PDB-4arm: Structure of the inactive pesticin T201A mutant

ID or keywords:

Entry

Database: PDB / ID: 4arm

Title

Structure of the inactive pesticin T201A mutant

Components

(PESTICIN) x 2

Keywords

TOXIN /

MURAMIDASE

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: 2.002 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4arm.cif.gz	294.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4arm.ent.gz	249 KB	Display	PDB format
PDBx/mmJSON format	4arm.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/4arm ftp://data.pdbj.org/pub/pdb/validation_reports/ar/4arm	HTTPS FTP

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Related structure data

Related structure data	4aqnC 4arjC 4arlC 4arpC 4arqC C: citing same article (ref.)
Similar structure data	4arq-2 2vv8-d 5jtc-d 5nyr-1 4arq-1 5nyp-1 5nyq-1 2pa3-d 4ayz-d 6tj5-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 - 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

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

1

A: PESTICIN

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

2

B: PESTICIN

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

Unit cell

Length a, b, c (Å)	65.623, 43.248, 133.201
Angle α, β, γ (deg.)	90.00, 99.36, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	PESTICIN Mass: 40312.176 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: T7, PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57159
#2: Protein	PESTICIN Mass: 40303.145 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: T7, PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57159
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, THR 201 TO ALA ENGINEERED RESIDUE IN CHAIN B, THR 201 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: 2.31 Å³/Da / Density % sol: 46.83 % / 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→44 Å / Num. obs: 50034 / % possible obs: 99.2 % / Observed criterion σ(I): 2.8 / Redundancy: 3.1 % / R_merge(I) obs: 0.09 / Net I/σ(I): 10.1
Reflection shell	Resolution: 2→2.12 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 2.8 / % possible all: 98.7

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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 / Resolution: 2.002→43.809 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 19.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2128	3503	7 %
R_work	0.176	-	-
obs	0.1786	50034	99.27 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 51.178 Å² / k_sol: 0.399 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.8547 Å²	0 Å²	0.6346 Å²
2-	-	-0.7729 Å²	0 Å²
3-	-	-	-2.0817 Å²

Refinement step

Cycle: LAST / Resolution: 2.002→43.809 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5512	0	0	667	6179

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5675
X-RAY DIFFRACTION	f_angle_d	0.826	7678
X-RAY DIFFRACTION	f_dihedral_angle_d	12.905	2148
X-RAY DIFFRACTION	f_chiral_restr	0.062	843
X-RAY DIFFRACTION	f_plane_restr	0.003	1010

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 (%)
2.0018-2.0292	0.2962	134	0.2406	1783	X-RAY DIFFRACTION	96
2.0292-2.0582	0.2414	142	0.2029	1886	X-RAY DIFFRACTION	100
2.0582-2.0889	0.2571	137	0.1958	1814	X-RAY DIFFRACTION	100
2.0889-2.1216	0.2202	141	0.1916	1881	X-RAY DIFFRACTION	100
2.1216-2.1564	0.2825	137	0.1909	1820	X-RAY DIFFRACTION	100
2.1564-2.1935	0.2621	140	0.1946	1862	X-RAY DIFFRACTION	100
2.1935-2.2334	0.2777	138	0.1908	1833	X-RAY DIFFRACTION	99
2.2334-2.2764	0.2367	141	0.1911	1863	X-RAY DIFFRACTION	100
2.2764-2.3228	0.2205	137	0.1836	1828	X-RAY DIFFRACTION	100
2.3228-2.3733	0.2294	143	0.1809	1892	X-RAY DIFFRACTION	100
2.3733-2.4285	0.2391	140	0.1783	1866	X-RAY DIFFRACTION	100
2.4285-2.4893	0.2071	136	0.1759	1812	X-RAY DIFFRACTION	100
2.4893-2.5566	0.2073	143	0.1696	1899	X-RAY DIFFRACTION	100
2.5566-2.6318	0.2459	140	0.1808	1851	X-RAY DIFFRACTION	100
2.6318-2.7167	0.2147	140	0.1762	1866	X-RAY DIFFRACTION	99
2.7167-2.8138	0.2339	138	0.1713	1824	X-RAY DIFFRACTION	100
2.8138-2.9264	0.2056	141	0.1795	1882	X-RAY DIFFRACTION	100
2.9264-3.0596	0.2554	140	0.1713	1856	X-RAY DIFFRACTION	100
3.0596-3.2209	0.2072	140	0.167	1866	X-RAY DIFFRACTION	100
3.2209-3.4226	0.2084	141	0.1596	1869	X-RAY DIFFRACTION	99
3.4226-3.6867	0.1962	140	0.161	1853	X-RAY DIFFRACTION	99
3.6867-4.0575	0.1797	140	0.155	1872	X-RAY DIFFRACTION	99
4.0575-4.6441	0.1553	143	0.1429	1896	X-RAY DIFFRACTION	99
4.6441-5.8488	0.1922	142	0.1731	1888	X-RAY DIFFRACTION	99
5.8488-43.8195	0.1959	149	0.2157	1969	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	0.1952	-0.2564	-0.3823	1.3388	-0.0828	1.4017	-0.0207	-0.5204	-0.0255	0.3504	0.0491	0.0106	0.2049	-0.7693	0.0644	0.4767	-0.1021	-0.0414	0.6088	0.0841	0.1457	-18.4628	-0.3112	-9.5528
2	2.9862	-0.2835	1.2453	2.5839	-0.931	2.251	-0.0082	-0.5892	-0.6204	0.512	-0.0387	-0.0724	0.793	0.2039	-0.0617	0.6086	0.0523	0.0309	0.6828	0.0972	0.2503	-6.6734	-6.1032	-6.1716
3	0.5891	0.1125	0.811	0.9301	0.2967	1.5559	-0.0898	-0.1314	0.1281	0.1527	0.1357	-0.1512	-0.2222	0.7173	0.0693	0.251	-0.0357	-0.0247	0.4639	-0.0218	0.1229	-4.1417	6.0283	-19.0677
4	0.7581	-0.0001	0.4553	1.5444	-0.4708	0.8978	0.018	0.077	-0.0222	-0.1186	0.0381	-0.0588	0.0223	0.1128	-0.0519	0.1061	-0.0023	0.0262	0.0664	-0.0211	0.1234	-2.4657	18.709	-56.5093
5	0.2514	0.187	-0.1153	1.2679	0.1275	0.5372	-0.0129	0.0543	-0.0365	-0.0197	0.0234	0.0299	0.0432	0.0014	-0.0263	0.1053	-0.0143	0.001	0.0824	0.0024	0.0989	0.8364	1.2434	-47.1258
6	1.8951	-0.2428	-0.0204	1.6983	-0.5051	2.2873	-0.0953	-0.2654	0.1069	0.2615	0.1423	-0.2741	0.0932	0.0604	0.0518	0.1303	0.0119	-0.0528	0.1066	-0.0101	0.13	11.0235	-0.699	-40.6703
7	0.6718	-0.2844	-0.7592	1.2004	0.5096	0.9389	-0.2134	-0.5305	0.1544	0.3465	0.0326	0.0393	0.2361	-0.2052	0.1027	0.4084	0.038	0.0243	0.619	-0.1166	0.2787	-48.6989	15.1892	-8.1078
8	0.9306	-0.0869	-0.4398	1.3985	0.7683	1.5364	0.0753	-0.3969	0.2967	0.2364	0.0183	-0.1387	-0.2537	0.1527	-0.0876	0.2646	0.0162	0.0184	0.3593	-0.0838	0.1723	-35.8982	14.9684	-19.9939
9	0.8083	0.0183	0.3896	0.8058	-0.3537	1.1816	0.002	0.0181	0.1151	0.0148	0.0275	0.0605	-0.1703	-0.0855	-0.0225	0.1034	0.0107	0.0232	0.103	-0.0023	0.109	-35.6527	17.281	-55.0542
10	1.6337	0.0928	-0.3578	1.2971	0.2886	0.8739	-0.0061	0.0942	-0.135	0.0309	0.1112	-0.1661	0.2597	0.0033	-0.1061	0.0944	-0.0037	-0.0283	0.1187	-0.0311	0.1383	-26.9669	-0.8234	-42.9278

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 14:58)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 59:75)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 76:163)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 164:252)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 253:336)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 337:359)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 13:75)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 76:164)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 165:277)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 278:359)

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