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

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Basic information

Entry
Database: PDB / ID: 4fft
TitleCrystal structure of Bacillus Subtilis expansin (EXLX1) in complex with mixed-linkage glucan
ComponentsExpansin-yoaJ
KeywordsCELLULOSE-BINDING PROTEIN / Cellulose
Function / homology
Function and homology information


extracellular region
Similarity search - Function
: / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Immunoglobulin-like / Beta Barrel ...: / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Expansin-YoaJ
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGeorgelis, N. / Yennawar, N.H. / Cosgrove, D.J.
CitationJournal: 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
DepositionJun 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Jun 24, 2015Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Expansin-yoaJ
B: Expansin-yoaJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8448
Polymers46,1932
Non-polymers1,6516
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.562, 56.562, 146.104
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#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-(1-3)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1315.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-3DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-3DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,8,7/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1/a4-b1_b3-c1_c4-d1_d4-e1_e4-f1_f3-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 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 Mixed-linkage glucan. Precipitant 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 Mixed-linkage glucan. Precipitant was 0.1 M sodium acetate pH 4.6, 2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 27, 2011
RadiationMonochromator: Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→75 Å / Num. all: 30482 / Num. obs: 30482 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.1-2.14197.5
2.31-2.37199.9
2.26-2.311100
2.22-2.26199.9
2.18-2.22199.9
2.14-2.18199.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.281 Å / SU ML: 0.32 / σ(F): 1.96 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 1535 5.05 %
Rwork0.1821 --
obs0.1846 30421 99.7 %
all-30482 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.029 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1706 Å20 Å2-0 Å2
2--2.1706 Å20 Å2
3----2.4692 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 110 221 3564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083433
X-RAY DIFFRACTIONf_angle_d1.2174659
X-RAY DIFFRACTIONf_dihedral_angle_d21.4351310
X-RAY DIFFRACTIONf_chiral_restr0.085515
X-RAY DIFFRACTIONf_plane_restr0.005581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.17520.32231440.24512933X-RAY DIFFRACTION99
2.1752-2.26220.28241750.22312858X-RAY DIFFRACTION100
2.2622-2.36510.28441410.23252845X-RAY DIFFRACTION100
2.3651-2.48980.30661510.23242921X-RAY DIFFRACTION100
2.4898-2.64560.27231690.21192882X-RAY DIFFRACTION100
2.6456-2.84970.25681370.19492882X-RAY DIFFRACTION100
2.8497-3.13620.27281570.1932941X-RAY DIFFRACTION100
3.1362-3.58920.23671400.1782860X-RAY DIFFRACTION100
3.5892-4.51910.16751610.1442867X-RAY DIFFRACTION100
4.5191-28.28360.19351600.16512897X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.0085-0.0036-0.00380.0007-0.00020.02420.00470.06160.0029-0.01490.00590.01220.0035-0.0217-0.0062-0.04690.30990.13640.37360.03440.2813-28.7566-50.3635-25.8546
20.0227-0.00020.00650.04950.02330.02430.03310.16850.0460.05670.01790.0816-0.0631-0.00920.03240.20540.10960.07930.3340.03460.2394-13.6301-56.0893-27.4272
30.00510.00090.00060.0079-0.0060.031-0.03280.05740.0291-0.0084-0.07690.0493-0.0437-0.0423-0.04840.01930.14880.13750.43650.00940.1941-19.0102-56.7073-32.1443
40.00090-0.00160.00230.00050.00230.0559-0.00650.0103-0.00020.02080.01190.001-0.008300.230.09690.0280.342-0.03170.3066-18.3308-65.6455-34.2547
50.0231-0.01020.01410.0071-0.0060.00780.0360.0792-0.00070.07940.06460.0878-0.0606-0.0730.020.16180.12150.07720.5729-0.03420.2876-23.8471-59.7199-35.1519
60.0125-0.02620.03540.0494-0.06750.07540.12630.04-0.05590.00860.0290.01630.07360.01110.01560.25530.05760.11290.24370.05790.276-5.8895-52.71-11.4701
70.0216-0.01160.00570.0253-0.01170.0048-0.00910.04990.04750.07930.0183-0.0564-0.1303-0.049200.33290.07950.09990.25970.01750.2873-9.1535-43.6675-11.748
80.01520.0132-0.01560.0088-0.01190.0101-0.0489-0.01710.0730.04210.0275-0.012-0.0537-0.0404-0.00250.3270.26080.14720.2495-0.00760.2116-14.0975-47.0596-6.1375
90.0015-0.0008-0.0010.00160.0010.00390.0285-0.0037-0.01150.00440.0422-0.00520.0362-0.002600.3648-0.06220.08440.5578-0.0180.43476.0021-49.6934-5.3459
100.00230.005-0.00410.0141-0.00270.00420.0618-0.0178-0.02230.0540.0931-0.0708-0.0003-0.048200.3050.08540.07390.30640.08370.327-11.4067-56.1102-8.078
119.1965-0.4558-1.98414.3117-6.5492.0001-0.01320.42290.4011-0.3036-0.116-0.2211-0.2377-0.1760.08710.37260.12620.04120.0870.04020.352728.0237-12.9822-10.7496
122.58910.62783.4190.15310.83114.53620.5059-0.0872-0.55190.4725-0.0798-0.45320.8189-0.1961-0.38630.44530.06220.00540.220.08080.365827.6049-34.0795-1.6232
135.0773-0.55944.83342.73380.25997.3226-0.16050.30370.1660.0566-0.01020.1568-0.0572-0.01050.16530.22910.07250.09760.24920.07890.283623.1666-24.8333-9.7665
142.60630.97632.77987.02683.50933.87620.0174-0.22470.03210.3671-0.049-0.1001-0.1047-0.15850.01370.36190.08760.06860.1730.07210.219228.7031-23.2494-2.7279
155.5341-2.4513.24047.9733-2.55735.2623-0.1532-0.46290.08071.02720.130.0355-0.4876-0.12380.05260.44640.11140.10280.17280.08020.289131.2766-20.26932.8113
164.0042-1.9527-1.91167.14127.9158.79090.09430.1970.1093-0.60980.462-1.0202-0.30.6024-0.50470.24550.06450.13280.33880.11130.331733.9577-28.9788-17.0141
175.29081.9811-0.36256.14090.28161.5942-0.2110.6043-0.51140.26580.17150.0490.1894-0.13330.03310.23270.04530.13810.3274-0.00630.318520.1326-39.0127-18.5434
182.9569-1.1886-3.99318.28254.38896.3862-0.09090.42240.1395-0.31370.00210.6598-0.1906-1.04130.09020.17810.07610.04020.43810.04690.326914.0375-34.3854-27.5388
192.66020.0309-0.21655.74391.36271.99810.00380.4618-0.2577-0.1682-0.14770.3217-0.0382-0.4150.13460.18270.09880.03520.39510.02390.252419.3861-36.464-24.7871
205.3952-2.4166-1.32374.94251.41865.0413-0.45020.3176-0.7372-0.05330.0237-0.27110.5968-0.25930.33390.17040.12230.10830.325-0.01170.162924.0569-43.2366-20.7982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:8)
2X-RAY DIFFRACTION2(chain A and resid 9:57)
3X-RAY DIFFRACTION3(chain A and resid 58:81)
4X-RAY DIFFRACTION4(chain A and resid 82:90)
5X-RAY DIFFRACTION5(chain A and resid 91:107)
6X-RAY DIFFRACTION6(chain A and resid 108:133)
7X-RAY DIFFRACTION7(chain A and resid 134:166)
8X-RAY DIFFRACTION8(chain A and resid 167:187)
9X-RAY DIFFRACTION9(chain A and resid 188:195)
10X-RAY DIFFRACTION10(chain A and resid 196:208)
11X-RAY DIFFRACTION11(chain B and resid 2:10)
12X-RAY DIFFRACTION12(chain B and resid 11:32)
13X-RAY DIFFRACTION13(chain B and resid 33:57)
14X-RAY DIFFRACTION14(chain B and resid 58:77)
15X-RAY DIFFRACTION15(chain B and resid 78:103)
16X-RAY DIFFRACTION16(chain B and resid 104:114)
17X-RAY DIFFRACTION17(chain B and resid 115:139)
18X-RAY DIFFRACTION18(chain B and resid 140:155)
19X-RAY DIFFRACTION19(chain B and resid 156:189)
20X-RAY DIFFRACTION20(chain B and resid 190:208)

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