PDB-6hc6: The structure of BSAP, a zinc aminopeptidase from Bacillus subtilis

ID or keywords:

Entry

Database: PDB / ID: 6hc6

Title

The structure of BSAP, a zinc aminopeptidase from Bacillus subtilis

Components

Aminopeptidase YwaD

Keywords

METAL BINDING PROTEIN / aminopeptidase / zinc binding protein / geobacillus stearothermophilus / PA-domain

Function / homology

Function and homology information

aminopeptidase B / bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.77 Å

Authors

Rogoulenko, E. / Lansky, S. / Faygenboim, R. / Cohen, T. / Alhadeff, R. / Shoham, Y. / Shoham, G.

Citation

Journal: To Be Published
Title: To be published
Authors: Alhadeff, R. / Faygenboim, R. / Lansky, S. / Rogoulenko, E. / Cohen, T. / Fundoiano-Hershcovitz, Y. / Feinberg, H. / Shoham, Y. / Shoham, G.

History

Deposition	Aug 14, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 28, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 15, 2023	Group: Advisory / Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type 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
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6hc6.cif.gz	504.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6hc6.ent.gz	418.5 KB	Display	PDB format
PDBx/mmJSON format	6hc6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6hc6_validation.pdf.gz	471.8 KB	Display	wwPDB validaton report
Full document	6hc6_full_validation.pdf.gz	481.2 KB	Display
Data in XML	6hc6_validation.xml.gz	54.8 KB	Display
Data in CIF	6hc6_validation.cif.gz	81.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hc/6hc6 ftp://data.pdbj.org/pub/pdb/validation_reports/hc/6hc6	HTTPS FTP

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Related structure data

Related structure data	1cp7S S: Starting model for refinement
Similar structure data	6hc7-1 6hc7-3 5n2i-2 6hc7-2 4cbh-1 4jes-d 4fq5-d 5gk9-d 2oqo-1 1vpa-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) 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

1cp7S

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 (4)

Deposited unit

A: Aminopeptidase YwaD

B: Aminopeptidase YwaD

C: Aminopeptidase YwaD

hetero molecules

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

1

A: Aminopeptidase YwaD

hetero molecules

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

2

B: Aminopeptidase YwaD

hetero molecules

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

3

C: Aminopeptidase YwaD

hetero molecules

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

Unit cell

Length a, b, c (Å)	224.922, 224.922, 42.502
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

#1: Protein	Aminopeptidase YwaD / Arginyl aminopeptidase / BSAP / Leucyl aminopeptidase Mass: 49515.082 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Gene: ywaD, BSU38470, ipa-8r / Production host: Escherichia coli (E. coli) References: UniProt: P25152, aminopeptidase B, bacterial leucyl aminopeptidase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1047 / 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	Density Matthews: 2.09 Å³/Da / Density % sol: 41.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 2K MME, 0.1M LiSO4, 4mM MnCl2, 0.1M acetate pH 5.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.954 Å / Relative weight: 1
Reflection	Resolution: 1.77→48.7 Å / Num. obs: 120817 / % possible obs: 100 % / Redundancy: 9.3 % / R_merge(I) obs: 0.068 / Net I/σ(I): 18.9
Reflection shell	Resolution: 1.77→1.8 Å / Redundancy: 8.6 % / R_merge(I) obs: 0.1089 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1CP7

1cp7

Resolution: 1.77→48.697 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.98

	R_factor	Num. reflection	% reflection
R_free	0.2027	2902	2.4 %
R_work	0.1647	-	-
obs	0.1656	120790	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.77→48.697 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9384	0	88	1047	10519

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9702
X-RAY DIFFRACTION	f_angle_d	0.823	13107
X-RAY DIFFRACTION	f_dihedral_angle_d	3.463	8158
X-RAY DIFFRACTION	f_chiral_restr	0.053	1462
X-RAY DIFFRACTION	f_plane_restr	0.005	1705

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 (%)
1.77-1.799	0.4419	159	0.3643	5476	X-RAY DIFFRACTION	100
1.799-1.8301	0.2579	98	0.2457	5618	X-RAY DIFFRACTION	100
1.8301-1.8633	0.2749	127	0.2078	5583	X-RAY DIFFRACTION	100
1.8633-1.8992	0.2153	161	0.1906	5512	X-RAY DIFFRACTION	100
1.8992-1.9379	0.2204	137	0.1915	5627	X-RAY DIFFRACTION	100
1.9379-1.9801	0.2294	156	0.1905	5470	X-RAY DIFFRACTION	100
1.9801-2.0262	0.2202	143	0.1912	5653	X-RAY DIFFRACTION	100
2.0262-2.0768	0.1992	165	0.1845	5498	X-RAY DIFFRACTION	100
2.0768-2.133	0.2117	111	0.1729	5647	X-RAY DIFFRACTION	100
2.133-2.1957	0.2071	126	0.1693	5568	X-RAY DIFFRACTION	100
2.1957-2.2666	0.2387	160	0.1687	5592	X-RAY DIFFRACTION	100
2.2666-2.3476	0.2145	143	0.1739	5603	X-RAY DIFFRACTION	100
2.3476-2.4416	0.2282	123	0.1716	5569	X-RAY DIFFRACTION	100
2.4416-2.5527	0.1988	154	0.1665	5590	X-RAY DIFFRACTION	100
2.5527-2.6873	0.2193	140	0.1687	5649	X-RAY DIFFRACTION	100
2.6873-2.8557	0.2248	107	0.1744	5643	X-RAY DIFFRACTION	100
2.8557-3.0761	0.2012	127	0.1702	5646	X-RAY DIFFRACTION	100
3.0761-3.3856	0.1898	158	0.1624	5617	X-RAY DIFFRACTION	100
3.3856-3.8753	0.1785	130	0.1424	5743	X-RAY DIFFRACTION	100
3.8753-4.8818	0.1655	137	0.1254	5691	X-RAY DIFFRACTION	100
4.8818-48.7155	0.1766	140	0.152	5893	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	3.1051	-1.6334	-0.0946	4.1191	0.9881	3.0931	-0.0085	-0.1482	-0.5333	0.328	0.0022	0.0083	0.2138	-0.0216	0.025	0.1448	-0.0173	-0.0412	0.1725	0.0389	0.2181	-81.5937	404.9178	51.1234
2	4.3247	-1.9137	-0.1618	2.1547	-0.1535	0.5275	0.0452	0.0833	0.3156	0.146	0.0899	0.1429	-0.0878	-0.0028	-0.14	0.177	-0.0067	0.0326	0.2038	0.0123	0.2373	-98.5576	431.0314	52.4671
3	2.7719	-0.1863	-0.3559	1.7429	0.0945	1.482	0.0637	0.5376	-0.0078	-0.0764	0.002	-0.2225	0.0379	0.0975	-0.0383	0.116	0.0214	-0.0189	0.2803	-0.0249	0.1485	-76.2446	415.3923	40.8973
4	1.1935	-0.2005	0.089	1.3379	-0.0082	1.3784	-0.016	-0.3056	0.1134	0.1674	0.0975	0.1483	-0.1223	-0.2779	-0.0606	0.1516	0.0105	0.036	0.2365	-0.0088	0.1369	-54.3061	384.6274	56.936
5	1.7971	-0.0295	0.0356	0.6118	-0.27	0.2574	-0.0347	0.0229	0.0141	0.0103	0.327	-0.7715	-0.1199	0.3275	-0.1965	0.2533	-0.0257	0.0097	0.3552	-0.2747	0.7306	-23.1941	391.9228	53.5795
6	1.6229	0.3061	-0.2972	2.1086	-0.0738	1.1854	0.1118	-0.4816	-0.0778	0.206	0.0213	-0.0407	0.1104	-0.1299	-0.0527	0.1319	-0.0072	-0.0172	0.1891	-0.0015	0.1077	-47.3001	376.9954	58.3121
7	1.7105	0.1004	0.5004	1.5925	-0.1685	1.3561	0.0431	0.0355	-0.177	-0.1636	0.0947	0.1471	0.1438	-0.1253	-0.1092	0.1369	-0.0423	-0.0248	0.1545	0.0055	0.1114	-52.3686	374.8414	44.7967
8	1.4832	0.6154	0.4546	1.3544	-0.9789	2.1618	-0.0428	0.2518	0.1449	-0.5333	0.0536	-0.0772	-0.143	0.06	0.01	0.2023	-0.0202	-0.004	0.1797	0.0013	0.1174	-47.6417	388.1086	39.8954
9	3.7665	0.6041	0.2942	2.5796	-0.0838	1.9977	0.0309	-0.0169	-0.2756	-0.2256	0.1708	0.0093	0.1024	-0.1567	-0.1542	0.1539	-0.0343	-0.0056	0.1614	-0.0185	0.0801	-53.0824	376.6458	41.3738
10	1.3625	0.3591	-0.5701	1.5166	-0.3496	1.6056	0.0933	-0.1717	0.1458	0.1807	-0.0416	-0.1512	-0.1173	0.2095	-0.0385	0.1595	-0.0468	-0.0227	0.2717	-0.0605	0.1481	-85.6838	378.012	47.3875
11	1.4819	-0.5531	-0.08	1.2165	-0.3334	1.431	0.2559	-0.2613	-0.6399	0.6416	0.0787	-0.6639	0.3624	0.2596	-0.2146	0.4004	-0.0259	-0.2747	0.3497	-0.0216	0.5395	-94.2849	358.1161	56.3547
12	0.7317	-0.1576	0.2889	0.6647	0.4366	0.5031	0.4261	0.1201	-0.5966	0.3294	0.1969	-0.7706	0.553	0.3789	0.166	0.3393	0.2134	-0.4807	0.1513	-0.0238	1.0468	-97.639	342.8023	45.304
13	1.6721	0.1557	0.2262	2.289	-0.1304	1.4493	0.1097	0.02	0.0908	0.0433	-0.004	0.0871	-0.0005	-0.0422	-0.0906	0.1223	-0.0243	0.0046	0.1904	-0.0225	0.0986	-98.8996	375.7287	41.3454
14	1.52	-0.3742	0.0031	2.3001	-0.2108	1.577	0.0577	0.2191	-0.0693	-0.2816	0.0169	0.0769	0.1347	0.0251	-0.075	0.1607	-0.0169	-0.0159	0.2344	-0.0354	0.1034	-93.2776	372.2008	34.1361

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 39 through 83 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 84 through 234 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 235 through 455 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 39 through 104 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 105 through 211 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 212 through 250 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 251 through 381 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 382 through 411 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 412 through 455 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 39 through 82 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 83 through 124 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 125 through 211 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 212 through 381 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 382 through 455 )

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