PDB-4ily: Abundantly secreted chitosanase from Streptomyces sp. SirexAA-E

ID or keywords:

Entry

Database: PDB / ID: 4ily

Title

Abundantly secreted chitosanase from Streptomyces sp. SirexAA-E

Components

Chitosanase

Keywords

HYDROLASE / Chitosanase / chitosan / biomass degradation

Function / homology

Function and homology information

chitosanase / chitosanase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function

Biological species

Streptomyces sp. SirexAA-E (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.835 Å

Authors

Bianchetti, C.M. / Takasuka, T.E. / Bergeman, L.F. / Fox, B.G.

History

Deposition	Jan 1, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ily.cif.gz	205.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4ily.ent.gz	165.2 KB	Display	PDB format
PDBx/mmJSON format	4ily.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4ily_validation.pdf.gz	421.3 KB	Display	wwPDB validaton report
Full document	4ily_full_validation.pdf.gz	422.1 KB	Display
Data in XML	4ily_validation.xml.gz	23.3 KB	Display
Data in CIF	4ily_validation.cif.gz	35.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/il/4ily ftp://data.pdbj.org/pub/pdb/validation_reports/il/4ily	HTTPS FTP

-
Related structure data

Related structure data	4ilt 4ilv 4im1 PDB Unreleased entry 4im4
Similar structure data	1chk-2 1chk-1 2peh-d 4l7s-2 4ec4-3 6cad-1 5e4h-2 4kpt-1 4pqn-d 3mpo-4 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Chitosanase

B: Chitosanase

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

1

A: Chitosanase

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

2

B: Chitosanase

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

Unit cell

Length a, b, c (Å)	39.067, 115.351, 57.339
Angle α, β, γ (deg.)	90.000, 107.080, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Chitosanase Mass: 27158.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. SirexAA-E (bacteria) / Gene: SACTE_5457 / Plasmid: PVP67K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G2NRC4, chitosanase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.9 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, 0.010 M MOPS pH 7.0) mixed in a 1:1 ratio with the Well Solution. Cryoprotected with 15% ethylene glycol, vapor diffusion, hanging drop, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97857 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2012 / Details: mirrors and beryllium lenses

Radiation

Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97857 Å / Relative weight: 1

Reflection

Resolution: 1.835→50 Å / Num. obs: 42074 / % possible obs: 99.3 % / Redundancy: 3.8 % / R_merge(I) obs: 0.106 / Χ²: 1.032 / Net I/σ(I): 9.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.835-1.87	2.6	0.449	1933	0.9	1	90.8
1.87-1.91	3	0.418	2019	0.929	1	97.4
1.91-1.94	3.2	0.365	2109	0.993	1	98.9
1.94-1.98	3.5	0.323	2110	0.973	1	99.8
1.98-2.03	3.7	0.304	2085	1.08	1	99.7
2.03-2.07	3.7	0.265	2122	1.161	1	99.9
2.07-2.12	3.8	0.226	2121	1.204	1	100
2.12-2.18	3.8	0.201	2129	1.192	1	100
2.18-2.25	3.8	0.18	2070	1.184	1	100
2.25-2.32	3.9	0.178	2152	1.214	1	100
2.32-2.4	4	0.166	2086	1.208	1	100
2.4-2.5	4	0.165	2144	1.25	1	100
2.5-2.61	4	0.162	2127	1.237	1	100
2.61-2.75	4.2	0.158	2095	1.158	1	100
2.75-2.92	4.2	0.137	2091	1.116	1	100
2.92-3.15	4.3	0.112	2134	1.046	1	100
3.15-3.46	4.3	0.093	2123	0.863	1	100
3.46-3.96	4.3	0.076	2136	0.8	1	100
3.96-4.99	4.3	0.058	2139	0.684	1	100
4.99-50	4.2	0.059	2149	0.496	1	99.7

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	6.5 Å	34.54 Å
Translation	6.5 Å	34.54 Å

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.835→34.542 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.19 / σ(F): 0 / Phase error: 20.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1951	2006	4.99 %
R_work	0.1566	-	-
obs	0.1585	40204	94.86 %

Solvent computation

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

Displacement parameters

B_iso max: 96.53 Å² / B_iso mean: 20.5534 Å² / B_iso min: 5.27 Å²

Refinement step

Cycle: LAST / Resolution: 1.835→34.542 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3732	0	0	518	4250

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3864
X-RAY DIFFRACTION	f_angle_d	1.035	5257
X-RAY DIFFRACTION	f_chiral_restr	0.08	539
X-RAY DIFFRACTION	f_plane_restr	0.005	726
X-RAY DIFFRACTION	f_dihedral_angle_d	13.738	1401

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.835-1.8804	0.3	121	0.2387	2217	2338	78
1.8804-1.9313	0.245	129	0.2046	2519	2648	88
1.9313-1.9881	0.2372	125	0.192	2643	2768	91
1.9881-2.0523	0.2361	139	0.1704	2681	2820	93
2.0523-2.1256	0.2182	145	0.1612	2689	2834	95
2.1256-2.2107	0.1992	151	0.1544	2724	2875	95
2.2107-2.3113	0.2267	141	0.1562	2803	2944	97
2.3113-2.4331	0.2329	147	0.1532	2787	2934	97
2.4331-2.5855	0.2166	155	0.1647	2795	2950	98
2.5855-2.7851	0.1988	151	0.1676	2831	2982	99
2.7851-3.0652	0.2275	150	0.1613	2846	2996	99
3.0652-3.5083	0.1672	155	0.1572	2862	3017	99
3.5083-4.4187	0.1419	145	0.1236	2905	3050	100
4.4187-34.5483	0.1716	152	0.1488	2896	3048	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	1.2815	0.3685	-0.4604	3.6174	0.4869	0.3009	0.0612	-0.0523	-0.1488	0.1467	-0.0136	-0.3886	-0.0347	0.119	-0.0389	0.132	-0.0322	-0.0221	0.1418	-0.0343	0.1396	-14.8939	-21.6554	-2.7928
2	2.5753	-0.1672	1.0412	1.5684	0.4269	2.3347	-0.0333	0.0051	0.2928	-0.0823	-0.0081	-0.0041	-0.2122	-0.0885	0.031	0.1293	-0.0167	0.0052	0.0752	-0.0063	0.1035	-22.1966	-2.6687	0.8523
3	0.5942	0.117	0.0826	1.3229	0.2014	0.0377	0.2441	-0.2444	-0.0121	0.5165	-0.2278	0.0026	0.2171	-0.1338	-0.0042	0.2558	-0.0583	-0.018	0.1462	-0.0069	0.0899	-21.4786	-23.6282	5.4679
4	1.863	1.1736	-0.1673	0.8512	-0.6503	2.6687	0.0927	-0.1735	0.073	0.2806	-0.2386	0.3193	-0.0012	-0.2581	-0.3385	0.2144	-0.0771	0.1149	0.2734	-0.106	0.2155	-36.6449	-28.1603	2.7271
5	1.1292	0.3785	-0.5157	3.645	-1.5945	3.4158	0.1588	-0.272	-0.0589	0.4614	-0.2292	0.2899	0.2652	-0.3429	-0.2801	0.2378	-0.1051	0.0205	0.173	-0.027	0.1511	-32.6663	-36.4643	-0.3893
6	7.0476	2.1222	0.9169	4.2569	-0.4471	5.2248	-0.1436	0.5897	0.4402	-0.5259	-0.092	0.7757	-0.4964	-0.7909	-0.0413	0.1642	0.0356	-0.0531	0.229	0.0006	0.1567	-29.6045	-28.2433	-13.2885
7	3.0303	0.4943	-0.2731	2.6219	0.2063	0.6315	0.0859	0.178	-0.4189	-0.0178	0.0856	-0.5123	0.1269	0.1098	-0.0705	0.1463	0.017	-0.043	0.1047	-0.044	0.1819	-17.4704	-35.0293	-8.5098
8	0.1661	0.1704	-0.6001	0.5266	-0.9759	2.5365	-0.1064	-0.1185	-0.1266	0.3226	0.0052	-0.0666	-0.8428	-0.1756	-0.0215	0.2515	0.0211	-0.0286	0.289	0.0043	0.1735	-26.2991	11.3375	-0.6596
9	0.4823	0.1721	0.2867	1.6345	0.2367	0.72	0.0644	-0.0744	-0.0884	0.0676	0.0464	-0.0712	0.179	-0.035	-0.1084	0.1059	-0.0086	-0.0158	0.1046	0.0235	0.0914	-30.6034	-4.7354	-29.2348
10	1.4214	1.2128	0.7041	2.5193	-1.739	4.0373	0.1276	-0.0908	-0.3292	0.2245	0.0449	-0.4348	0.4419	0.1364	0.1326	0.2696	0.023	-0.1302	0.1249	0.0437	0.3183	-23.7049	-20.2519	-24.7134
11	2.9799	-0.1932	-0.5681	2.7887	0.6945	2.6658	-0.002	0.0558	-0.575	-0.0628	-0.0061	0.0335	0.5342	-0.1081	-0.0146	0.2281	0.0005	-0.0974	0.0996	0.0177	0.1744	-29.8935	-18.6998	-31.2729
12	0.6175	1.3434	-0.5396	5.7459	-1.8128	0.9514	0.1295	-0.1976	-0.0442	0.2587	-0.1598	-0.2335	0.0184	0.1402	0.029	0.0784	-0.0003	-0.0319	0.1179	0.002	0.0919	-24.0219	3.4918	-22.6762
13	1.0751	-0.015	-0.3172	1.1451	0.0747	1.2482	-0.0186	0.0559	-0.052	-0.0217	-0.0087	-0.207	-0.015	0.1932	0.0189	0.0487	-0.0181	-0.0113	0.1232	0.0049	0.0954	-21.1006	10.8279	-34.3187
14	1.5503	-0.2133	-0.3738	3.5762	1.2969	4.0911	-0.041	0.1421	0.1779	-0.0491	-0.0459	-0.1153	-0.268	0.2072	-0.0095	0.059	-0.0124	0.0048	0.1002	0.0373	0.1158	-21.593	19.4069	-36.555
15	2.2558	0.551	-0.0958	1.7326	-0.551	1.4999	-0.0186	0.032	0.0581	-0.077	-0.0554	0.1686	-0.0107	-0.1607	0.0177	0.0528	0.0128	0.0033	0.1045	-0.0024	0.0911	-36.3433	15.1675	-35.4233

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 54:89 )	A
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 90:159 )	A
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 160:202 )	A
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 203:221 )	A
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 222:249 )	A
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 250:261 )	A
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 262:289 )	A
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 41:59 )	B
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 60:120 )	B
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 121:136 )	B
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 137:159 )	B
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 160:188 )	B
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 189:221 )	B
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 222:249 )	B
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 250:289 )	B

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi