PDB-4ufq: Structure of a novel Hyaluronidase (Hyal_Sk) from Streptomyces ko...

ID or keywords:

Entry

Database: PDB / ID: 4ufq

Title

Structure of a novel Hyaluronidase (Hyal_Sk) from Streptomyces koganeiensis.

Components

Hyaluronidase

Keywords

HYDROLASE

Function / homology

Hyaluronidase, bacterial / Hyaluronidase protein (HylP) / hyalurononglucosaminidase activity / capsule polysaccharide biosynthetic process / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / DI(HYDROXYETHYL)ETHER / Hyaluronidase

Function and homology information

Biological species

Streptomyces koganeiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.45 Å

Authors

Gavira, J.A. / Messina, L. / Pernagallo, S. / Unciti-Broceta, J.D. / Conejero-Muriel, M. / Diaz-Mochon, J.J. / Vaccaro, S. / Caruso, S. / Musumeci, L. / Bisicchia, S. / Di Pasquale, R.

Citation

Journal: FEBS Lett. / Year: 2016
Title: Identification and Characterization of a Bacterial Hyaluronidase and its Production in Recombinant Form.
Authors: Messina, L. / Gavira, J.A. / Pernagallo, S. / Unciti-Broceta, J.D. / Sanchez Martin, R.M. / Diaz-Mochon, J.J. / Vaccaro, S. / Conejero-Muriel, M. / Pineda-Molina, E. / Caruso, S. / Musumeci, ...

History

Deposition	Mar 18, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 29, 2016	Group: Database references
Revision 1.2	Jul 13, 2016	Group: Database references / Structure summary
Revision 1.3	Aug 10, 2016	Group: Database references
Revision 1.4	Mar 29, 2017	Group: Database references / Source and taxonomy
Revision 1.5	Aug 23, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ufq.cif.gz	251.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4ufq.ent.gz	219.2 KB	Display	PDB format
PDBx/mmJSON format	4ufq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ufq_validation.pdf.gz	468.5 KB	Display	wwPDB validaton report
Full document	4ufq_full_validation.pdf.gz	471.3 KB	Display
Data in XML	4ufq_validation.xml.gz	22.5 KB	Display
Data in CIF	4ufq_validation.cif.gz	33.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uf/4ufq ftp://data.pdbj.org/pub/pdb/validation_reports/uf/4ufq	HTTPS FTP

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Related structure data

Similar structure data	3u3x-3 5ako-d 3u3x-2 1yru-d 4v2k-1 1zot-d 3u3x-1 3hbu-d 4ia3-1 1go7-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	#220 - Apr 2018 Dehalogenases similarity (2) #111 - Mar 2009 Hydrogenase similarity (2)

Deposited unit

A: Hyaluronidase

B: Hyaluronidase

hetero molecules

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

1

B: Hyaluronidase

hetero molecules

B: Hyaluronidase

hetero molecules

B: Hyaluronidase

hetero molecules

defined by author&software
66.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Hyaluronidase

hetero molecules

A: Hyaluronidase

hetero molecules

A: Hyaluronidase

hetero molecules

defined by author&software
68.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.884, 66.884, 483.942
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-2142- HOH
2	1	A-2152- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Hyaluronidase Mass: 21745.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces koganeiensis (bacteria) / Plasmid: PCR-TOPO-BLUNTII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: A0A0U2E2J7

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Non-polymers , 6 types, 435 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.4 Å³/Da / Density % sol: 48.93 % / Description: NONE
Crystal grow	Details: COUNTERDIFFUSION; 30% V/V PEG8K, 0.2 M AMMONIUM SULPHATE

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALBA

/ Beamline: XALOC / Wavelength: 0.90753, 0.97942

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2014 / Details: MIRRORS

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.90753	1
2	0.97942	1

Reflection

Resolution: 1.45→52.24 Å / Num. obs: 75047 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 19 % / B_iso Wilson estimate: 15.6 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 20.49

Reflection shell

Resolution: 1.45→1.5 Å / Redundancy: 17 % / R_merge(I) obs: 1 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software

Name	Classification
XDS	data reduction
SCALA	data scaling
SHELXDE	phasing
MLPHARE	phasing
PHENIX	refinement

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 1.45→52.244 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 16.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1743	3831	5.1 %
R_work	0.1495	-	-
obs	0.1508	74977	99.88 %

Solvent computation

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

Displacement parameters

B_iso mean: 27.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→52.244 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2987	0	78	417	3482

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3239
X-RAY DIFFRACTION	f_angle_d	1.299	4425
X-RAY DIFFRACTION	f_dihedral_angle_d	11.826	1148
X-RAY DIFFRACTION	f_chiral_restr	0.072	531
X-RAY DIFFRACTION	f_plane_restr	0.006	579

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 (%)
1.45-1.4684	0.3092	127	0.2463	2591	X-RAY DIFFRACTION	100
1.4684-1.4877	0.2711	143	0.2215	2613	X-RAY DIFFRACTION	100
1.4877-1.5081	0.2455	144	0.2135	2574	X-RAY DIFFRACTION	100
1.5081-1.5296	0.2348	143	0.1995	2587	X-RAY DIFFRACTION	100
1.5296-1.5524	0.2271	136	0.197	2626	X-RAY DIFFRACTION	100
1.5524-1.5767	0.232	131	0.1919	2581	X-RAY DIFFRACTION	99
1.5767-1.6026	0.229	137	0.1792	2577	X-RAY DIFFRACTION	99
1.6026-1.6302	0.2063	156	0.1806	2620	X-RAY DIFFRACTION	100
1.6302-1.6598	0.2275	130	0.1695	2587	X-RAY DIFFRACTION	100
1.6598-1.6918	0.2217	139	0.1644	2613	X-RAY DIFFRACTION	100
1.6918-1.7263	0.2004	147	0.1525	2591	X-RAY DIFFRACTION	100
1.7263-1.7638	0.1715	144	0.1537	2635	X-RAY DIFFRACTION	100
1.7638-1.8049	0.1754	156	0.1548	2603	X-RAY DIFFRACTION	100
1.8049-1.85	0.1682	137	0.147	2623	X-RAY DIFFRACTION	100
1.85-1.9	0.1665	169	0.1427	2589	X-RAY DIFFRACTION	100
1.9-1.9559	0.1585	145	0.1439	2617	X-RAY DIFFRACTION	100
1.9559-2.0191	0.1659	133	0.1374	2634	X-RAY DIFFRACTION	100
2.0191-2.0912	0.162	133	0.1416	2643	X-RAY DIFFRACTION	100
2.0912-2.175	0.1553	121	0.1358	2649	X-RAY DIFFRACTION	100
2.175-2.274	0.1928	139	0.1314	2646	X-RAY DIFFRACTION	100
2.274-2.3938	0.1634	147	0.1344	2652	X-RAY DIFFRACTION	100
2.3938-2.5438	0.1589	135	0.1429	2643	X-RAY DIFFRACTION	100
2.5438-2.7402	0.1552	145	0.1376	2662	X-RAY DIFFRACTION	100
2.7402-3.016	0.1734	150	0.1431	2681	X-RAY DIFFRACTION	100
3.016-3.4523	0.1777	137	0.1418	2709	X-RAY DIFFRACTION	100
3.4523-4.3492	0.1427	155	0.1398	2724	X-RAY DIFFRACTION	100
4.3492-52.2783	0.1835	152	0.1638	2876	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	3.1931	2.4788	-0.2945	2.7834	0.796	1.9419	-0.1681	0.504	0.1136	-0.3265	0.0472	-0.0288	-0.0117	0.1593	0.0992	0.2889	-0.011	-0.0064	0.2983	0.0419	0.0966	1.8521	1.5911	113.1578
2	0.6581	-0.045	0.0682	0.8355	0.1103	0.982	0.0079	0.1571	-0.0257	-0.1177	-0.0265	-0.005	0.0063	-0.0156	0.0222	0.1669	-0.0052	0.0099	0.1756	0.0026	0.0956	0.3561	-1.1484	128.2131
3	0.6755	-0.5627	0.1764	2.7964	-0.2563	1.3052	0.033	0.1181	-0.0031	-0.0763	-0.0583	0.0608	0.0216	-0.0644	0.0187	0.1177	0.0011	-0.0173	0.1182	-0.0112	0.0903	-6.7352	-1.3871	139.3349
4	1.267	0.8829	-0.0628	0.6	0.1739	1.7047	0.0462	0.0521	-0.0895	-0.0295	-0.0397	-0.2375	0.0324	0.1528	-0.0236	0.0848	0.0052	-0.0031	0.1058	0.0065	0.0754	6.579	-2.2514	147.4913
5	1.335	-0.26	-0.0286	0.0777	-0.1637	3.0517	-0.0136	0.0369	-0.0409	-0.0191	-0.0306	0.0962	0.0107	-0.5656	0.0032	0.0791	0.0022	-0.0048	0.1629	-0.0127	0.0837	-9.7054	1.0594	157.5503
6	1.1959	0.0802	0.3135	0.7424	-0.0694	4.5997	-0.0491	-0.1487	0.0665	0.1476	-0.0032	0.1129	-0.1518	-0.5239	0.0477	0.1412	0.0132	0.017	0.1785	0.001	0.1077	-5.9243	1.8333	177.969
7	2.0422	0.6165	-1.2107	3.8424	-1.8521	1.891	-0.2198	-0.4097	-0.1317	0.2261	0.026	0.0033	-0.4878	0.2515	0.3151	0.6741	-0.0093	-0.0133	0.7284	-0.0513	0.1879	0.5339	2.6379	96.1
8	2.488	0.2975	-0.2367	1.786	-0.1295	2.2769	-0.0467	-0.4115	-0.3775	0.2008	-0.1577	-0.2374	0.3908	0.196	0.2035	0.5266	0.0501	-0.0036	0.5325	0.0727	0.2424	4.7292	-7.259	84.7519
9	3.136	2.6854	-0.9053	5.1738	-0.7198	2.165	-0.074	-0.1775	0.0119	0.2418	-0.0898	0.2397	-0.1455	-0.3289	0.0899	0.4033	-0.001	-0.0018	0.4841	-0.051	0.2288	-5.9241	5.1986	77.2833
10	5.1574	1.744	1.812	1.3665	1.1748	3.6178	0.0549	-0.3929	-0.1541	0.2485	-0.1285	-0.0661	0.4173	0.0448	0.0271	0.411	0.0291	0.0027	0.3162	0.0388	0.1843	2.6826	-8.0467	69.6626
11	1.5075	1.6132	-0.9419	2.6202	-2.2576	2.7129	-0.0472	-0.1016	0.0288	0.4437	0.0756	0.3192	-0.1321	-0.5189	0.0076	0.2922	0.0328	0.0241	0.3778	-0.0119	0.2308	-11.8081	1.6812	63.1317
12	7.8805	-3.6031	-1.7042	2.0463	0.1612	1.2944	0.0324	-0.2968	0.2175	0.1501	-0.0788	-0.1569	-0.2049	0.1125	0.0277	0.3107	-0.0141	-0.0445	0.3254	-0.023	0.1989	7.7692	7.5247	60.4447
13	0.8379	0.1297	-0.1487	0.6149	-0.5355	2.3946	-0.0499	-0.0979	-0.0734	0.0417	-0.0247	-0.061	0.1789	0.1379	0.0753	0.1522	0.0093	0.0058	0.124	0.0015	0.1624	5.7715	-4.5358	37.6602

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 6 THROUGH 25 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 26 THROUGH 65 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 66 THROUGH 85 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 86 THROUGH 115 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 116 THROUGH 145 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 146 THROUGH 217 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 7 THROUGH 26 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 27 THROUGH 46 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 47 THROUGH 66 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 67 THROUGH 86 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 87 THROUGH 106 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 107 THROUGH 116 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 117 THROUGH 217 )

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