PDB-4fer: Crystal structure of Bacillus Subtilis expansin (EXLX1) in comple...

ID or keywords:

Entry

Database: PDB / ID: 4fer

Title

Crystal structure of Bacillus Subtilis expansin (EXLX1) in complex with cellohexaose

Components

Expansin-yoaJ

Keywords

CELLULOSE-BINDING PROTEIN /

Expansin / bacteria autolysis

Function / homology

Function and homology information

extracellular region
Similarity search - Function

Biological species

Bacillus subtilis subsp. subtilis (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.099 Å

Authors

Georgelis, N. / Yennawar, N.H. / Cosgrove, D.J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for entropy-driven cellulose binding by a type-A cellulose-binding module (CBM) and bacterial expansin.
Authors: Georgelis, N. / Yennawar, N.H. / Cosgrove, D.J.

History

Deposition	May 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 22, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 26, 2012	Group: Database references
Revision 1.2	Jun 24, 2015	Group: Derived calculations
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Feb 28, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fe/4fer ftp://data.pdbj.org/pub/pdb/validation_reports/fe/4fer	HTTPS FTP

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Related structure data

Related structure data	4fftC 4fg2C 4fg4C 2bh0 3d30 C: citing same article (ref.)
Similar structure data	4fg4-d 3oqs-d 4fft-d 4b18-d 1ee4-2 6bw1-d 5ctt-d 3zio-d 6p6a-d 6d7m-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	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Expansin-yoaJ

B: Expansin-yoaJ

hetero molecules

47.9 kDa, 2 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)	58.205, 58.205, 147.277
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein

Expansin-yoaJ / EXLX1

Mass: 23096.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: yoaJ, BSU18630 / Production host:

Escherichia coli (E. coli) / References: UniProt: O34918

#2: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ... / beta-cellohexaose

Type: oligosaccharide

, Oligosaccharide

/ Class: Metabolism

/ Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellohexaose

Descriptor	Type	Program
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}	LINUCS	PDB-CARE

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Non-polymers , 4 types, 240 molecules

#3: Chemical	ChemComp-ACY / ACETIC ACID / Acetic acid Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.12 Å³/Da / Density % sol: 60.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: EXLX1 was concentrated to 30 mg/ml in 25 mM HEPES pH 7.5 in the presence of 5 mM cellohexaose. Precipitant used was 0.1 M sodium acetate pH 4.6, 2 M ammonium sulfate, VAPOR DIFFUSION, ...Details: EXLX1 was concentrated to 30 mg/ml in 25 mM HEPES pH 7.5 in the presence of 5 mM cellohexaose. Precipitant used was 0.1 M sodium acetate pH 4.6, 2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal

Density Matthews: 3.12 Å³/Da / Density % sol: 60.55 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: EXLX1 was concentrated to 30 mg/ml in 25 mM HEPES pH 7.5 in the presence of 5 mM cellohexaose. Precipitant used was 0.1 M sodium acetate pH 4.6, 2 M ammonium sulfate, VAPOR DIFFUSION, ...

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Data collection

Diffraction

Mean temperature: 93 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 28, 2010 / Details: Varimax

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.1→75 Å / Num. all: 32370 / Num. obs: 32507 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

Reflection shell

Resolution (Å)	Diffraction-ID	% possible all
2.31-2.37	1	100
2.26-2.31	1	100
2.22-2.26	1	99.9
2.18-2.22	1	99.4
2.14-2.18	1	98.7
2.1-2.14	1	99.6

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Processing

Software

Name	Version	Classification
CrystalClear		data collection
PHENIX	(phenix.refine: 1.7.3_928)	model building
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.7.3_928	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.099→23.846 Å / SU ML: 0.29 / σ(F): 1.97 / Phase error: 20.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2055	1611	4.96 %
R_work	0.1671	-	-
obs	0.169	32460	99.65 %
all	-	32507	-

Solvent computation

Shrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.43 Å² / k_sol: 0.41 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.4877 Å²	0 Å²	0 Å²
2-	-	2.4877 Å²	-0 Å²
3-	-	-	1.5143 Å²

Refinement step

Cycle: LAST / Resolution: 2.099→23.846 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3233	0	107	232	3572

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3419
X-RAY DIFFRACTION	f_angle_d	1.195	4635
X-RAY DIFFRACTION	f_dihedral_angle_d	26.879	1385
X-RAY DIFFRACTION	f_chiral_restr	0.086	504
X-RAY DIFFRACTION	f_plane_restr	0.004	577

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 (%)
2.0994-2.1744	0.2929	170	0.2032	3068	X-RAY DIFFRACTION	99
2.1744-2.2614	0.2788	143	0.1935	3113	X-RAY DIFFRACTION	100
2.2614-2.3642	0.2552	166	0.1823	3077	X-RAY DIFFRACTION	100
2.3642-2.4887	0.2371	158	0.1856	3087	X-RAY DIFFRACTION	100
2.4887-2.6445	0.2186	153	0.1729	3140	X-RAY DIFFRACTION	100
2.6445-2.8484	0.2372	157	0.1699	3070	X-RAY DIFFRACTION	100
2.8484-3.1344	0.2177	173	0.1644	3106	X-RAY DIFFRACTION	100
3.1344-3.5867	0.1623	162	0.1522	3068	X-RAY DIFFRACTION	100
3.5867-4.5138	0.1776	164	0.149	3064	X-RAY DIFFRACTION	99
4.5138-23.847	0.1923	165	0.1735	3056	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	-0.0031	-0.0276	-0.0064	-0.0185	0.0059	0.0026	0.3676	-0.3695	0.1364	0.6233	0.0712	-0.1054	-0.0574	0.1015	0.0003	0.1376	0.0436	-0.0079	0.1159	-0.0042	0.1927	2.0364	69.0316	16.6606
2	0.0246	0.0143	-0.0053	0.018	0.0112	0.0169	0.0172	-0.1662	0.0953	0.2693	-0.0106	0.3065	-0.1399	-0.1079	-0	0.321	0.0857	0.0407	0.3168	0.0083	0.3048	3.9444	66.6293	31.3125
3	0.0238	-0.0324	0.1916	0.4063	0.2352	0.3776	-0.0592	0.0478	-0.0322	0.0722	0.0373	0.0561	-0.0285	0.0531	0	0.1805	-0.0056	-0.0084	0.1686	0.0456	0.1933	15.3013	57.1207	23.7952
4	0.1283	-0.0186	0.0859	0.1094	-0.1404	0.1552	-0.0799	0.0401	0.1408	0.0707	-0.061	-0.2167	-0.1833	0.0153	-0.2868	0.2245	0.0063	-0.0495	0.1005	0.0367	0.1685	13.8694	68.7204	25.0543
5	0.0337	-0.0052	-0.0507	0.0339	0.0463	0.0974	0.064	0.2288	0.0283	0.2198	0.4439	0.253	0.1579	0.3266	0.1533	0.3043	-0.0066	0.0461	0.1737	0.1645	0.1387	13.0314	53.7214	31.2286
6	0.019	-0.0309	0.054	0.0508	0.0008	-0.0149	0.0689	-0.0382	-0.1532	0.3792	-0.049	-0.011	-0.0919	0.1707	0.0002	0.2131	0.004	0.0018	0.2038	0.0144	0.1689	13.6147	62.1547	30.8236
7	0.0031	0.0679	0.0162	0.0007	-0.0797	0.0593	0.0154	-0.2223	0.2359	0.3023	-0.01	0.0206	-0.6559	-0.2134	-0.0001	0.3735	-0.0223	-0.0198	0.2147	0.0316	0.2076	17.1735	69.7586	36.2803
8	-0.0021	0.0182	-0.039	-0.0055	-0.0195	-0.0082	-0.043	0.1349	-0.2195	-0.0501	0.0392	0.1355	-0.5352	-0.0985	-0.0002	0.2665	-0.0004	-0.0156	0.1873	0.0255	0.1963	7.4653	68.3803	22.0491
9	0.1017	0.066	0.2617	0.2577	-0.0705	0.2626	0.083	0.0716	0.0087	-0.2903	-0.0434	0.0767	0.0054	0.0791	0.0001	0.1928	0.0084	-0.0149	0.1456	0.0243	0.1748	13.3281	51.3573	8.7892
10	0.0508	0.0558	-0.0194	0.0721	-0.0182	0.0349	0.2685	0.1527	-0.0126	-0.1245	0.3854	0.051	0.0713	-0.1358	0.1156	0.606	0.0135	-0.8081	0.5463	-0.4955	-0.4421	1.4991	43.7226	-1.9694
11	0.5543	-0.1127	-0.2208	0.1375	-0.1348	0.1162	-0.0755	-0.1888	-0.2859	-0.089	0.0789	0.2103	-0.0433	-0.0929	0.0267	0.1955	-0.0246	-0.0303	0.124	0.0206	0.2726	8.5	44.3149	11.6345
12	0.365	0.2807	-0.0297	0.3051	-0.153	0.1794	-0.0049	0.1319	0.308	-0.5976	0.2257	0.2623	0.3988	-0.5526	0.1014	0.28	0.0011	-0.1221	0.1784	-0.0169	0.1247	5.6274	54.2745	3.9986
13	0.0221	0.0044	-0.0756	0.0147	0.0207	0.051	-0.2474	0.061	0.0557	-0.0103	-0.0678	0.1373	0.815	0.3334	-0.1231	0.6252	0.1245	-0.0038	0.3054	0.0189	0.2052	13.4724	48.6147	-1.1557
14	0.0565	0.0412	-0.0202	0.0107	-0.0257	0.0268	0.5937	0.1176	-0.3208	-0.1688	-0.4138	0.115	-0.3032	0.2718	-0.0034	0.4521	0.1371	-0.0942	0.2622	0.0119	0.2826	22.0011	37.2844	5.292
15	0.2233	0.1633	0.0802	0.119	-0.0246	0.097	0.1482	0.3139	0.112	-0.2399	-0.1352	-0.0828	-0.0177	0.0307	0.0063	0.2419	0.0577	0.0239	0.2015	0.0377	0.1731	15.3679	57.3624	4.4446
16	7.486	6.2612	-2.2311	7.5735	1.8555	6.4978	-0.466	-1.3127	-1.3492	1.4549	-0.3843	-1.426	1.5502	1.6696	0.2504	0.3326	0.1005	-0.0781	0.3347	0.0144	0.2573	-1.1965	-2.5663	15.3232
17	6.656	-1.8769	3.01	4.4146	-4.0043	3.961	-0.2515	-0.2469	0.4785	-0.5263	-0.0561	0.1157	-0.1072	-0.689	0.1939	0.2006	0.0728	-0.0281	0.2369	0.0039	0.3314	-1.8991	0.7906	1.5546
18	2.3641	1.0681	0.4396	1.9454	0.6598	2.2818	-0.0554	0.1296	0.1295	-0.0456	-0.0411	0.002	-0.0301	0.1112	0.1057	0.1954	0.0412	-0.0072	0.1579	0.0507	0.1755	10.994	10.0233	1.9409
19	4.9797	1.2295	0.8924	4.3963	1.5958	3.7913	-0.1417	0.0446	-0.2072	-0.0853	0.1238	-0.1099	0.3339	-0.0623	-0.0062	0.1624	0.0387	0.0562	0.0933	0.0364	0.078	8.249	2.3269	0.6731
20	7.0867	0.4925	-1.8981	4.1819	-1.0169	3.9383	-0.0849	0.392	0.3345	-0.3232	0.1229	0.1608	0.208	-0.2785	-0.0264	0.2047	-0.0057	-0.0193	0.1667	0.0444	0.1248	6.0662	3.9996	-3.7796
21	8.5589	-1.5937	-4.3795	5.702	1.0666	9.0134	-0.2313	1.0091	-0.7458	-1.0477	-0.124	0.2171	0.2985	-0.9558	0.1957	0.3537	-0.075	0.0452	0.2366	-0.0006	0.1763	5.7664	-3.3764	-9.215
22	3.7219	2.8243	5.7743	5.1528	3.3181	9.3074	0.5524	-0.0307	-0.0807	0.1116	-0.4223	-0.0901	0.9888	0.0623	-0.3396	0.2401	0.0152	0.0213	0.1585	0.0324	0.1489	5.2519	-0.9464	8.1426
23	3.8851	2.6905	0.163	8.418	0.3314	1.8579	-0.0607	-0.0067	-0.0683	-0.2389	-0.0038	-0.5852	0.0596	0.21	0.0681	0.1664	0.0252	-0.0048	0.1663	0.0187	0.1771	21.1021	13.7465	13.4934
24	9.3152	-5.7641	-5.5773	4.2065	2.093	6.0942	-0.2056	-1.0181	0.3295	1.1274	0.4973	-1.1243	-0.5597	0.2704	-0.1783	0.482	0.0491	-0.1187	0.1238	0.0013	0.3391	18.4293	32.5366	17.8821
25	2.5254	0.2505	-1.1185	4.2152	2.3987	2.6619	-0.1975	-0.0703	-0.0811	0.457	0.028	-0.1322	0.1418	0.0791	0.1552	0.1949	0.0239	-0.0289	0.1388	0.0493	0.1597	13.8941	13.773	16.3812
26	7.827	3.54	3.0235	3.6622	5.0423	7.7436	-0.3617	-1.0133	0.8328	0.8408	0.2069	0.3641	-1.5867	0.1655	0.0993	0.7838	-0.0739	0.0228	0.4695	-0.1325	0.1615	12.6362	24.3539	30.7922
27	4.4014	0.3331	0.1957	4.8162	0.7601	3.0858	0.0129	-0.2685	0.4898	0.5056	-0.0553	-0.1028	0.0774	0.0203	-0.0121	0.2721	0.0418	-0.0233	0.1432	-0.0046	0.2985	13.317	23.485	17.6974
28	5.5991	1.7294	0.7546	3.7009	-0.2403	3.8414	0.0884	-0.4673	0.3015	0.7185	-0.092	0.0804	0.152	-0.179	0.0057	0.2794	0.0339	0.0138	0.2097	-0.0184	0.16	15.0518	13.6291	23.2037
29	1.4341	-2.8825	-1.8491	8.7079	0.2519	6.6724	0.7327	0.0446	0.3428	0.0542	-0.1361	-0.927	-0.6909	0.7246	-0.446	0.4113	-0.06	-0.2983	-0.1217	0.2766	0.7982	26.4056	30.3084	13.3603
30	7.5129	3.7634	-3.3077	6.4296	-4.0497	6.654	0.0173	-0.4071	-0.3548	0.1749	0.0141	-0.077	0.2015	0.2116	-0.0978	0.1958	0.0528	-0.0695	0.1302	0.0117	0.193	21.5624	10.9972	18.552

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:5)
2	X-RAY DIFFRACTION	2	(chain A and resid 6:10)
3	X-RAY DIFFRACTION	3	(chain A and resid 11:54)
4	X-RAY DIFFRACTION	4	(chain A and resid 55:70)
5	X-RAY DIFFRACTION	5	(chain A and resid 71:75)
6	X-RAY DIFFRACTION	6	(chain A and resid 76:87)
7	X-RAY DIFFRACTION	7	(chain A and resid 88:101)
8	X-RAY DIFFRACTION	8	(chain A and resid 102:107)
9	X-RAY DIFFRACTION	9	(chain A and resid 108:143)
10	X-RAY DIFFRACTION	10	(chain A and resid 144:149)
11	X-RAY DIFFRACTION	11	(chain A and resid 150:166)
12	X-RAY DIFFRACTION	12	(chain A and resid 167:182)
13	X-RAY DIFFRACTION	13	(chain A and resid 183:189)
14	X-RAY DIFFRACTION	14	(chain A and resid 190:196)
15	X-RAY DIFFRACTION	15	(chain A and resid 197:208)
16	X-RAY DIFFRACTION	16	(chain B and resid 2:5)
17	X-RAY DIFFRACTION	17	(chain B and resid 6:10)
18	X-RAY DIFFRACTION	18	(chain B and resid 11:54)
19	X-RAY DIFFRACTION	19	(chain B and resid 55:75)
20	X-RAY DIFFRACTION	20	(chain B and resid 76:88)
21	X-RAY DIFFRACTION	21	(chain B and resid 89:101)
22	X-RAY DIFFRACTION	22	(chain B and resid 102:107)
23	X-RAY DIFFRACTION	23	(chain B and resid 108:122)
24	X-RAY DIFFRACTION	24	(chain B and resid 123:126)
25	X-RAY DIFFRACTION	25	(chain B and resid 127:143)
26	X-RAY DIFFRACTION	26	(chain B and resid 144:149)
27	X-RAY DIFFRACTION	27	(chain B and resid 150:171)
28	X-RAY DIFFRACTION	28	(chain B and resid 172:189)
29	X-RAY DIFFRACTION	29	(chain B and resid 190:196)
30	X-RAY DIFFRACTION	30	(chain B and resid 197:208)

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