PDB-5kig: PSEUDO T4 LYSOZYME MUTANT - Y88F

ID or keywords:

Entry

Database: PDB / ID: 5kig

Title

PSEUDO T4 LYSOZYME MUTANT - Y88F

Components

Endolysin

Lysin

Keywords

HYDROLASE / HALOGEN BONDS / T4 LYSOZYME

Function / homology

Function and homology information

viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process /

lysozyme /

lysozyme activity /

cytolysis / defense response to bacterium / host cell cytoplasm
Similarity search - Function

Biological species

Enterobacteria phage T4 (virus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Scholfield, M.R.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2017
Title: Structure-Energy Relationships of Halogen Bonds in Proteins.
Authors: Scholfield, M.R. / Ford, M.C. / Carlsson, A.C. / Butta, H. / Mehl, R.A. / Ho, P.S.

History

Deposition	Jun 16, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 19, 2017	Group: Database references
Revision 1.2	Jun 14, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Sep 27, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5kig.cif.gz	54 KB	Display	PDBx/mmCIF format
PDB format	pdb5kig.ent.gz	40.7 KB	Display	PDB format
PDBx/mmJSON format	5kig.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kig_validation.pdf.gz	286.1 KB	Display	wwPDB validaton report
Full document	5kig_full_validation.pdf.gz	287.2 KB	Display
Data in XML	5kig_validation.xml.gz	12.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ki/5kig ftp://data.pdbj.org/pub/pdb/validation_reports/ki/5kig	HTTPS FTP

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Related structure data

Related structure data	5khzC 5ki1C 5ki2C 5ki3C 5ki8C 5kiiC 5kimC 5kioC 1l63S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1lye-d 231l-d 1l71-d 3g3x-d 123l-d 1l61-d 2b74-d 104l-1 1l91-d 1l77-d 1d3j-d 1lpy-d 232l-d 1lyg-d 1dyg-d 1qtc-d 1l87-d 1cvk-d 1i6s-d 160l-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	#9 - Sep 2000 Lysozyme similarity (6) #100 - Apr 2008 Adrenergic Receptors similarity (6) #136 - Apr 2011 Nanobodies similarity (6) #164 - Aug 2013 Serotonin Receptor similarity (6) #217 - Jan 2018 Opioid Receptors similarity (4)

Deposited unit

A: Endolysin

hetero molecules

19.6 kDa, 1 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)	60.368, 60.368, 96.571
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-478- HOH
2	1	A-485- HOH

#1: Protein	Endolysin / Lysin / Lysis protein / Lysozyme / Muramidase Mass: 19441.246 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P00720, lysozyme
#2: Chemical	ChemComp-HED / 2-HYDROXYETHYL DISULFIDE Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.48 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 2.0M KPO4, 50MM 2-HYDROXYETHYLDISULFIDE, 50MM 2-MERCAPTOETHANOL, PH6.9

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å

Detector

Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 15, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Resolution: 1.5→50 Å / Num. obs: 33527 / % possible obs: 99.3 % / Redundancy: 8.1 % / B_iso Wilson estimate: 12.1 Å² / R_merge(I) obs: 0.061 / R_pim(I) all: 0.021 / R_rim(I) all: 0.064 / Χ²: 2.423 / Net I/av σ(I): 42.296 / Net I/σ(I): 18.2 / Num. measured all: 269948

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.5-1.53	3.3	0.399	1	94.8
1.53-1.55	5.7	0.367	1	99.7
1.55-1.58	6.5	0.345	1	100
1.58-1.62	6.7	0.292	1	100
1.62-1.65	7	0.268	1	100
1.65-1.69	7.1	0.248	1	100
1.69-1.73	6.9	0.216	1	100
1.73-1.78	7.3	0.19	1	100
1.78-1.83	7.7	0.174	1	99.9
1.83-1.89	7.2	0.149	1	99.6
1.89-1.96	4.9	0.142	1	98.2
1.96-2.04	8.1	0.108	1	99.9
2.04-2.13	7.2	0.096	1	99.9
2.13-2.24	8.5	0.083	1	99.4
2.24-2.38	8.2	0.072	1	98.8
2.38-2.56	11.2	0.066	1	99.8
2.56-2.82	10.7	0.058	1	99.8
2.82-3.23	13.2	0.049	1	99.9
3.23-4.07	8.3	0.04	1	97.5
4.07-50	14.2	0.032	1	99.1

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.10_2155	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1L63

1l63

Resolution: 1.5→22.988 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.75

	R_factor	Num. reflection	% reflection
R_free	0.1956	3747	5.97 %
R_work	0.1626	-	-
obs	0.1645	62766	98.1 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 51.84 Å² / B_iso mean: 16.3394 Å² / B_iso min: 3.68 Å²

Refinement step

Cycle: final / Resolution: 1.5→22.988 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1291	0	8	335	1634
B_iso mean	-	-	35.63	27.97	-
Num. residues	-	-	-	-	162

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1457
X-RAY DIFFRACTION	f_angle_d	0.797	1987
X-RAY DIFFRACTION	f_chiral_restr	0.066	218
X-RAY DIFFRACTION	f_plane_restr	0.005	260
X-RAY DIFFRACTION	f_dihedral_angle_d	19.144	605

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4928-1.5117	0.2814	102	0.265	1697	1799	75
1.5117-1.5316	0.2971	142	0.2266	2150	2292	96
1.5316-1.5525	0.2474	127	0.2106	2197	2324	99
1.5525-1.5747	0.2014	140	0.1882	2211	2351	100
1.5747-1.5982	0.2011	148	0.1792	2238	2386	100
1.5982-1.6232	0.2477	138	0.1878	2239	2377	100
1.6232-1.6498	0.2189	136	0.1778	2222	2358	100
1.6498-1.6782	0.204	146	0.1832	2255	2401	100
1.6782-1.7087	0.2006	132	0.1768	2187	2319	100
1.7087-1.7416	0.2084	146	0.1717	2248	2394	100
1.7416-1.7771	0.2282	145	0.1713	2290	2435	100
1.7771-1.8157	0.2179	137	0.1709	2157	2294	100
1.8157-1.858	0.1799	143	0.1633	2218	2361	100
1.858-1.9044	0.2016	127	0.1776	2135	2262	96
1.9044-1.9559	0.2001	145	0.1812	2114	2259	96
1.9559-2.0134	0.1659	150	0.1574	2232	2382	100
2.0134-2.0783	0.1966	144	0.1637	2224	2368	100
2.0783-2.1526	0.1786	144	0.1516	2235	2379	100
2.1526-2.2387	0.1919	138	0.1524	2171	2309	98
2.2387-2.3405	0.1907	152	0.1593	2119	2271	97
2.3405-2.4637	0.1967	138	0.1575	2227	2365	100
2.4637-2.6179	0.2217	134	0.1627	2255	2389	100
2.6179-2.8197	0.2107	140	0.166	2181	2321	100
2.8197-3.1028	0.2548	142	0.171	2237	2379	100
3.1028-3.5504	0.1485	128	0.1433	2253	2381	99
3.5504-4.4678	0.144	132	0.1269	2098	2230	96
4.4678-22.9904	0.1827	151	0.1582	2229	2380	100

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