PDB-4arp: Structure of the inactive pesticin E178A mutant

ID or keywords:

Entry

Database: PDB / ID: 4arp

Title

Structure of the inactive pesticin E178A mutant

Components

PESTICIN

Keywords

HYDROLASE /

MURAMIDASE / INACTIVE MUTANT

Function / homology

Function and homology information

metabolic process /

lysozyme activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function

Biological species

YERSINIA PESTIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.296 Å

Authors

Zeth, K. / Patzer, S.I. / Albrecht, R. / Braun, V.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Structure and Mechanistic Studies of Pesticin, a Bacterial Homolog of Phage Lysozymes.
Authors: Patzer, S.I. / Albrecht, R. / Braun, V. / Zeth, K.

History

Deposition	Apr 25, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 2, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 30, 2012	Group: Other
Revision 1.2	Jul 18, 2012	Group: Other
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4arp.cif.gz	280.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4arp.ent.gz	229.6 KB	Display	PDB format
PDBx/mmJSON format	4arp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ar/4arp ftp://data.pdbj.org/pub/pdb/validation_reports/ar/4arp	HTTPS FTP

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Related structure data

Related structure data	4aqnSC 4arjC 4arlC 4armC 4arqC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4arl-2 4arl-1 6fne-1 6gmn-4 1oxv-1 4arm-2 1gt0-d 1oxu-2 5j19-d 1oxv-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#217 - Jan 2018 Opioid Receptors similarity (1) #9 - Sep 2000 Lysozyme similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #136 - Apr 2011 Nanobodies similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (1)

Deposited unit

A: PESTICIN

B: PESTICIN

80.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PESTICIN

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

2

B: PESTICIN

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

Unit cell

Length a, b, c (Å)	44.641, 127.829, 158.359
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PESTICIN Mass: 40032.867 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57159
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, GLU 178 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 178 TO ALA

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.41 % / Description: NONE
Crystal grow	pH: 7 / Details: pH 7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→79 Å / Num. obs: 41466 / % possible obs: 99.6 % / Observed criterion σ(I): 2.1 / Redundancy: 7.7 % / B_iso Wilson estimate: 36.83 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.3→2.43 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.81 / Mean I/σ(I) obs: 2.1 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AQN

4aqn

Resolution: 2.296→79.18 Å / SU ML: 0.39 / σ(F): 2.01 / Phase error: 24.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.256	2072	5 %
R_work	0.2112	-	-
obs	0.2134	41385	99.61 %

Solvent computation

Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 62.368 Å² / k_sol: 0.365 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-7.3705 Å²	0 Å²	0 Å²
2-	-	14.5822 Å²	0 Å²
3-	-	-	-7.2117 Å²

Refinement step

Cycle: LAST / Resolution: 2.296→79.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5396	0	0	304	5700

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.021	5695
X-RAY DIFFRACTION	f_angle_d	1.177	7417
X-RAY DIFFRACTION	f_dihedral_angle_d	14.36	2057
X-RAY DIFFRACTION	f_chiral_restr	0.086	820
X-RAY DIFFRACTION	f_plane_restr	0.005	969

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 (%)
2.2955-2.3489	0.3577	129	0.3171	2449	X-RAY DIFFRACTION	94
2.3489-2.4077	0.367	135	0.2787	2562	X-RAY DIFFRACTION	100
2.4077-2.4728	0.291	138	0.2568	2619	X-RAY DIFFRACTION	100
2.4728-2.5455	0.3079	135	0.2404	2548	X-RAY DIFFRACTION	100
2.5455-2.6277	0.2741	137	0.2394	2637	X-RAY DIFFRACTION	100
2.6277-2.7216	0.291	135	0.2199	2554	X-RAY DIFFRACTION	100
2.7216-2.8306	0.2753	138	0.2266	2620	X-RAY DIFFRACTION	100
2.8306-2.9594	0.2848	138	0.2221	2611	X-RAY DIFFRACTION	100
2.9594-3.1155	0.2884	137	0.2199	2602	X-RAY DIFFRACTION	100
3.1155-3.3107	0.2648	138	0.2144	2623	X-RAY DIFFRACTION	100
3.3107-3.5663	0.2345	139	0.2076	2633	X-RAY DIFFRACTION	100
3.5663-3.9251	0.2364	139	0.2002	2640	X-RAY DIFFRACTION	100
3.9251-4.4931	0.2326	141	0.1764	2676	X-RAY DIFFRACTION	100
4.4931-5.6606	0.2316	143	0.1716	2706	X-RAY DIFFRACTION	100
5.6606-79.2266	0.2258	150	0.2222	2833	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	0.0592	-0.0933	-0.1147	0.0957	0.1284	0.1442	-0.1069	0.275	-0.0256	-0.4924	0.2152	-0.0037	0.2439	0.1848	0.0331	0.7846	0.1385	0.0351	1.0584	-0.3449	-0.0324	16.6497	-8.8716	-1.0529
2	0.5304	-0.1912	0.1113	0.0476	-0.0568	0.2715	-0.0233	0.0823	0.0594	0.0038	-0.0063	0.0092	-0.0261	0.0534	0.0095	0.2161	0.023	0.0058	0.2455	0.0112	0.2531	20.816	5.6703	32.689
3	0.5224	-0.0168	0.2209	0.5608	-0.0002	0.095	0.1221	-0.0156	-0.0436	0.0061	0.0708	0.0618	0.15	0.1138	-0.0855	0.7796	-0.0498	0.0901	0.842	0.1494	0.5563	-0.5223	21.4173	53.8058
4	0.3848	-0.0034	0.2412	0.0108	-0.0112	0.1606	0.0415	-0.1824	-0.0524	0.0789	-0.0251	-0.0239	-0.0126	0.0205	-0.0026	0.9051	0.1225	0.0205	0.4196	0.0861	0.3067	8.6394	23.4833	55.6463
5	0.0119	0.0152	0.0171	0.0812	-0.0409	0.0953	-0.0133	-0.0025	-0.0015	-0.0251	0.0144	0.0204	0.0175	-0.0065	-0.0104	1.0211	-0.0086	-0.1465	0.7559	0.0834	0.7263	15.6079	31.6498	61.8859
6	0.8264	0.0575	0.0626	0.4892	-0.0303	0.0192	-0.065	-0.4414	-0.019	0.4796	0.1448	0.1902	-0.2292	-0.2067	-0.0244	0.5086	0.0464	0.0657	0.4163	0.0285	0.2765	0.9011	35.8167	45.8422
7	0.2909	0.0686	-0.3609	0.284	0.0572	0.5282	0.0909	-0.0009	0.0779	0.0366	-0.0595	0.0331	-0.016	-0.1683	-0.0026	0.1893	-0.003	0.0129	0.2631	-0.0427	0.2246	-5.4228	44.249	19.6058
8	0.0681	0.0008	-0.0557	0.0423	-0.0124	0.1049	0.015	-0.0462	0.0031	-0.0661	0.0802	-0.0576	-0.0825	0.0319	-0.0146	0.1756	-0.0768	0.0417	0.2664	-0.0785	0.1395	-6.2272	41.2583	-0.3025
9	0.0625	0.0151	0.107	0.0419	0.0552	0.2174	0.0638	-0.0273	-0.0469	0.0007	0.0304	-0.046	-0.0213	0.0663	-0.0487	0.1456	-0.0182	-0.0118	0.2152	-0.0383	0.2033	-11.5699	28.473	9.9306
10	0.1896	0.0625	0.255	0.0783	0.0786	0.3484	0.0357	-0.1284	0.0327	-0.057	0.0341	0.0611	-0.0335	0.0005	-0.0021	0.2133	0.0091	0.0026	0.3513	-0.0393	0.2249	-17.0793	37.8998	0.8676
11	0.3645	0.0014	0.004	0.1177	0.0339	0.0165	0.0597	-0.0958	-0.0052	-0.0066	-0.0684	-0.0532	-0.021	-0.1208	-0.0023	0.15	-0.0004	-0.016	0.2997	-0.0122	0.2043	-1.239	33.8047	19.1113
12	0.2551	0.007	0.1519	0.1664	-0.1734	0.8984	-0.0555	0.2075	-0.0845	0.0436	-0.06	0.0323	-0.0821	0.1248	0.0403	0.0804	-0.011	-0.0066	0.1896	-0.0261	0.1312	9.6652	39.837	18.4298
13	0.053	-0.0362	0.088	0.1935	-0.0705	0.1629	0.0152	0.1927	0.0105	-0.0909	-0.0491	-0.1523	0.0298	0.0696	0.0242	0.1272	-0.0248	0.0139	0.3491	0.0159	0.2238	14.7972	48.6405	14.9169
14	0.1715	-0.0635	0.2265	0.1593	0.0016	0.3495	-0.061	0.0028	0.1646	0.0711	-0.0954	0.0158	-0.0484	-0.0368	0.0831	0.1772	0.0057	-0.0206	0.1798	-0.0524	0.2249	8.2299	51.876	22.3216

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 13:152)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 153:357)
3	X-RAY DIFFRACTION	3	CHAIN B AND (RESSEQ 13:37)
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESSEQ 38:65)
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESSEQ 66:75)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 76:165)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 166:182)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 183:200)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 201:236)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 237:252)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 253:277)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 278:310)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 311:336)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 337:357)

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