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- PDB-4fg4: Crystal structure of Bacillus Subtilis expansin (EXLX1) in comple... -

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Basic information

Entry
Database: PDB / ID: 4fg4
TitleCrystal structure of Bacillus Subtilis expansin (EXLX1) in complex with hemithiocellodextrin
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
hemithiocellodextrin / Expansin-YoaJ
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.701 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 3, 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 / 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_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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _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)47,0703
Polymers46,1932
Non-polymers8771
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.039, 58.039, 146.801
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)-4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta- ...beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-1-thio-beta-D-glucopyranose / hemithiocellodextrin


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 876.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: hemithiocellodextrin
DescriptorTypeProgram
WURCS=2.0/2,5,4/[a2122h-1b_1-5_1*S][a2122h-1b_1-5]/1-2-2-2-2/a4-b1_b4-c1*S*_c4-d1_d4-e1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Glcp1SH]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.09 Å3/Da / Density % sol: 60.2 %
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 hemithiocellodextrin. 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 hemithiocellodextrin. 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 11, 2012
RadiationMonochromator: Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 14815 / Num. obs: 14815 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.7-2.75198.7
2.97-3.04199
2.91-2.97199
2.85-2.91199.4
2.8-2.85198.9
2.75-2.8198.8

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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: 2.701→23.777 Å / SU ML: 0.47 / σ(F): 1.98 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 748 5.05 %random
Rwork0.1878 ---
obs0.191 14805 97.57 %-
all-14815 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.4796 Å20 Å20 Å2
2--11.4796 Å2-0 Å2
3---9.7385 Å2
Refinement stepCycle: LAST / Resolution: 2.701→23.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 56 127 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093376
X-RAY DIFFRACTIONf_angle_d1.1954579
X-RAY DIFFRACTIONf_dihedral_angle_d14.6651230
X-RAY DIFFRACTIONf_chiral_restr0.077499
X-RAY DIFFRACTIONf_plane_restr0.005576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7011-2.90930.40691640.28552883X-RAY DIFFRACTION99
2.9093-3.20150.28091640.21422814X-RAY DIFFRACTION99
3.2015-3.66330.24871490.1782865X-RAY DIFFRACTION99
3.6633-4.60990.19451440.15792781X-RAY DIFFRACTION98
4.6099-23.77750.23761270.17582714X-RAY DIFFRACTION94

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