PDB-9joc: CRYSTAL STRUCTURE OF ENDO-1,3-FUCANASE (FUN168D) FROM GH168 FAMILY

ID or keywords:

Entry

Database: PDB / ID: 9joc

Title

CRYSTAL STRUCTURE OF ENDO-1,3-FUCANASE (FUN168D) FROM GH168 FAMILY

Components

endo-1.3-fucanase

Keywords

HYDROLASE / Endo-1.3-fucanase / GH168

Function / homology

Hypothetical glycosyl hydrolase family 15 / Hypothetical glycosyl hydrolase family 15 / Uncharacterized protein

Function and homology information

Biological species

Wenyingzhuangia fucanilytica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.29 Å

Authors

Chen, G.N. / Chang, Y.G.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Structure of endo-1.3-fucanase (Fun168D) from GH168 family at 1.29 Angstroms resulution.
Authors: Chen, G.N. / Chang, Y.G.

History

Deposition	Sep 24, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Nov 27, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9joc.cif.gz	229.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9joc.ent.gz	186 KB	Display	PDB format
PDBx/mmJSON format	9joc.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/jo/9joc ftp://data.pdbj.org/pub/pdb/validation_reports/jo/9joc	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: endo-1.3-fucanase

44.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	84.449, 84.449, 93.114
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

Components on special symmetry positions

ID	Model	Components
1	1	A-917- HOH

#1: Protein	endo-1.3-fucanase Mass: 44452.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wenyingzhuangia fucanilytica (bacteria) Gene: AXE80_08865 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B1Y6G8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 42.96 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium chloride, 20% w/v Polyethylene glycol 3,350, pH 6.3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.29→73.13 Å / Num. obs: 93037 / % possible obs: 98.7 % / Redundancy: 8.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.042 / R_pim(I) all: 0.014 / R_rim(I) all: 0.044 / Χ²: 0.79 / Net I/σ(I): 25.1
Reflection shell	Resolution: 1.29→1.36 Å / % possible obs: 92 % / Redundancy: 3.7 % / R_merge(I) obs: 0.374 / Num. measured all: 46926 / Num. unique obs: 12605 / CC_1/2: 0.886 / R_pim(I) all: 0.218 / R_rim(I) all: 0.435 / Χ²: 0.43 / Net I/σ(I) obs: 2.7

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Processing

Software

Name	Version	Classification
Aimless		data scaling
PHENIX	1.20.1-4487-000	refinement
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.29→31.28 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1565	3901	2.15 %
R_work	0.1369	-	-
obs	0.1373	93037	97.46 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.29→31.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2945	0	0	517	3462

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3028
X-RAY DIFFRACTION	f_angle_d	1.098	4110
X-RAY DIFFRACTION	f_dihedral_angle_d	5.911	402
X-RAY DIFFRACTION	f_chiral_restr	0.088	448
X-RAY DIFFRACTION	f_plane_restr	0.01	531

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 (%)
1.29-1.31	0.2597	119	0.2451	5164	X-RAY DIFFRACTION	80
1.31-1.32	0.2462	107	0.2338	5573	X-RAY DIFFRACTION	85
1.32-1.34	0.2306	112	0.218	5723	X-RAY DIFFRACTION	88
1.34-1.36	0.2171	130	0.2009	5972	X-RAY DIFFRACTION	91
1.36-1.38	0.2212	137	0.1935	6127	X-RAY DIFFRACTION	94
1.38-1.4	0.1956	143	0.1896	6298	X-RAY DIFFRACTION	97
1.4-1.42	0.1775	140	0.1681	6396	X-RAY DIFFRACTION	98
1.42-1.44	0.1631	136	0.1615	6474	X-RAY DIFFRACTION	99
1.44-1.47	0.1581	148	0.154	6445	X-RAY DIFFRACTION	99
1.47-1.5	0.198	148	0.1455	6562	X-RAY DIFFRACTION	100
1.5-1.53	0.153	146	0.1395	6459	X-RAY DIFFRACTION	100
1.53-1.56	0.1803	142	0.1375	6520	X-RAY DIFFRACTION	100
1.56-1.59	0.1799	148	0.1366	6532	X-RAY DIFFRACTION	100
1.59-1.63	0.1449	142	0.1316	6489	X-RAY DIFFRACTION	100
1.63-1.67	0.1529	141	0.1401	6502	X-RAY DIFFRACTION	100
1.67-1.71	0.1776	144	0.138	6457	X-RAY DIFFRACTION	100
1.71-1.76	0.1408	143	0.1344	6565	X-RAY DIFFRACTION	100
1.76-1.82	0.131	144	0.131	6487	X-RAY DIFFRACTION	100
1.82-1.89	0.1751	143	0.1378	6499	X-RAY DIFFRACTION	100
1.89-1.96	0.145	150	0.1307	6502	X-RAY DIFFRACTION	100
1.96-2.05	0.1548	142	0.1217	6515	X-RAY DIFFRACTION	100
2.05-2.16	0.1237	134	0.1237	6533	X-RAY DIFFRACTION	100
2.16-2.29	0.1484	142	0.126	6500	X-RAY DIFFRACTION	100
2.29-2.47	0.1468	138	0.1282	6547	X-RAY DIFFRACTION	100
2.47-2.72	0.1739	150	0.1323	6514	X-RAY DIFFRACTION	100
2.72-3.11	0.1659	142	0.1366	6494	X-RAY DIFFRACTION	100
3.11-3.92	0.1385	146	0.1236	6490	X-RAY DIFFRACTION	100
3.92-10	0.1496	144	0.1369	6504	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	1.402	-0.8372	-0.5686	1.4871	0.8609	1.779	0.0769	0.2025	0.0181	-0.1303	-0.1007	0.0289	-0.1651	-0.1273	0.025	0.1238	0.0245	-0.0234	0.144	-0.0017	0.1118	23.4244	2.64	-10.2898
2	1.5004	-0.5849	-0.1864	0.8124	0.1394	0.8793	-0.0111	0.0573	-0.0478	-0.0277	-0.0113	-0.0001	-0.0036	-0.0295	0.0091	0.1026	-0.0049	0.0017	0.0891	0.0015	0.0971	42.605	-5.5673	-10.0712
3	2.5289	-1.4527	0.4478	2.1561	-0.6969	1.9191	0.0056	0.0943	0.2352	0.0191	-0.0202	-0.1707	-0.1313	0.1468	0.0062	0.1319	-0.0084	-0.0044	0.1276	-0.0074	0.1548	50.6429	2.7619	-5.552
4	0.7474	0.2201	-0.5659	1.0149	-0.5934	2.034	0.0017	-0.0786	0.0307	0.0132	-0.0126	-0.1025	0.0009	0.1421	0.0082	0.1315	0.0166	-0.0092	0.1298	-0.0213	0.1409	38.6275	3.7533	5.2968
5	1.0613	-0.0549	-0.1636	0.8443	-0.0867	1.792	0.0263	-0.0651	-0.0524	0.0734	-0.032	-0.0503	0.0498	0.1124	0.012	0.1223	0.0164	-0.007	0.1255	-0.0129	0.1293	31.8596	2.3164	10.8598
6	1.8447	0.1782	-0.1688	1.9238	0.5684	1.5291	-0.0239	-0.0199	-0.1857	0.0724	-0.0548	0.2056	0.1585	-0.1286	0.0753	0.1199	-0.0055	-0.0046	0.122	-0.0049	0.1274	20.2529	-3.2723	10.3666
7	0.7562	-0.2161	-0.0456	1.7313	0.8583	1.1545	0.0209	0.0427	0.0046	-0.0082	-0.1217	0.2022	-0.0399	-0.1965	0.0999	0.1246	0.0214	-0.0141	0.1377	-0.0142	0.12	18.9409	4.346	2.9214
8	1.8499	-0.0009	0.9821	1.8094	-0.7574	3.0712	-0.0104	-0.0673	0.0484	0.0665	0.0364	0.1663	-0.153	-0.21	-0.0145	0.1077	0.0161	0.0085	0.115	-0.0254	0.116	19.8459	9.2033	18.884

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 90 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 91 through 188 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 189 through 209 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 210 through 253 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 254 through 290 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 291 through 319 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 320 through 358 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 359 through 388 )

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