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- PDB-4w89: Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1... -

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Basic information

Entry
Database: PDB / ID: 4w89
TitleCrystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from metagenomic library, in complex with cellotriose
ComponentsXyloglucan-specific endo-beta-1,4-glucanase
KeywordsHYDROLASE / glycoside hydrolase / cell wall degrading enzyme / GH5 family
Function / homology
Function and homology information


xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
alpha-cellotriose / Xyloglucan-specific endo-beta-1,4-glucanase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSantos, C.R. / Cordeiro, R.L. / Wong, D.W.S. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/13309-0, 2014/07135-1 Brazil
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 ...citation / entity / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _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
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement 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 / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / refine_hist / struct_asym / struct_conn / struct_conn_type / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: 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: Xyloglucan-specific endo-beta-1,4-glucanase
B: Xyloglucan-specific endo-beta-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2946
Polymers76,2372
Non-polymers1,0574
Water1,67593
1
A: Xyloglucan-specific endo-beta-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6473
Polymers38,1181
Non-polymers5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xyloglucan-specific endo-beta-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6473
Polymers38,1181
Non-polymers5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.704, 96.704, 95.719
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Xyloglucan-specific endo-beta-1,4-glucanase


Mass: 38118.262 Da / Num. of mol.: 2
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: D2K7Z0, xyloglucan-specific endo-beta-1,4-glucanase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.39 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, PEG400, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 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: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 38307 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 47.973 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.191 / Rrim(I) all: 0.211 / Χ2: 0.95 / Net I/σ(I): 10.01 / Num. measured all: 211116
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
2.4-2.550.61933503633261071.42596.4
2.55-2.720.77132791594657781.09497.20.9952.25
2.72-2.940.89231047552454060.797.90.6373.84
2.94-3.220.96227958509849860.42997.80.396.21
3.22-3.60.98324289459445070.24798.10.2249.98
3.6-4.150.99320656404439850.13998.50.12516.34
4.15-5.070.99617389344734220.09499.30.08422.15
5.07-7.130.99614814264626370.09499.70.08523.41
7.130.9998669148914790.03799.30.03341.66

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native structure of XEG5A

Resolution: 2.4→43.2 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.898 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1922 5 %RANDOM
Rwork0.2204 36412 --
obs0.2222 36412 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.08 Å2 / Biso mean: 40.001 Å2 / Biso min: 20.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.64 Å20 Å2
2--0.64 Å2-0 Å2
3----2.07 Å2
Refinement stepCycle: final / Resolution: 2.4→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5374 0 70 93 5537
Biso mean--64.16 35.33 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.025580
X-RAY DIFFRACTIONr_bond_other_d0.0010.025076
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9387614
X-RAY DIFFRACTIONr_angle_other_deg0.678311676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2965676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01625.214280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05115868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8551522
X-RAY DIFFRACTIONr_chiral_restr0.0530.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021314
X-RAY DIFFRACTIONr_mcbond_it1.043.9492710
X-RAY DIFFRACTIONr_mcbond_other1.043.9482709
X-RAY DIFFRACTIONr_mcangle_it1.7295.9193384
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 134 -
Rwork0.286 2655 -
all-2789 -
obs--95.64 %

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