PDB-4arl: Structure of the inactive pesticin D207A mutant

ID or keywords:

Entry

Database: PDB / ID: 4arl

Title

Structure of the inactive pesticin D207A mutant

Components

PESTICIN

Keywords

HYDROLASE /

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: 1.999 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 16, 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	Sep 5, 2012	Group: Derived calculations
Revision 1.4	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status 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	4arl.cif.gz	285.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4arl.ent.gz	235.6 KB	Display	PDB format
PDBx/mmJSON format	4arl.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	4aqnC 4arjC 4armC 4arpC 4arqC C: citing same article (ref.)
Similar structure data	4arm-2 4arp-2 4arp-1 4arq-1 4arq-2 5nyj-9 6tj6-d 5xzw-1 2vv8-d 1z47-2 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

80.6 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)	35.323, 92.620, 225.916
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-2152- HOH

#1: Protein	PESTICIN Mass: 40289.160 Da / Num. of mol.: 2 / 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: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, ASP 207 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 207 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: 2.3 Å³/Da / Density % sol: 46.5 % / 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→58 Å / Num. obs: 50456 / % possible obs: 97.8 % / Observed criterion σ(I): 2.5 / Redundancy: 5.4 % / B_iso Wilson estimate: 31.79 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shell	Resolution: 2→2.12 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / % possible all: 91

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.7_650)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.999→58.43 Å / SU ML: 0.3 / σ(F): 1.5 / Phase error: 22.67 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2414	2000	4 %
R_work	0.1962	-	-
obs	0.1981	50456	97.77 %

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.722 Å² / k_sol: 0.336 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.5223 Å²	0 Å²	0 Å²
2-	-	-2.0584 Å²	0 Å²
3-	-	-	-5.4639 Å²

Refinement step

Cycle: LAST / Resolution: 1.999→58.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5451	0	0	283	5734

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.019	5808
X-RAY DIFFRACTION	f_angle_d	1.257	7573
X-RAY DIFFRACTION	f_dihedral_angle_d	14.234	2114
X-RAY DIFFRACTION	f_chiral_restr	0.1	836
X-RAY DIFFRACTION	f_plane_restr	0.007	996

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 (%)
1.999-2.049	0.3094	125	0.2849	3038	X-RAY DIFFRACTION	87
2.049-2.1044	0.3034	136	0.2517	3285	X-RAY DIFFRACTION	94
2.1044-2.1663	0.2998	139	0.231	3356	X-RAY DIFFRACTION	97
2.1663-2.2362	0.2995	140	0.2343	3423	X-RAY DIFFRACTION	98
2.2362-2.3162	0.2817	142	0.2131	3438	X-RAY DIFFRACTION	99
2.3162-2.4089	0.218	143	0.2107	3446	X-RAY DIFFRACTION	99
2.4089-2.5185	0.2645	145	0.2146	3537	X-RAY DIFFRACTION	99
2.5185-2.6513	0.2912	144	0.2096	3450	X-RAY DIFFRACTION	100
2.6513-2.8174	0.2472	143	0.2002	3487	X-RAY DIFFRACTION	99
2.8174-3.035	0.2543	144	0.2063	3494	X-RAY DIFFRACTION	99
3.035-3.3404	0.2169	146	0.1953	3533	X-RAY DIFFRACTION	99
3.3404-3.8236	0.2714	147	0.192	3546	X-RAY DIFFRACTION	99
3.8236-4.817	0.2011	148	0.1591	3600	X-RAY DIFFRACTION	99
4.817-58.4545	0.2064	158	0.1839	3823	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	0.9538	-0.3107	-0.5747	0.2917	0.411	0.6008	0.1046	0.1655	-0.0856	-0.047	0.099	-0.1813	-0.1332	-0.1657	-0.0705	0.4424	0.0121	0.0331	0.683	0.0263	0.3479	-7.4291	8.4511	-45.9308
2	0.9598	-0.1767	0.1441	0.7312	-0.365	1.1074	0.0428	0.7029	0.4574	-0.498	0.1613	-0.0187	0.6614	-0.4808	0.4621	0.2108	-0.1705	-0.0501	0.4447	-0.0308	-0.0979	-11.9878	9.3281	-34.1529
3	0.2866	0.1886	-0.1437	0.1757	-0.0955	0.0963	-0.1123	-0.0907	0.1052	0.0298	0.2048	-0.2353	0.1003	0.0981	0.2869	0.1557	0.0577	-0.0013	0.1449	-0.0999	0.2626	12.0402	29.0692	-7.6913
4	0.6522	-0.2654	-0.1571	0.2687	0.179	0.3856	-0.0152	-0.0571	-0.0112	0.0762	0.0822	-0.154	0.0606	0.0724	0.132	0.1047	0.0064	-0.0042	0.0845	-0.0444	0.2256	7.7365	20.0906	-7.6437
5	0.0429	0.0448	-0.049	0.206	-0.3696	0.6749	-0.0551	0.1016	0.14	0.1699	0.0449	0.0076	-0.0598	-0.3541	-0.0136	0.0786	0.006	0.0136	0.1831	-0.02	0.242	-7.5123	13.1153	-4.26
6	0.1039	-0.0367	0.1375	0.2436	0.1162	1.1378	-0.0308	0.0382	-0.0252	-0.0037	0.0362	-0.1576	-0.0075	0.3389	0.0634	0.4577	0.2467	-0.0249	0.9138	0.0862	0.2024	-11.3799	55.8219	-54.1382
7	0.0428	0.0157	0.0089	0.0237	0.0129	0.008	-0.0393	0.0909	0.0112	-0.0079	0.1017	-0.0117	0.0409	-0.0363	-0.0157	0.599	0.2034	-0.04	1.0606	-0.0612	0.2414	-9.4833	47.8113	-57.6831
8	0.3298	-0.084	0.1343	0.1579	-0.2158	0.481	0.1415	0.2808	0.2555	-0.1445	-0.0739	0.0478	-0.0674	-0.4715	0.2477	0.4404	0.1116	-0.0477	0.629	0.0123	0.0946	-14.0304	53.5036	-41.5481
9	0.7559	0.2111	-0.1969	0.203	0.0644	0.1623	0.044	0.1982	0.4474	-0.5184	0.2243	-0.392	-0.4654	0.2583	-0.0154	0.4644	-0.0844	0.1528	0.2434	-0.0605	0.4276	10.1985	72.982	-19.3727
10	0.4422	-0.0968	0.0286	0.3769	0.5523	0.9441	-0.0102	-0.0127	0.0406	-0.1464	0.0519	-0.1499	-0.1102	0.0591	-0.0083	0.247	-0.0332	0.0127	0.1218	-0.0202	0.1943	4.1748	61.0952	-16.236

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 13:37)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 38:164)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 165:222)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 223:336)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 337:360)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 11:30)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 31:58)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 59:164)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 165:228)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 229:357)

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