3799	-0.7768	0.2002	0.465	0.0199	-0.0113	-0.2806	0.9169	-0.3998	0.1673	-0.1677	0.0238	0.2894	-0.105	0.1495	-13.2827	0.0119	35.5364
21	15.3761	-1.3594	-18.8343	1.419	2.2449	34.2779	0.2047	-0.4622	0.1148	0.334	-0.1306	-0.0573	-0.8256	0.789	-0.0741	0.1849	-0.1157	-0.0173	0.1505	-0.0917	0.1693	-9.0626	3.4706	33.4812
22	31.3807	-8.5109	-9.2822	16.6574	6.3093	3.7484	0.3826	-2.1958	0.7022	0.8653	-0.0492	-0.7301	0.1283	0.4764	-0.3334	0.6614	-0.2828	-0.1162	0.6699	-0.116	0.2545	-6.5782	5.2039	48.1422
23	13.9635	-1.7735	2.7011	16.0912	-6.5815	22.2959	-0.3579	0.0868	-0.6669	-0.1404	-0.0896	-0.4915	-0.127	0.0235	0.4475	0.119	-0.1722	-0.0346	0.3287	-0.0355	0.3738	0.5199	1.8959	39.0592
24	32.4418	-13.362	-6.4634	10.9658	3.5276	6.7926	0.2338	0.549	1.3609	0.335	-0.2377	-0.1715	-0.4643	0.1796	0.0039	0.2902	-0.1372	-0.0411	0.3094	-0.0867	0.3247	-7.7255	7.8718	35.7511

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	315 - 332
2	X-RAY DIFFRACTION	2	A	333 - 354
3	X-RAY DIFFRACTION	3	A	355 - 371
4	X-RAY DIFFRACTION	4	A	372 - 378
5	X-RAY DIFFRACTION	5	A	379 - 387
6	X-RAY DIFFRACTION	6	A	388 - 395
7	X-RAY DIFFRACTION	7	B	315 - 336
8	X-RAY DIFFRACTION	8	B	337 - 353
9	X-RAY DIFFRACTION	9	B	354 - 368
10	X-RAY DIFFRACTION	10	B	369 - 377
11	X-RAY DIFFRACTION	11	B	378 - 389
12	X-RAY DIFFRACTION	12	B	390 - 395
13	X-RAY DIFFRACTION	13	C	317 - 329
14	X-RAY DIFFRACTION	14	C	330 - 344
15	X-RAY DIFFRACTION	15	C	345 - 360
16	X-RAY DIFFRACTION	16	C	361 - 371
17	X-RAY DIFFRACTION	17	C	372 - 382
18	X-RAY DIFFRACTION	18	C	385 - 397
19	X-RAY DIFFRACTION	19	D	317 - 333
20	X-RAY DIFFRACTION	20	D	334 - 343
21	X-RAY DIFFRACTION	21	D	344 - 356
22	X-RAY DIFFRACTION	22	D	357 - 366
23	X-RAY DIFFRACTION	23	D	367 - 374
24	X-RAY DIFFRACTION	24	D	375 - 393

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