PDB-6ica: The crystal structure of Legionella pneumophila LapA aminopeptidase

ID or keywords:

Entry

Database: PDB / ID: 6ica

Title

The crystal structure of Legionella pneumophila LapA aminopeptidase

Components

Aminopeptidase

Keywords

HYDROLASE / Legionella pneumophila / aminopeptidase / type II secretion / catalytic activity

Function / homology

Peptidase M28 family / metalloexopeptidase activity / Peptidase M28 / Peptidase family M28 / aminopeptidase activity / proteolysis / metal ion binding / ACETATE ION / Aminopeptidase

Function and homology information

Biological species

Legionella pneumophila subsp. pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.195 Å

Authors

Honghua, G. / Nannan, Z.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: The crystal structure of Legionella pneumophila LapA aminopeptidase
Authors: Honghua, G. / Nannan, Z.

History

Deposition	Sep 5, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ica.cif.gz	460.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6ica.ent.gz	377.3 KB	Display	PDB format
PDBx/mmJSON format	6ica.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ica_validation.pdf.gz	485.8 KB	Display	wwPDB validaton report
Full document	6ica_full_validation.pdf.gz	495.1 KB	Display
Data in XML	6ica_validation.xml.gz	46.7 KB	Display
Data in CIF	6ica_validation.cif.gz	67.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ic/6ica ftp://data.pdbj.org/pub/pdb/validation_reports/ic/6ica	HTTPS FTP

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Related structure data

Related structure data	5gneS S: Starting model for refinement
Similar structure data	5o59-1 4czo-d 4czr-d 2rfz-3 4czq-d 5m0l-d 4d5p-d 2rfz-4 4czp-d 2rfy-3 Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5gneS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (2)

Deposited unit

A: Aminopeptidase

B: Aminopeptidase

C: Aminopeptidase

hetero molecules

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

1

A: Aminopeptidase

hetero molecules

defined by author&software
Evidence: gel filtration
48.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Aminopeptidase

hetero molecules

defined by author&software
48.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Aminopeptidase

hetero molecules

defined by author&software
48.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.424, 121.913, 130.812
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 3 molecules ABC

#1: Protein	Aminopeptidase Mass: 48227.312 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2814 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZRR6

#1: Protein

Aminopeptidase

Mass: 48227.312 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2814 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZRR6

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Non-polymers , 5 types, 666 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.33 Å³/Da / Density % sol: 47.13 %
Crystal grow	Temperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium sulfate, 20% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97876 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97876 Å / Relative weight: 1
Reflection	Resolution: 2.195→50 Å / Num. obs: 69504 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC_1/2: 0.995 / R_pim(I) all: 0.052 / Net I/σ(I): 13
Reflection shell	Resolution: 2.2→2.27 Å / Num. unique obs: 3400 / CC_1/2: 0.829 / R_pim(I) all: 0.247

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5GNE

5gne

Resolution: 2.195→34.518 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.17

	R_factor	Num. reflection	% reflection
R_free	0.1834	3444	4.96 %
R_work	0.1433	-	-
obs	0.1453	69432	99.71 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.195→34.518 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8740	0	89	644	9473

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	9036
X-RAY DIFFRACTION	f_angle_d	1.136	12267
X-RAY DIFFRACTION	f_dihedral_angle_d	14.123	3223
X-RAY DIFFRACTION	f_chiral_restr	0.048	1370
X-RAY DIFFRACTION	f_plane_restr	0.006	1566

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 (%)
2.1948-2.2249	0.2561	143	0.1839	2515	X-RAY DIFFRACTION	97
2.2249-2.2567	0.2288	159	0.1781	2565	X-RAY DIFFRACTION	100
2.2567-2.2903	0.2299	143	0.168	2602	X-RAY DIFFRACTION	100
2.2903-2.3261	0.2313	126	0.1629	2635	X-RAY DIFFRACTION	100
2.3261-2.3642	0.2243	133	0.159	2584	X-RAY DIFFRACTION	100
2.3642-2.405	0.2104	146	0.1563	2604	X-RAY DIFFRACTION	100
2.405-2.4487	0.216	118	0.1557	2624	X-RAY DIFFRACTION	100
2.4487-2.4958	0.2087	147	0.1429	2608	X-RAY DIFFRACTION	100
2.4958-2.5467	0.206	128	0.1436	2628	X-RAY DIFFRACTION	100
2.5467-2.6021	0.1947	150	0.1428	2625	X-RAY DIFFRACTION	100
2.6021-2.6626	0.1682	135	0.1398	2623	X-RAY DIFFRACTION	100
2.6626-2.7292	0.2165	138	0.1378	2633	X-RAY DIFFRACTION	100
2.7292-2.8029	0.191	139	0.1424	2603	X-RAY DIFFRACTION	100
2.8029-2.8854	0.1455	126	0.135	2660	X-RAY DIFFRACTION	100
2.8854-2.9784	0.1974	138	0.1387	2628	X-RAY DIFFRACTION	100
2.9784-3.0848	0.1808	120	0.1393	2645	X-RAY DIFFRACTION	100
3.0848-3.2083	0.2055	140	0.1439	2644	X-RAY DIFFRACTION	100
3.2083-3.3542	0.2011	117	0.1418	2672	X-RAY DIFFRACTION	100
3.3542-3.5308	0.1409	119	0.1351	2682	X-RAY DIFFRACTION	100
3.5308-3.7518	0.1606	164	0.1256	2617	X-RAY DIFFRACTION	100
3.7518-4.0411	0.159	164	0.1266	2642	X-RAY DIFFRACTION	100
4.0411-4.447	0.1351	160	0.1192	2668	X-RAY DIFFRACTION	100
4.447-5.0887	0.1656	133	0.1223	2705	X-RAY DIFFRACTION	100
5.0887-6.4045	0.21	108	0.1621	2758	X-RAY DIFFRACTION	100
6.4045-34.522	0.1755	150	0.1726	2818	X-RAY DIFFRACTION	99

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	1.3879	-0.55	0.125	1.2955	-0.5738	2.2602	-0.0265	0.0946	-0.2221	-0.1183	-0.0787	-0.1649	0.3205	0.1069	0.1006	0.1824	-0.0213	0.0609	0.1955	0.0022	0.1697	28.9689	-32.3437	-17.6998
2	2.3396	0.1	-1.0456	3.0003	0.5531	1.9359	0.075	0.8051	0.0985	-0.528	-0.0231	0.2754	-0.0999	-0.0793	-0.0741	0.3221	-0.0419	-0.0186	0.3689	0.088	0.1981	21.3157	-26.3823	-22.183
3	0.6218	0.1957	-0.212	1.3923	0.4392	1.4884	0.1563	0.0983	0.2929	-0.0431	-0.1024	0.0118	-0.7163	0.0171	-0.0354	0.2378	0.061	-0.0244	0.2288	0.0989	0.2832	15.5536	-9.5547	-2.1661
4	0.7362	0.2424	-0.0635	1.477	-0.1547	0.8423	-0.0116	0.043	0.0936	-0.0055	0.0241	-0.0098	-0.0443	-0.0052	-0.0089	0.0971	-0.0068	0.0039	0.1253	0.0375	0.1286	14.1392	-20.6664	0.5377
5	1.498	0.2141	0.2983	1.4505	0.3903	2.2778	-0.0194	-0.2204	0.3945	0.2442	-0.191	-0.2862	-0.5768	0.3673	0.186	0.3821	-0.1282	-0.0963	0.3119	-0.0136	0.332	26.3174	-19.3464	43.7782
6	0.0824	-0.025	-0.054	0.0331	-0.1681	1.1549	0.006	-0.3284	-0.0236	0.1696	0.0062	-0.0573	-0.1143	0.1117	-0.0228	0.5537	0.0247	0.0323	0.4676	0.0293	0.2825	12.5562	-42.265	62.2002
7	0.8377	-0.1246	-0.096	0.9702	-0.204	1.4161	-0.0351	-0.0328	0.0145	0.0322	0.0366	-0.0268	0.0383	0.0141	-0.0032	0.1129	0.0336	-0.0176	0.1108	-0.0086	0.0817	10.4233	-39.9337	38.634
8	1.4635	-0.1371	0.146	2.3777	0.1668	1.0947	0.0479	-0.2494	0.1613	0.4065	0.262	0.24	-0.2825	-0.4145	-0.1234	0.4274	0.1991	0.1305	0.3287	0.0226	0.2878	15.9312	-46.4275	86.4957
9	1.1367	-0.1685	-0.8248	0.2604	-0.2268	1.1072	-0.1039	0.1351	0.829	-0.0576	0.316	0.1027	-0.9409	0.0878	-0.2232	0.7069	0.0735	0.0123	0.3113	0.047	0.5326	24.7518	-36.9456	80.3638
10	1.124	-1.0974	-0.0043	1.2435	0.1616	0.1448	0.0182	0.3271	0.239	-0.2815	-0.0206	-0.2016	-0.1337	-0.001	-0.0026	0.4182	0.0002	0.0296	0.2602	0.0356	0.266	37.2712	-55.4338	51.1663
11	0.6825	0.0595	-0.1389	1.5361	-0.1158	1.1518	-0.0163	0.0355	0.0101	0.045	0.0545	-0.0089	-0.0632	-0.0636	-0.0235	0.0865	0.0175	-0.0334	0.1053	-0.0007	0.0973	32.1585	-59.0387	69.5665

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 47 through 96 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 97 through 117 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118 through 158 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 159 through 424 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 47 through 123 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 124 through 146 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 147 through 424 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 47 through 96 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 97 through 134 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 135 through 158 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 159 through 424 )

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