PDB-4aqn: Crystal structure of pesticin from Y. pestis

ID or keywords:

Entry

Database: PDB / ID: 4aqn

Title

Crystal structure of pesticin from Y. pestis

Components

PESTICIN

Keywords

TOXIN /

BACTERIOCIN /

COLICIN /

THREE DOMAINS /

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 /

SAD / Resolution: 1.98 Å

Authors

Zeth, K. / Albrecht, R.

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 19, 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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Download

PDBx/mmCIF format	4aqn.cif.gz	285.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4aqn.ent.gz	241.6 KB	Display	PDB format
PDBx/mmJSON format	4aqn.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/aq/4aqn ftp://data.pdbj.org/pub/pdb/validation_reports/aq/4aqn	HTTPS FTP

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Related structure data

Related structure data	4arjC 4arlC 4armC 4arpC 4arqC C: citing same article (ref.)
Similar structure data	4arq-d 3ez0-d 4mt0-d 1nvm-1 5ksa-d 2hdx-d 5swz-2 3pik-d 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

hetero molecules

80.2 kDa, 2 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)	36.550, 86.780, 122.270
Angle α, β, γ (deg.)	90.00, 96.14, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	PESTICIN Mass: 40090.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Production host: ESCHERICIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57159
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	OTHER_DETAILS: PESTICIN FROM Y. PESTIS WAS CLONED INTO E. COLI WITH NO OVERHANGING RESIDUES.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.8 % / Description: NONE
Crystal grow	pH: 7.5 / Details: 18% PEG 8000, 0.2 M MGCL2, 0.1 M HEPES PH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→48 Å / Num. obs: 52797 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / R_merge(I) obs: 0.1 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
SHARP		phasing
DM		phasing
BUCCANEER		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.98→29.819 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 25.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2369	2640	5 %
R_work	0.1896	-	-
obs	0.192	52797	99.75 %

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.153 Å² / k_sol: 0.309 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.4564 Å²	0 Å²	0.9968 Å²
2-	-	-1.1051 Å²	0 Å²
3-	-	-	-0.3513 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→29.819 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5392	0	1	385	5778

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5520
X-RAY DIFFRACTION	f_angle_d	1.133	7459
X-RAY DIFFRACTION	f_dihedral_angle_d	14.788	2075
X-RAY DIFFRACTION	f_chiral_restr	0.079	824
X-RAY DIFFRACTION	f_plane_restr	0.004	977

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 (%)
1.98-2.016	0.3593	141	0.3242	2683	X-RAY DIFFRACTION	100
2.016-2.0548	0.3323	138	0.2972	2616	X-RAY DIFFRACTION	100
2.0548-2.0967	0.3191	138	0.2737	2623	X-RAY DIFFRACTION	100
2.0967-2.1423	0.3118	140	0.2647	2664	X-RAY DIFFRACTION	100
2.1423-2.1921	0.3363	137	0.2555	2599	X-RAY DIFFRACTION	100
2.1921-2.2469	0.2888	139	0.2314	2641	X-RAY DIFFRACTION	100
2.2469-2.3076	0.2498	139	0.2179	2631	X-RAY DIFFRACTION	100
2.3076-2.3755	0.2618	136	0.2119	2586	X-RAY DIFFRACTION	100
2.3755-2.4521	0.2692	141	0.2126	2684	X-RAY DIFFRACTION	100
2.4521-2.5397	0.2804	138	0.2011	2621	X-RAY DIFFRACTION	100
2.5397-2.6414	0.2619	139	0.2029	2639	X-RAY DIFFRACTION	100
2.6414-2.7615	0.2734	139	0.1997	2647	X-RAY DIFFRACTION	100
2.7615-2.907	0.2734	138	0.2083	2629	X-RAY DIFFRACTION	100
2.907-3.0889	0.2638	140	0.2036	2649	X-RAY DIFFRACTION	100
3.0889-3.3271	0.2163	140	0.1865	2671	X-RAY DIFFRACTION	100
3.3271-3.6614	0.223	139	0.1734	2636	X-RAY DIFFRACTION	100
3.6614-4.19	0.198	138	0.1529	2622	X-RAY DIFFRACTION	100
4.19-5.2742	0.1824	140	0.1427	2653	X-RAY DIFFRACTION	99
5.2742-29.8221	0.2017	140	0.1685	2663	X-RAY DIFFRACTION	98

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	2.1009	-0.1215	-0.1947	1.5549	-1.461	5.1459	0.0158	0.736	-0.3115	-0.1754	0.1408	-0.0183	-0.0328	0.005	-0.1233	0.2118	-0.0729	-0.0079	0.5013	-0.0992	0.191	16.4256	10.8567	21.8774
2	2.0961	1.0522	-0.2432	3.685	0.4026	0.6749	0.1324	-0.104	-0.019	0.4145	-0.1367	0.1448	-0.0113	0.0355	0.015	0.2397	0.0567	0.0287	0.202	0.0403	0.1871	-0.7579	-0.8065	52.2974
3	0.9906	-0.5859	0.1833	2.1904	0.0097	6.4412	0.1591	-0.5312	0.4732	-0.0206	0.1265	0.3228	0.4451	-0.0365	-0.3677	0.4563	-0.1118	-0.0038	1.0298	0.0283	0.4035	-21.6444	9.4353	121.6766
4	1.7146	0.1578	-0.1419	0.7487	0.8137	4.6646	0.1413	-0.8138	0.4176	0.178	-0.3804	0.1501	-0.0307	-1.2472	-0.0577	0.3103	-0.071	0.057	0.8839	-0.1406	0.0239	-24.9272	12.1576	108.7904
5	2.6297	-1.8668	-0.9167	3.7958	1.023	1.608	-0.1177	-0.0509	-0.1272	0.0962	0.1254	-0.1921	0.251	0.0776	-0.0192	0.216	-0.0352	-0.0121	0.1438	-0.0039	0.1538	-5.0747	-0.3857	80.9914
6	6.273	-1.041	-2.6594	3.4917	2.0417	8.0521	0.4348	0.1589	-0.2764	-0.3883	-0.485	0.5508	-0.3622	-1.1672	0.0731	0.2801	-0.0153	-0.0815	0.2952	-0.031	0.2869	-21.9676	6.297	77.9668

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 13:164)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 165:357)
3	X-RAY DIFFRACTION	3	CHAIN B AND (RESSEQ 13:39)
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESSEQ 40:164)
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESSEQ 165:336)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 337:357)

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