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- PDB-4w8a: Crystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4-gl... -

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Basic information

Entry
Database: PDB / ID: 4w8a
TitleCrystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library, in the native form
ComponentsExo-xyloglucanase
KeywordsHYDROLASE / glycoside hydrolase / celll wall degrading enzyme / GH5 family
Function / homology
Function and homology information


beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.72 Å
AuthorsSantos, C.R. / Cordeiro, R.L. / Wong, D.W.S. / Murakami, M.T.
CitationJournal: Biochemistry / Year: 2015
Title: Structural Basis for Xyloglucan Specificity and alpha-d-Xylp(1 6)-d-Glcp Recognition at the -1 Subsite within the GH5 Family.
Authors: Dos Santos, C.R. / Cordeiro, R.L. / Wong, D.W. / Murakami, M.T.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exo-xyloglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3428
Polymers42,6821
Non-polymers6617
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.951, 120.951, 59.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Exo-xyloglucanase


Mass: 42681.840 Da / Num. of mol.: 1 / Fragment: unp residues 139-516
Source method: isolated from a genetically manipulated source
Details: cow's rumen
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: D2XML9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 57.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: ammonium sulfate, sodium citrate, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 50907 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 17.562 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.046 / Χ2: 0.921 / Net I/σ(I): 45.99 / Num. measured all: 538560
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allRmerge(I) obsMean I/σ(I) obs
1.72-1.820.98861266843970800.17283.9
1.82-1.950.99686638796278720.12698.90.1222.85
1.95-2.10.99882902737772980.08698.90.08232.38
2.1-2.310.99977181680667670.06399.40.0642.86
2.31-2.580.99967723617061440.05199.60.04949.23
2.58-2.970.99956824544854380.0499.80.03859
2.97-3.64146139464246390.02899.90.02677.45
3.64-5.12137649360536050.0211000.0297.17
5.12122238207120640.01699.70.01696.91

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.72→42.28 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.525 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1488 2651 5.1 %RANDOM
Rwork0.1054 49509 --
obs0.1075 49509 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.44 Å2 / Biso mean: 11.214 Å2 / Biso min: 4.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.26 Å2-0 Å2
2--0.26 Å2-0 Å2
3----0.86 Å2
Refinement stepCycle: final / Resolution: 1.72→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 38 493 3543
Biso mean--25.99 23.13 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193121
X-RAY DIFFRACTIONr_bond_other_d0.0010.022768
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9164248
X-RAY DIFFRACTIONr_angle_other_deg0.94336351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29625.127158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73515463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.117159
X-RAY DIFFRACTIONr_chiral_restr0.1320.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02774
X-RAY DIFFRACTIONr_mcbond_it1.7090.8631543
X-RAY DIFFRACTIONr_mcbond_other1.7090.8631542
X-RAY DIFFRACTIONr_mcangle_it1.9251.3021927
X-RAY DIFFRACTIONr_rigid_bond_restr4.81335889
X-RAY DIFFRACTIONr_sphericity_free23.954599
X-RAY DIFFRACTIONr_sphericity_bonded7.92756212
LS refinement shellResolution: 1.72→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 147 -
Rwork0.124 2703 -
all-2850 -
obs--70.77 %

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