PDB-5xep: Crystal structure of BRP39, a chitinase-like protein, at 2.6 Angs...

ID or keywords:

Entry

Database: PDB / ID: 5xep

Title

Crystal structure of BRP39, a chitinase-like protein, at 2.6 Angstorm resolution

Components

Chitinase-3-like protein 1

Keywords

SUGAR BINDING PROTEIN / Tim barrel / Apoptosis

Function / homology

Function and homology information

response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / positive regulation of peptidyl-threonine phosphorylation / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / Neutrophil degranulation / lung development / response to interleukin-1 ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Mohanty, A.K. / Fisher, A.J. / Choudhary, S. / Kaushik, J.K.

Citation

Journal: To be published
Title: Crystal Structure of BRP39, a signalling glycoprotein expressed during mammary gland apoptosis.
Authors: Mohanty, A.K. / Fisher, A.J. / Yu, Z. / Pradeep, M.A. / Janjanam, J. / Kaushik, J.K.

History

Deposition	Apr 5, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 11, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5xep_validation.pdf.gz	490.5 KB	Display	wwPDB validaton report
Full document	5xep_full_validation.pdf.gz	506.8 KB	Display
Data in XML	5xep_validation.xml.gz	75.9 KB	Display
Data in CIF	5xep_validation.cif.gz	104.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xe/5xep ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xep	HTTPS FTP

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Related structure data

Related structure data	1ljyS S: Starting model for refinement
Similar structure data	3wj7-d 3q68-d 6j7i-2 6j7i-1 1hr6-4 3wkt-2 6j7a-2 5ip2-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	#62 - Feb 2005 Major Histocompatibility Complex similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #88 - Apr 2007 Clathrin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #166 - Oct 2013 Proteasome similarity (1) #176 - Aug 2014 Dynein similarity (1) #177 - Sep 2014 Apoptosomes similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1)

Deposited unit

A: Chitinase-3-like protein 1

B: Chitinase-3-like protein 1

C: Chitinase-3-like protein 1

D: Chitinase-3-like protein 1

E: Chitinase-3-like protein 1

F: Chitinase-3-like protein 1

hetero molecules

258 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chitinase-3-like protein 1

B: Chitinase-3-like protein 1

C: Chitinase-3-like protein 1

hetero molecules

defined by author
Evidence: gel filtration
129 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Chitinase-3-like protein 1

E: Chitinase-3-like protein 1

F: Chitinase-3-like protein 1

defined by author
Evidence: gel filtration
129 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	130.610, 81.320, 229.330
Angle α, β, γ (deg.)	90.00, 105.86, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Chitinase-3-like protein 1 / BRP39 protein / Breast regression protein 39 / Cartilage glycoprotein 39 / GP-39 Mass: 43057.074 Da / Num. of mol.: 6 / Fragment: UNP residues 9-389 / Mutation: E104G, G340R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Tissue: Mammary gland / Gene: Chi3l1, Brp39, Chil1 / Organ: Breast / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B(DE3) / References: UniProt: Q61362
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.75 % / Description: Thin rectangular plates
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 20% PEG6000, 1M LiCl2, 0.1M Bicine buffer, pH 9.0

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Data collection

Diffraction	Mean temperature: 297 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: MAR CCD 130 mm / Detector: CCD / Date: Mar 13, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.6→100 Å / Num. obs: 71290 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.78 % / B_iso Wilson estimate: 34.6 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.085 / Net I/σ(I): 13.08
Reflection shell	Resolution: 2.6→2.67 Å / Redundancy: 3.78 % / R_merge(I) obs: 0.486 / Mean I/σ(I) obs: 2.97 / Num. unique obs: 5288 / CC_1/2: 0.834 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
XDS		data reduction
XDS		data scaling
PHENIX	1.11.1_2575	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1LJY

1ljy

Resolution: 2.6→38.27 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.87

	R_factor	Num. reflection	% reflection
R_free	0.2309	3610	5.06 %
R_work	0.1898	-	-
obs	0.1919	71282	99.72 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→38.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17268	0	8	438	17714

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	17733
X-RAY DIFFRACTION	f_angle_d	0.759	23978
X-RAY DIFFRACTION	f_dihedral_angle_d	12.122	10451
X-RAY DIFFRACTION	f_chiral_restr	0.046	2541
X-RAY DIFFRACTION	f_plane_restr	0.006	3067

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 (%)
2.6-2.6342	0.3344	140	0.2604	2616	X-RAY DIFFRACTION	100
2.6342-2.6703	0.3061	143	0.2499	2599	X-RAY DIFFRACTION	100
2.6703-2.7085	0.3369	132	0.2374	2586	X-RAY DIFFRACTION	100
2.7085-2.7489	0.308	139	0.2367	2602	X-RAY DIFFRACTION	100
2.7489-2.7918	0.2979	137	0.2355	2545	X-RAY DIFFRACTION	100
2.7918-2.8376	0.2718	128	0.2271	2629	X-RAY DIFFRACTION	100
2.8376-2.8865	0.2873	144	0.2287	2577	X-RAY DIFFRACTION	100
2.8865-2.939	0.326	119	0.2387	2611	X-RAY DIFFRACTION	100
2.939-2.9955	0.2875	157	0.2369	2559	X-RAY DIFFRACTION	100
2.9955-3.0566	0.2934	129	0.2356	2611	X-RAY DIFFRACTION	100
3.0566-3.123	0.2812	139	0.2263	2595	X-RAY DIFFRACTION	100
3.123-3.1956	0.2823	141	0.214	2593	X-RAY DIFFRACTION	100
3.1956-3.2755	0.2649	134	0.212	2566	X-RAY DIFFRACTION	100
3.2755-3.364	0.2473	130	0.2136	2636	X-RAY DIFFRACTION	100
3.364-3.4629	0.2461	151	0.2194	2558	X-RAY DIFFRACTION	100
3.4629-3.5746	0.2584	150	0.1987	2579	X-RAY DIFFRACTION	100
3.5746-3.7023	0.2018	145	0.1876	2612	X-RAY DIFFRACTION	100
3.7023-3.8504	0.2052	145	0.1739	2635	X-RAY DIFFRACTION	100
3.8504-4.0255	0.23	140	0.1689	2563	X-RAY DIFFRACTION	100
4.0255-4.2374	0.1931	129	0.1612	2599	X-RAY DIFFRACTION	100
4.2374-4.5025	0.1829	143	0.1469	2629	X-RAY DIFFRACTION	100
4.5025-4.8496	0.1571	146	0.1416	2576	X-RAY DIFFRACTION	99
4.8496-5.3364	0.1836	141	0.1524	2616	X-RAY DIFFRACTION	100
5.3364-6.1059	0.2075	143	0.1793	2607	X-RAY DIFFRACTION	99
6.1059-7.6826	0.2366	135	0.1905	2692	X-RAY DIFFRACTION	100
7.6826-38.2744	0.166	130	0.1551	2681	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	0.0359	0.049	-0.0262	0.0717	-0.0662	0.2913	-0.0526	-0.2466	-0.0696	0.0133	0.0397	0.0865	0.1318	-0.0467	-0.0001	0.1425	0.1086	0.0108	0.2857	0.065	0.3155	41.6885	65.5407	30.4814
2	0.0217	0.0092	0.0015	0.0276	-0.034	0.0389	-0.0416	-0.1296	-0.0643	0.0708	0.0368	0.0247	0.0497	0.0658	-0.0085	0.1686	0.0711	-0.048	0.341	0.0311	0.3082	47.6396	74.0384	36.5216
3	0.0423	0.0248	0.0491	0.0197	0.0399	0.0638	-0.0723	-0.1223	0.0785	0.0582	0.1369	-0.0399	0.0149	0.182	-0.0263	0.0826	0.0974	-0.0969	0.3239	-0.041	0.2142	53.8709	78.0562	32.2596
4	0.0104	-0.0137	-0.0028	0.0224	-0.0003	0.0042	-0.0374	0.0382	0.0683	0.0371	-0.0146	0.0212	-0.04	-0.0171	0.0002	0.1515	-0.0448	0.0682	0.1828	-0.0646	0.2736	46.5485	86.2345	5.6013
5	0.0907	0.0166	-0.0156	0.091	0.0825	0.1454	0.0416	0.0478	-0.1298	-0.1216	0.0267	-0.0144	-0.015	0.0752	0.0849	0.0369	0.0033	-0.0136	0.1318	-0.0317	0.2098	44.3589	72.4332	10.2884
6	0.1385	0.0018	-0.1875	0.1083	-0.021	0.3313	0.1265	-0.1318	0.004	0.0373	0.0796	-0.008	-0.0212	0.336	0.0971	0.1814	0.056	-0.0594	0.2946	-0.0871	0.2032	35.0684	102.4127	36.6468
7	0.0675	-0.0834	0.0417	0.1001	-0.0504	0.0305	0.0186	-0.0957	-0.0355	0.1226	0.1309	-0.042	-0.0311	0.1011	0.0191	0.3834	-0.0162	-0.0174	0.2932	-0.0406	0.1378	25.1936	101.2475	43.3511
8	0.1362	0.0129	-0.2024	0.1235	-0.157	0.4856	0.1154	-0.0112	0.0536	0.1605	0.1583	0.0003	-0.0911	-0.0623	0.3791	0.1943	0.0796	0.0033	0.2041	-0.0343	0.0953	18.3988	105.7272	40.9187
9	0.0201	-0.0256	-0.0027	0.1021	0.0453	0.0348	0.031	-0.0059	-0.0246	0.02	0.0372	0.0374	0.0011	-0.0766	0.0724	0.0831	0.1237	-0.0452	0.1695	0.1403	0.2989	12.4049	104.5254	13.3783
10	0.0944	-0.0372	-0.0217	0.2625	0.0596	0.451	0.0592	0.0509	0.0772	0.0243	0.2094	-0.0177	-0.2157	0.03	0.46	0.0679	0.0791	-0.0047	0.0964	0.0128	0.1653	26.3213	107.9164	17.865
11	0.0282	0.0332	-0.027	0.0422	-0.0325	0.1455	0.1246	-0.0402	0.0442	0.1433	0.0889	0.0939	-0.108	-0.1665	0.115	0.3315	-0.0667	0.238	0.3158	0.0272	0.644	6.0066	77.8207	36.2437
12	0.0477	0.024	0.0775	0.0382	0.0735	0.1995	0.0877	-0.0682	-0.0369	0.1341	0.0526	0.0776	0.0561	-0.0277	0.0324	0.3588	-0.0782	0.1578	0.3639	0.0729	0.4901	12.2482	68.3076	39.8778
13	0.1427	-0.0803	0.0359	0.0643	-0.065	0.2677	0.1514	-0.1134	-0.1348	0.1641	-0.0376	0.1472	0.1532	-0.0663	0.1121	0.3534	-0.1718	0.1036	0.2134	0.0242	0.4438	11.7037	61.3028	34.9234
14	0.0946	0.0895	0.0383	0.1201	0.0115	0.0337	-0.0035	0.0314	-0.0541	0.0129	-0.0209	-0.0002	0.0652	-0.0087	-0.0547	0.2178	-0.1076	-0.125	0.3109	-0.0719	0.4449	13.9373	65.6049	7.4958
15	0.0381	0.0785	-0.0329	0.1501	-0.0857	0.0537	0.0339	0.1674	-0.0504	0.0734	0.1634	0.437	0.1738	-0.3497	0.4128	-0.2501	-0.1675	0.0004	0.2455	0.1073	0.6001	4.5555	73.9482	15.2731
16	0.0832	0.0253	0.0257	0.0064	0.0056	0.0105	0.0825	0.1266	-0.0348	-0.0197	0.0936	0.0047	-0.0787	-0.1676	0.0026	0.6283	-0.0615	-0.0356	0.4212	0.1238	0.294	-0.9841	77.1557	73.3445
17	0.018	0.0099	0.0116	0.014	-0.0104	0.0303	0.0545	0.1158	0.0064	-0.1052	0.1227	0.0598	-0.0202	-0.0844	-0.0001	0.6078	-0.0193	-0.1064	0.3703	0.0635	0.2712	9.0093	75.4815	66.8258
18	0.0869	0.0039	-0.084	0.0296	0.011	0.0829	0.0978	0.095	0.1081	-0.0627	0.1179	0.0348	-0.0887	0.0344	0.1326	0.4597	-0.0605	0.0283	0.3505	0.0643	0.1459	15.8497	80.0543	69.0778
19	0.0102	-0.0077	0.0115	0.0086	-0.0062	0.0159	0.0054	-0.0078	0.0162	0.0341	0.0193	-0.035	-0.01	0.037	-0.008	0.4819	-0.0477	0.0663	0.2261	-0.1188	0.2405	21.4965	80.8433	96.5616
20	0.2346	-0.005	-0.0842	0.4329	-0.2906	0.7676	0.03	0.0113	0.1954	0.0144	0.1986	-0.0458	-0.3252	-0.1417	0.2938	0.5194	-0.0457	0.0772	0.1291	0.0056	0.1208	7.581	83.9413	91.712
21	0.0233	0.0069	-0.0294	0.0278	0.0014	0.034	0.0975	0.0965	-0.0148	-0.2078	0.046	-0.0245	-0.0996	0.0315	-0	0.3729	0.0414	0.0252	0.3453	-0.0786	0.3997	28.6165	52.9078	75.2499
22	0.0109	-0.0025	0.0012	0.0334	-0.0328	0.0319	0.0182	0.0386	0.0052	-0.0728	0.0278	0.003	0.0858	-0.1	0	0.3496	0.0197	-0.0116	0.358	-0.1151	0.319	22.4178	43.1109	72.2272
23	0.0319	0.0049	0.0323	0.0252	0.0208	0.035	0.012	0.0532	-0.1673	0.0141	0.0712	-0.0093	0.2028	-0.0296	0.0028	0.3828	0.0042	-0.0005	0.2854	-0.1058	0.3316	23.1823	36.3476	77.5921
24	0.0006	0.0002	-0.0002	0.0027	-0.0011	0.0008	0.0397	0.0066	-0.0606	0.031	0.0004	0.0295	0.0707	0.0138	0.0003	0.3171	-0.0104	-0.1739	0.2932	0.0247	0.3478	20.9835	43.0559	104.7731
25	0.1719	-0.0683	-0.0768	0.1447	-0.129	0.3832	0.0518	-0.1266	-0.0442	0.2004	0.1253	-0.2813	-0.0413	0.1848	0.1829	0.292	0.0257	-0.0988	0.2521	-0.0956	0.2515	29.6771	50.3738	96.4772
26	0.0439	-0.0422	0.0289	0.041	-0.0259	0.0383	0.0166	0.221	0.023	0.0125	-0.0045	0.0687	0.0995	0.0064	-0.002	0.372	-0.1548	-0.0088	0.4812	-0.0467	0.3509	-7.1958	41.0345	80.6136
27	0.0107	-0.0085	-0.0095	0.0078	0.0084	0.0088	-0.0766	0.18	0.0015	-0.0416	-0.0325	0.0247	-0.0727	0.0237	-0.0001	0.5072	-0.1812	-0.096	0.5944	0.0157	0.5107	-13.332	49.1304	74.1949
28	0.0218	0.0081	-0.0027	0.0221	-0.0348	0.0396	-0.0719	0.2809	-0.0247	-0.0168	0.1452	0.1865	0.0395	-0.1882	0.0012	0.3206	-0.1115	-0.1177	0.5269	0.0472	0.4747	-19.6103	53.2132	78.2791
29	0.0044	-0.0013	-0.0038	0.0035	-0.0017	0.0052	-0.0182	0.0173	0.036	-0.0037	-0.0462	0.0215	0.0305	-0.0264	-0.0002	0.4028	-0.0006	0.0846	0.2352	0.0142	0.3114	-12.8165	61.1071	104.1573
30	0.0713	0.0475	-0.0069	0.0515	-0.0031	0.0996	-0.041	0.0485	-0.0857	0.2259	0.0293	0.2678	0.0138	-0.0467	0.0007	0.3901	-0.082	0.0524	0.2484	-0.0465	0.3004	-10.1676	48.6707	100.5249

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 22:82)
2	X-RAY DIFFRACTION	2	(chain A and resid 83:121)
3	X-RAY DIFFRACTION	3	(chain A and resid 122:213)
4	X-RAY DIFFRACTION	4	(chain A and resid 214:234)
5	X-RAY DIFFRACTION	5	(chain A and resid 235:381)
6	X-RAY DIFFRACTION	6	(chain B and resid 22:82)
7	X-RAY DIFFRACTION	7	(chain B and resid 83:121)
8	X-RAY DIFFRACTION	8	(chain B and resid 122:213)
9	X-RAY DIFFRACTION	9	(chain B and resid 214:234)
10	X-RAY DIFFRACTION	10	(chain B and resid 235:381)
11	X-RAY DIFFRACTION	11	(chain C and resid 22:82)
12	X-RAY DIFFRACTION	12	(chain C and resid 83:121)
13	X-RAY DIFFRACTION	13	(chain C and resid 122:213)
14	X-RAY DIFFRACTION	14	(chain C and resid 214:234)
15	X-RAY DIFFRACTION	15	(chain C and resid 235:381)
16	X-RAY DIFFRACTION	16	(chain D and resid 22:82)
17	X-RAY DIFFRACTION	17	(chain D and resid 83:121)
18	X-RAY DIFFRACTION	18	(chain D and resid 122:213)
19	X-RAY DIFFRACTION	19	(chain D and resid 214:234)
20	X-RAY DIFFRACTION	20	(chain D and resid 235:381)
21	X-RAY DIFFRACTION	21	(chain E and resid 22:82)
22	X-RAY DIFFRACTION	22	(chain E and resid 83:121)
23	X-RAY DIFFRACTION	23	(chain E and resid 122:213)
24	X-RAY DIFFRACTION	24	(chain E and resid 214:234)
25	X-RAY DIFFRACTION	25	(chain E and resid 235:381)
26	X-RAY DIFFRACTION	26	(chain F and resid 22:82)
27	X-RAY DIFFRACTION	27	(chain F and resid 83:121)
28	X-RAY DIFFRACTION	28	(chain F and resid 122:213)
29	X-RAY DIFFRACTION	29	(chain F and resid 214:234)
30	X-RAY DIFFRACTION	30	(chain F and resid 235:381)

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