PDB-5dll: Aminopeptidase N (pepN) from Francisella tularensis subsp. tulare...

ID or keywords:

Entry

Database: PDB / ID: 5dll

Title

Aminopeptidase N (pepN) from Francisella tularensis subsp. tularensis SCHU S4

Components

Aminopeptidase N

Keywords

HYDROLASE / conserved gene / putative drug target function / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / zinc ion binding
Similarity search - Function

Biological species

Francisella tularensis subsp. tularensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.51 Å

Authors

Borek, D. / Raczynska, J. / Dubrovska, I. / Grimshaw, S. / Minasov, G. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Otwinowski, Z. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272200700058C	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	Contract No. HHSN272201200026C	United States

Citation

Journal: To Be Published
Title: Aminopeptidase N (pepN) from Francisella tularensis subsp. tularensis SCHU S4
Authors: Borek, D. / Raczynska, J. / Dubrovska, I. / Grimshaw, S. / Minasov, G. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Otwinowski, Z. / Center for Structural Genomics of Infectious Diseases

History

Deposition	Sep 7, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 23, 2015	Group: Derived calculations
Revision 1.2	Jul 20, 2016	Group: Data collection
Revision 1.3	Sep 27, 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 1.4	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 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

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Download

PDBx/mmCIF format	5dll.cif.gz	359.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5dll.ent.gz	293 KB	Display	PDB format
PDBx/mmJSON format	5dll.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5dll_validation.pdf.gz	443.2 KB	Display	wwPDB validaton report
Full document	5dll_full_validation.pdf.gz	444.4 KB	Display
Data in XML	5dll_validation.xml.gz	29.5 KB	Display
Data in CIF	5dll_validation.cif.gz	41 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dl/5dll ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dll	HTTPS FTP

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Related structure data

Related structure data	2dq6S S: Starting model for refinement
Similar structure data	4r5v-d 5y1t-d 4k5m-d 6eab-d 5lhd-4 3f73-1 4kx9-d 4j3b-d 4kxd-d 6m8p-18 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP04077

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Aminopeptidase N

hetero molecules

100 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)	75.670, 75.670, 161.042
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

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Protein , 1 types, 1 molecules A

#1: Protein	Aminopeptidase N Mass: 99243.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria) Strain: SCHU S4 / Schu 4 / Gene: pepN, FTT_1793c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NE65, membrane alanyl aminopeptidase

#1: Protein

Aminopeptidase N

Mass: 99243.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: pepN, FTT_1793c / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q5NE65, membrane alanyl aminopeptidase

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Non-polymers , 5 types, 80 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.68 Å³/Da / Density % sol: 54.14 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Sodium iodide 0.1 M Bis Tris propane pH 6.5 20% (w/v) PEG

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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: Mar 4, 2010
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.5→65.53 Å / Num. obs: 26293 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / R_merge(I) obs: 0.104 / R_sym value: 0.104 / Net I/σ(I): 15.2
Reflection shell	Resolution: 2.5→2.52 Å / Redundancy: 3.8 % / R_merge(I) obs: 0 / Mean I/σ(I) obs: 0.921 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2DQ6

2dq6

Resolution: 2.51→65.53 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.876 / SU B: 27.106 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25998	1412	5.1 %	RANDOM
R_work	0.19303	-	-	-
obs	0.19653	26293	78.35 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 57.348 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.33 Å²	0.17 Å²	-0 Å²
2-	-	0.33 Å²	-0 Å²
3-	-	-	-1.07 Å²

Refinement step

Cycle: 1 / Resolution: 2.51→65.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6867	0	22	62	6951

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.019	7028
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6693
X-RAY DIFFRACTION	r_angle_refined_deg	0.931	1.948	9490
X-RAY DIFFRACTION	r_angle_other_deg	0.674	3	15393
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.281	5	855
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.34	25.269	353
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.347	15	1272
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.351	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	1050
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	8012
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1633
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	4.043	3.092	3420
X-RAY DIFFRACTION	r_mcbond_other	4.04	3.091	3419
X-RAY DIFFRACTION	r_mcangle_it	5.88	4.633	4275
X-RAY DIFFRACTION	r_mcangle_other	5.88	4.634	4276
X-RAY DIFFRACTION	r_scbond_it	4.905	3.491	3608
X-RAY DIFFRACTION	r_scbond_other	4.863	3.491	3603
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.09	5.063	5209
X-RAY DIFFRACTION	r_long_range_B_refined	8.906	24.448	7740
X-RAY DIFFRACTION	r_long_range_B_other	8.904	24.448	7738
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.507→2.572 Å

	R_factor	Num. reflection	% reflection
R_free	0.265	29	-
R_work	0.292	468	-
obs	-	-	19.12 %

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	6.2577	-3.2088	1.4648	7.2594	-4.8009	3.285	0.2414	-0.9557	0.0303	0.1235	-0.0593	0.1194	-0.1358	0.1648	-0.1821	0.2864	0.0487	0.0649	0.3039	-0.0076	0.3459	-53.5903	-46.2504	68.7724
2	1.3349	0.6909	-0.3935	1.7344	0.0695	2.3569	-0.0796	-0.0935	-0.0224	0.2976	0.1436	0.0839	0.0134	-0.2394	-0.064	0.1547	0.0972	0.0114	0.2865	0.04	0.0764	-68.6455	-28.8101	73.367
3	1.2562	1.5325	0.1185	3.5443	0.4659	1.2028	-0.1395	0.1009	-0.0937	0.0166	0.3218	-0.0448	-0.11	-0.013	-0.1823	0.193	0.0661	0.0297	0.2566	0.0121	0.1677	-60.5045	-21.3193	66.4441
4	2.0155	-0.4192	-0.7119	2.3381	0.2338	1.586	-0.2356	-0.0866	0.0889	0.1882	0.2391	0.0386	-0.1964	-0.2222	-0.0035	0.2869	0.1378	-0.0475	0.225	0.0227	0.1371	-64.2755	-13.1168	59.2953
5	2.2947	1.1483	-0.001	2.1866	-0.6417	3.0579	-0.0086	0.0138	0.0599	0.1377	0.0608	-0.0231	-0.2583	-0.0241	-0.0522	0.1624	0.0419	-0.0271	0.1558	0.0263	0.1237	-52.0969	-16.1202	48.0588
6	0.7451	0.2012	-0.4179	1.2175	-0.9591	1.8061	-0.1601	0.1294	-0.1021	0.034	0.0146	-0.1747	0.0619	0.0277	0.1455	0.168	0.0056	0.0283	0.2666	0.0321	0.1786	-46.3265	-28.1154	47.8886
7	2.7571	0.2193	-0.226	1.3837	-0.1982	2.7137	-0.3229	0.0042	-0.1952	-0.0607	0.0405	-0.0189	0.3044	0.0743	0.2824	0.2251	0.0381	0.0555	0.1544	-0.014	0.1148	-45.3921	-40.1854	50.2929
8	1.9898	-0.7886	-0.6523	1.919	2.3945	3.1029	-0.3487	-0.2659	-0.6285	0.3836	0.2359	0.1177	0.5752	0.3048	0.1128	0.4961	0.2152	0.2509	0.3474	0.0072	0.5021	-34.1002	-54.0035	44.6645
9	1.5759	-0.1387	0.8188	3.2103	1.4528	1.1855	0.1491	0.5429	-0.6787	-0.0202	0.1196	0.2654	0.2224	0.4083	-0.2687	0.6051	0.1428	0.0029	0.5232	-0.3166	0.599	-34.2028	-49.9343	34.626
10	2.9937	3.6952	-6.4745	4.7024	-9.1102	38.2195	-0.3222	0.0047	-0.5593	-0.3595	-0.1145	-0.497	1.0487	-0.1289	0.4368	0.2388	0.0437	0.1701	0.2691	-0.1906	0.4877	-31.8234	-58.3686	31.5938
11	2.8926	0.1149	-0.2297	1.2557	0.1087	0.0342	-0.1609	0.4305	-0.2961	-0.2076	0.1208	-0.0748	0.024	-0.0135	0.04	0.2692	0.0366	0.1003	0.3804	-0.1033	0.1917	-22.8186	-41.8444	36.3801
12	4.13	-0.5685	2.9584	4.3674	-1.6682	2.5147	-0.0609	-0.4922	0.4473	-0.3031	-0.6081	-1.3263	0.0889	-0.2648	0.669	0.2885	0.0457	0.0875	0.6695	0.11	0.5164	-9.8594	-33.439	33.3729
13	49.6536	11.6786	-14.1553	2.8364	-4.5671	21.8941	-0.5241	-0.4753	0.6683	-0.1543	-0.064	0.1132	0.0476	-0.6584	0.5881	0.4263	0.0424	-0.0295	0.3671	-0.0972	0.2351	-20.92	-26.0738	26.5099
14	0.937	-0.397	0.8837	1.8972	-1.5351	4.4423	-0.01	0.0172	-0.0101	-0.0125	0.0225	-0.012	0.1386	0.0492	-0.0125	0.0587	0.0333	0.0091	0.2648	-0.0061	0.1209	-15.0409	-29.6225	44.0055
15	5.3524	-2.3378	0.6535	2.3631	0.6859	1.2753	0.0772	0.1669	-0.2367	-0.2109	-0.0888	0.0195	-0.1373	-0.0083	0.0115	0.1127	-0.0133	-0.0138	0.3378	0.1558	0.1895	-21.5841	-15.2634	34.4081
16	1.8878	-1.3936	-0.2386	3.4823	-1.0375	3.2145	-0.0885	-0.0187	0.3519	0.388	-0.0363	-0.2117	-0.2282	0.2175	0.1248	0.3078	-0.0517	-0.0642	0.3187	0.0847	0.2202	-17.6198	-8.5279	43.1132
17	6.5131	-2.3943	-3.3105	5.8296	4.2527	4.9399	0.2064	-0.0596	0.4975	0.0356	0.1339	-0.0969	-0.9675	0.2406	-0.3403	0.7161	-0.0618	-0.0658	0.3513	0.0512	0.4741	-16.8767	-3.042	52.1625
18	6.2631	-3.302	3.3486	4.689	-1.9549	3.4448	0.0034	0.0022	0.089	0.0021	-0.0988	-0.1908	-0.3386	-0.015	0.0953	0.2647	0.0267	-0.0034	0.2083	0.0553	0.0849	-20.7097	-10.7094	57.2517
19	0.1542	-0.4304	0.5024	2.1508	-2.1681	2.2985	-0.1986	-0.0729	0.0175	0.2573	0.161	-0.0342	-0.4268	-0.0821	0.0377	0.3717	0.07	-0.0236	0.3787	0.0164	0.1282	-21.0618	-17.8955	66.5057
20	2.7513	-1.4784	-2.161	3.2681	1.0257	3.9633	-0.1471	-0.0373	-0.3901	0.0963	-0.0472	0.2845	0.1508	-0.1237	0.1943	0.1663	0.0373	0.0269	0.1646	0.0416	0.1588	-21.885	-31.1481	72.4958

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	11 - 20
2	X-RAY DIFFRACTION	2	A	21 - 118
3	X-RAY DIFFRACTION	3	A	119 - 159
4	X-RAY DIFFRACTION	4	A	160 - 207
5	X-RAY DIFFRACTION	5	A	208 - 290
6	X-RAY DIFFRACTION	6	A	291 - 349
7	X-RAY DIFFRACTION	7	A	350 - 439
8	X-RAY DIFFRACTION	8	A	440 - 486
9	X-RAY DIFFRACTION	9	A	487 - 515
10	X-RAY DIFFRACTION	10	A	516 - 526
11	X-RAY DIFFRACTION	11	A	527 - 579
12	X-RAY DIFFRACTION	12	A	580 - 592
13	X-RAY DIFFRACTION	13	A	593 - 598
14	X-RAY DIFFRACTION	14	A	599 - 645
15	X-RAY DIFFRACTION	15	A	646 - 687
16	X-RAY DIFFRACTION	16	A	688 - 720
17	X-RAY DIFFRACTION	17	A	721 - 733
18	X-RAY DIFFRACTION	18	A	734 - 761
19	X-RAY DIFFRACTION	19	A	762 - 813
20	X-RAY DIFFRACTION	20	A	814 - 864

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Yorodumi