PDB-4fg2: Crystal structure of Bacillus Subtilis expansin (EXLX1) in comple...

ID or keywords:

Entry

Database: PDB / ID: 4fg2

Title

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

Components

Expansin-yoaJ

Keywords

CELLULOSE-BINDING PROTEIN /

Cellulose

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	Jun 2, 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.pdbx_synonyms / _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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PDBx/mmCIF format	4fg2.cif.gz	179.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4fg2.ent.gz	144.6 KB	Display	PDB format
PDBx/mmJSON format	4fg2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fg/4fg2 ftp://data.pdbj.org/pub/pdb/validation_reports/fg/4fg2	HTTPS FTP

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Related structure data

Related structure data	4ferC 4fftC 4fg4C 2bh0 3d30 C: citing same article (ref.)
Similar structure data	4fft-d 4fg4-d 3fex-3 3v71-d 4fer-d 5y7m-2 1q1t-d 3oqs-d 1un0-1 5j2z-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 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)	57.192, 57.192, 146.330
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#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-glucopyranose / beta-cellotetraose

Type: oligosaccharide

, Oligosaccharide

/ Class: Metabolism

/ Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose

Descriptor	Type	Program
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-ACY / ACETIC ACID /

Acetic acid

Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.99 Å³/Da / Density % sol: 58.88 %
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 80 mM cellotetraose. Precipitant was 0.1 M sodium acetate pH 4.6 and 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 80 mM cellotetraose. Precipitant was 0.1 M sodium acetate pH 4.6 and 2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal

Density Matthews: 2.99 Å³/Da / Density % sol: 58.88 %

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 80 mM cellotetraose. Precipitant was 0.1 M sodium acetate pH 4.6 and 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: Apr 29, 2011

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: 30220 / Num. obs: 30220 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

Reflection shell

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

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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→28.065 Å / SU ML: 0.38 / σ(F): 1.96 / Phase error: 27.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2608	1517	5.06 %
R_work	0.2072	-	-
obs	0.2099	29993	95.97 %
all	-	30220	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 47.491 Å² / k_sol: 0.414 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.8087 Å²	0 Å²	0 Å²
2-	-	8.8087 Å²	-0 Å²
3-	-	-	2.6749 Å²

Refinement step

Cycle: LAST / Resolution: 2.099→28.065 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3234	0	53	185	3472

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3370
X-RAY DIFFRACTION	f_angle_d	1.087	4567
X-RAY DIFFRACTION	f_dihedral_angle_d	22.587	1330
X-RAY DIFFRACTION	f_chiral_restr	0.077	494
X-RAY DIFFRACTION	f_plane_restr	0.005	578

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	0.3031	138	0.2653	2926	X-RAY DIFFRACTION	99
2.1744-2.2614	0.3237	182	0.2534	2961	X-RAY DIFFRACTION	100
2.2614-2.3643	0.3723	168	0.2736	2933	X-RAY DIFFRACTION	99
2.3643-2.4889	0.4045	160	0.2918	2964	X-RAY DIFFRACTION	99
2.4889-2.6447	0.3558	135	0.2583	2882	X-RAY DIFFRACTION	99
2.6447-2.8487	0.3159	143	0.2283	3011	X-RAY DIFFRACTION	99
2.8487-3.135	0.2345	148	0.2063	2912	X-RAY DIFFRACTION	99
3.135-3.5879	0.226	162	0.1794	2853	X-RAY DIFFRACTION	96
3.5879-4.5173	0.244	134	0.1775	2281	X-RAY DIFFRACTION	77
4.5173-28.0676	0.2115	147	0.187	2753	X-RAY DIFFRACTION	93

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	0.0022	0.0002	-0.0054	0.0041	0.005	0.026	0.0051	-0.0278	0.0064	0.0098	0.0167	-0.0039	0.0065	0.0088	-0.0037	0.2095	0.1736	0.0356	0.3088	-0.1165	0.2991	-1.2141	-34.3392	24.0947
2	0.0153	-0.0177	-0.0132	0.0217	0.0154	0.0111	-0.019	-0.0005	-0.0095	0.0057	-0.0151	-0.0197	0.0122	0.0153	-0.0116	0.346	0.2255	0.0207	0.3856	-0.053	0.2905	-11.6893	-29.8012	38.6684
3	0.0091	-0.0078	-0.0214	0.0194	0.0081	0.0442	-0.0959	0.0026	-0.0674	0.0562	0.0592	-0.0247	0.0244	-0.0043	-0.0722	0.0962	0.2131	0.0762	0.4376	-0.2903	0.1752	-13.5647	-24.0255	26.1913
4	0.0382	-0.0145	0.0003	0.0068	-0.0009	0.0006	-0.0425	-0.0083	-0.0062	0.0224	0.0085	-0.0004	0.0223	0.0021	-0.0139	0.2447	0.1441	0.0722	0.3438	-0.1223	0.239	-13.661	-29.0469	31.4152
5	0.0208	-0.0038	-0.025	0.0265	-0.0346	0.0854	-0.0717	-0.044	0.002	0.068	0.0284	-0.0209	0.04	0.0725	-0.0452	0.2271	0.1728	0.0734	0.4842	-0.1505	0.2311	-13.451	-28.5492	34.8528
6	0.0011	-0	0.0013	0.0004	0.0003	0.002	-0.0045	-0.0005	-0.0006	0.0245	0.0018	-0	0.0137	-0.0032	-0	0.3731	0.0885	0.1234	0.3956	0.0003	0.4419	-19.3623	-37.8745	36.6961
7	0.023	-0.0197	0.0094	0.019	-0.0125	0.0058	-0.0937	0.0274	-0.0927	0.0937	0.132	-0.0055	0.0479	0.0713	0.0872	0.2194	0.1724	0.033	0.3777	-0.1543	0.2332	-12.1307	-32.9729	27.8292
8	0.0271	-0.0099	0.008	0.0027	-0.0037	0.005	-0.0603	-0.0439	-0.0161	-0.0469	-0.0289	0.0042	-0.0033	-0.0649	-0.1264	0.1091	0.0444	0.0379	0.406	-0.215	0.3095	-12.4016	-15.0829	12.9187
9	0.0497	0.0544	0.0409	0.0684	0.0449	0.0488	-0.0899	0.0888	0.1138	-0.0188	0.0219	-0.03	-0.0472	0.0523	-0.0429	0.1537	-0.0031	-0.006	0.4225	-0.1499	0.3066	-5.0955	-10.6091	10.6273
10	0.0116	0.0069	0.0024	0.0059	-0.002	0.0074	-0.0019	-0.01	-0.0099	0.0005	-0.0115	-0.0127	-0.0039	0.0215	0.0018	0.1167	-0.0085	-0.0055	0.3655	-0.1038	0.2386	-6.7653	-14.3779	2.4374
11	0.007	-0.0001	-0.0248	0.006	0.0058	0.0799	0.0458	0.013	0.0283	-0.0174	0.0106	-0.0014	-0.106	0.0259	-0.0181	0.1699	0.0357	0.0756	0.4318	-0.1483	0.2619	-9.4724	-16.4882	7.4833
12	0.0428	0.0063	-0.0248	0.0015	-0.0015	0.0184	-0.021	0.04	0.0103	-0.0065	-0.0228	0.0499	-0.0034	-0.024	-0.0122	0.137	0.0324	-0.0237	0.4031	-0.208	0.2958	-15.0105	-22.0386	8.3
13	5.6168	-1.0864	-5.9912	6.5566	-1.1185	7.2075	-0.4736	-3.0629	1.4761	1.3544	0.8307	-0.0415	-0.6976	0.5887	-0.3723	0.341	0.1177	0.0106	0.8544	-0.2657	0.551	1.8959	36.1544	17.2612
14	7.7475	6.358	6.9029	5.2179	5.6652	6.1504	-0.2991	0.3239	-0.0809	-0.3575	0.5235	-0.6203	-0.4584	0.6333	-0.2215	0.2078	-0.0185	0.0761	0.5867	-0.2595	0.514	1.6628	31.6307	1.5753
15	1.9118	0.0992	0.2872	3.095	-0.6512	2.033	-0.1977	0.211	-0.1373	-0.085	0.3175	0.2042	0.1108	-0.0658	-0.1381	0.1598	0.0268	-0.0457	0.5328	-0.1691	0.3127	-10.1847	23.6128	6.4016
16	3.5379	0.3626	0.2071	2.2087	-0.7271	0.6331	-0.2654	0.3999	0.1618	-0.209	0.2721	-0.2343	-0.0289	0.2174	-0.0594	0.195	-0.0702	-0.0182	0.6548	-0.2126	0.312	-6.6997	30.0715	2.9136
17	5.0321	2.021	1.7001	2.2078	1.2161	3.3437	-0.2759	-0.0504	0.0736	-0.2592	0.307	0.1607	-0.0731	0.0538	-0.0457	0.2096	-0.0957	-0.0294	0.6102	-0.188	0.3015	-7.0589	31.0822	-0.819
18	8.2068	3.5508	4.5061	2.9915	1.8939	2.4761	-0.5235	2.2075	-0.0925	-0.7716	0.8286	-0.6271	-0.3859	1.4615	-0.3089	0.3708	-0.2378	-0.0587	0.9455	-0.0766	0.4736	-6.4631	36.939	-8.9329
19	8.0027	2.3314	-0.486	1.4467	-1.9352	7.3795	0.1871	-0.1297	0.0651	-0.0499	0.1011	-0.0715	-0.1596	0.84	-0.26	0.1352	0.0154	-0.0807	0.3776	-0.1859	0.3727	-2.4911	34.0379	5.5022
20	0.7649	-0.5721	-0.7546	0.9694	0.3615	0.8242	-0.0411	0.1536	-0.0987	-0.0158	-0.1414	0.2815	0.1784	-0.0144	0.182	0.2405	0.1144	0.0127	0.4863	-0.2079	0.4286	-19.6921	20.8822	17.5145
21	4.7273	-6.164	4.1974	2.0002	-9.4859	2	-0.1413	-0.8368	-0.3447	2.0055	1.366	-0.0125	-1.4979	-0.5133	-1.222	0.6374	0.1899	-0.0939	0.3723	-0.1071	0.6319	-18.2989	0.9537	22.1639
22	1.8246	-0.9343	-0.4192	4.7134	1.3265	1.9954	-0.2064	0.0129	-0.3628	0.5364	0.1019	0.1113	0.3821	0.2764	0.079	0.2825	0.1441	-0.0066	0.4217	-0.1615	0.372	-11.7144	13.1624	22.3852
23	6.3087	5.7512	-0.4467	9.5317	0.689	1.9652	0.0102	-0.4929	0.0958	0.8083	-0.1329	0.3171	0.142	0.059	0.1144	0.2759	0.1735	-0.0106	0.4771	-0.1193	0.2701	-15.4471	16.3591	26.5016
24	7.3238	-1.5382	-2.0088	6.8046	3.6027	6.4673	-0.032	-0.091	0.3387	0.5105	-0.18	0.6496	0.3495	-0.255	0.2862	0.1411	0.1057	0.0524	0.2802	-0.0564	0.1658	-20.9838	19.0154	20.7244

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:7)
2	X-RAY DIFFRACTION	2	(chain A and resid 8:14)
3	X-RAY DIFFRACTION	3	(chain A and resid 15:59)
4	X-RAY DIFFRACTION	4	(chain A and resid 60:75)
5	X-RAY DIFFRACTION	5	(chain A and resid 76:88)
6	X-RAY DIFFRACTION	6	(chain A and resid 89:93)
7	X-RAY DIFFRACTION	7	(chain A and resid 94:114)
8	X-RAY DIFFRACTION	8	(chain A and resid 115:140)
9	X-RAY DIFFRACTION	9	(chain A and resid 141:167)
10	X-RAY DIFFRACTION	10	(chain A and resid 168:173)
11	X-RAY DIFFRACTION	11	(chain A and resid 174:195)
12	X-RAY DIFFRACTION	12	(chain A and resid 196:208)
13	X-RAY DIFFRACTION	13	(chain B and resid 2:6)
14	X-RAY DIFFRACTION	14	(chain B and resid 7:12)
15	X-RAY DIFFRACTION	15	(chain B and resid 13:57)
16	X-RAY DIFFRACTION	16	(chain B and resid 58:76)
17	X-RAY DIFFRACTION	17	(chain B and resid 77:90)
18	X-RAY DIFFRACTION	18	(chain B and resid 91:96)
19	X-RAY DIFFRACTION	19	(chain B and resid 97:107)
20	X-RAY DIFFRACTION	20	(chain B and resid 108:120)
21	X-RAY DIFFRACTION	21	(chain B and resid 121:125)
22	X-RAY DIFFRACTION	22	(chain B and resid 126:169)
23	X-RAY DIFFRACTION	23	(chain B and resid 170:193)
24	X-RAY DIFFRACTION	24	(chain B and resid 194:208)

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