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- PDB-4w87: Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1... -

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Basic information

Entry
Database: PDB / ID: 4w87
TitleCrystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from metagenomic library, in complex with a xyloglucan oligosaccharide
ComponentsXyloglucan-specific endo-beta-1,4-glucanase
KeywordsHYDROLASE / glycoside hydrolase / cell wall degrading enzyme / GH5
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
Xyloglucan-specific endo-beta-1,4-glucanase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _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 / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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.name / _chem_comp.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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)77,5586
Polymers76,2372
Non-polymers1,3224
Water5,134285
1
A: Xyloglucan-specific endo-beta-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7793
Polymers38,1181
Non-polymers6612
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)38,7793
Polymers38,1181
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.504, 96.504, 95.857
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 / Fragment: unp residues 92-430
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 alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 636.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}}}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.: 285 / 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: 3.38 Å3/Da / Density % sol: 63.66 %
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: 2.15→50 Å / Num. obs: 53072 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 36.459 Å2 / Rmerge F obs: 0.992 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.223 / Χ2: 0.88 / Net I/σ(I): 7.72 / Num. measured all: 285791
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
2.15-2.280.51444681877684331.3596.1
2.28-2.440.69343225829780550.98597.10.8912.03
2.44-2.630.79639890765374270.757970.6842.79
2.63-2.880.90436202706368610.50197.10.4534.25
2.88-3.220.9733443642662900.2997.90.2637.2
3.22-3.720.9928741563855520.1598.50.13611.91
3.72-4.540.99625590475947220.08999.20.08118.34
4.54-6.40.99621815368936770.08499.70.07720.73
6.40.99712204206220550.06699.70.06127.95

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Processing

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

Resolution: 2.15→43.14 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.202 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 2696 5.1 %RANDOM
Rwork0.1879 50382 --
obs0.1903 50382 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.48 Å2 / Biso mean: 30.885 Å2 / Biso min: 17.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.2 Å2-0 Å2
2--0.2 Å20 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 2.15→43.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5374 0 88 285 5747
Biso mean--57.13 31.05 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.025600
X-RAY DIFFRACTIONr_bond_other_d0.0010.025104
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.9427644
X-RAY DIFFRACTIONr_angle_other_deg0.858311726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1325.214280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12715868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7121522
X-RAY DIFFRACTIONr_chiral_restr0.0970.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021314
X-RAY DIFFRACTIONr_mcbond_it2.2712.9212710
X-RAY DIFFRACTIONr_mcbond_other2.2672.922709
X-RAY DIFFRACTIONr_mcangle_it3.0724.3743384
LS refinement shellResolution: 2.149→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 189 -
Rwork0.266 3617 -
all-3806 -
obs--95.68 %

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