PDB-4phi: Crystal structure of HEWL with hexatungstotellurate(VI)

ID or keywords:

Entry

Database: PDB / ID: 4phi

Title

Crystal structure of HEWL with hexatungstotellurate(VI)

Components

Lysozyme C

Keywords

HYDROLASE /

polyoxometalate / Anderson Evans type

Function / homology

Function and homology information

Lactose synthesis /

Antimicrobial peptides / Neutrophil degranulation /

beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process /

lysozyme /

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

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.811 Å

Authors

Bijelic, A. / Molitor, C. / Mauracher, S.G. / Al-Oweini, R. / Kortz, U. / Rompel, A.

Citation

Journal: Chembiochem / Year: 2015
Title: Hen Egg-White Lysozyme Crystallisation: Protein Stacking and Structure Stability Enhanced by a Tellurium(VI)-Centred Polyoxotungstate.
Authors: Bijelic, A. / Molitor, C. / Mauracher, S.G. / Al-Oweini, R. / Kortz, U. / Rompel, A.

History

Deposition	May 6, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jan 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 21, 2015	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4phi.cif.gz	311.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4phi.ent.gz	267.6 KB	Display	PDB format
PDBx/mmJSON format	4phi.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/ph/4phi ftp://data.pdbj.org/pub/pdb/validation_reports/ph/4phi	HTTPS FTP

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Related structure data

Similar structure data	6gcj-d 5evh-d 1sl5-d 4j6k-5 4zy7-1 6sru-7 5iri-2 5u64-d 6pwt-d 6d4a-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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (3) #136 - Apr 2011 Nanobodies similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (3) #9 - Sep 2000 Lysozyme similarity (3) #142 - Oct 2011 PDB Pioneers similarity (3)

Deposited unit

A: Lysozyme C

B: Lysozyme C

C: Lysozyme C

D: Lysozyme C

hetero molecules

70.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lysozyme C

hetero molecules

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

2

Idetical with deposited unit
defined by author&software

3

B: Lysozyme C

hetero molecules

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

4

C: Lysozyme C

hetero molecules

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

5

D: Lysozyme C

hetero molecules

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

Unit cell

Length a, b, c (Å)	60.010, 60.010, 261.840
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-302- HOH

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV Mass: 14331.160 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 663 molecules

#2: Chemical	ChemComp-TEW / 6-tungstotellurate(VI) Mass: 1614.626 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O₂₄TeW₆
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1.2 M sodium chloride, 0.1 M sodium acetate pH 4.8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0207 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0207 Å / Relative weight: 1
Reflection	Resolution: 1.811→29.25 Å / Num. obs: 80356 / % possible obs: 99.99 % / Redundancy: 19.6 % / R_merge(I) obs: 0.19 / R_sym value: 0.19 / Net I/σ(I): 15.72
Reflection shell	Resolution: 1.81→1.859 Å / Redundancy: 17.8 % / R_merge(I) obs: 1.702 / Num. measured obs: 80356 / Num. unique all: 4520 / R_sym value: 1.7 / % possible all: 99.89

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.811→29.247 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1995	4149	4.99 %
R_work	0.187	-	-
obs	0.1876	83164	100 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.811→29.247 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3868	0	268	646	4782

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4311
X-RAY DIFFRACTION	f_angle_d	0.717	6388
X-RAY DIFFRACTION	f_dihedral_angle_d	11.209	1381
X-RAY DIFFRACTION	f_chiral_restr	0.025	563
X-RAY DIFFRACTION	f_plane_restr	0.002	696

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 (%)
1.8105-1.8311	0.3015	134	0.259	2591	X-RAY DIFFRACTION	100
1.8311-1.8526	0.2569	139	0.254	2630	X-RAY DIFFRACTION	100
1.8526-1.8752	0.2548	139	0.2522	2707	X-RAY DIFFRACTION	100
1.8752-1.8989	0.2254	135	0.2439	2579	X-RAY DIFFRACTION	100
1.8989-1.9239	0.2438	138	0.2465	2655	X-RAY DIFFRACTION	100
1.9239-1.9503	0.2454	140	0.2387	2632	X-RAY DIFFRACTION	100
1.9503-1.9781	0.2182	137	0.2271	2629	X-RAY DIFFRACTION	100
1.9781-2.0076	0.2575	134	0.2283	2640	X-RAY DIFFRACTION	100
2.0076-2.039	0.2205	139	0.2163	2600	X-RAY DIFFRACTION	100
2.039-2.0724	0.1942	146	0.219	2708	X-RAY DIFFRACTION	100
2.0724-2.1082	0.2542	136	0.2139	2557	X-RAY DIFFRACTION	100
2.1082-2.1465	0.25	141	0.2122	2664	X-RAY DIFFRACTION	100
2.1465-2.1877	0.2189	145	0.2168	2628	X-RAY DIFFRACTION	100
2.1877-2.2324	0.2459	138	0.2044	2655	X-RAY DIFFRACTION	100
2.2324-2.2809	0.2416	136	0.2049	2610	X-RAY DIFFRACTION	100
2.2809-2.3339	0.2153	137	0.2049	2609	X-RAY DIFFRACTION	100
2.3339-2.3923	0.2312	140	0.1909	2676	X-RAY DIFFRACTION	100
2.3923-2.4569	0.2096	138	0.2006	2601	X-RAY DIFFRACTION	100
2.4569-2.5292	0.1807	139	0.1987	2649	X-RAY DIFFRACTION	100
2.5292-2.6108	0.1919	144	0.191	2659	X-RAY DIFFRACTION	100
2.6108-2.704	0.1804	143	0.1843	2609	X-RAY DIFFRACTION	100
2.704-2.8122	0.1766	134	0.1793	2630	X-RAY DIFFRACTION	100
2.8122-2.9401	0.1892	134	0.1679	2635	X-RAY DIFFRACTION	100
2.9401-3.0949	0.1988	135	0.175	2648	X-RAY DIFFRACTION	100
3.0949-3.2886	0.187	141	0.1634	2627	X-RAY DIFFRACTION	100
3.2886-3.5421	0.1589	141	0.1563	2657	X-RAY DIFFRACTION	100
3.5421-3.8978	0.1889	133	0.1591	2616	X-RAY DIFFRACTION	100
3.8978-4.4602	0.1528	143	0.1428	2635	X-RAY DIFFRACTION	100
4.4602-5.6128	0.1594	132	0.1692	2641	X-RAY DIFFRACTION	100
5.6128-29.2505	0.2216	138	0.195	2638	X-RAY DIFFRACTION	100

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