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- PDB-4w7v: Crystal structure of XacCel5A in complex with cellobiose -

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Basic information

Entry
Database: PDB / ID: 4w7v
TitleCrystal structure of XacCel5A in complex with cellobiose
ComponentsCellulase
KeywordsHYDROLASE / (a/b)8-barrel glycosyl hydrolase family 5 cellulase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / Cellulase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsPaiva, J.H. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/13309-0 and 2014/07135-1 Brazil
CitationJournal: To Be Published
Title: Crystal structure of XacCel5A in complex with cellobiose
Authors: Paiva, J.H. / Murakami, M.T.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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 / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3673
Polymers36,6821
Non-polymers6852
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.186, 81.756, 48.168
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

21A-581-

HOH

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Components

#1: Protein Cellulase


Mass: 36682.418 Da / Num. of mol.: 1 / Fragment: unp residues 42-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: egl, XAC0030 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PRD3
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium cacodylate, 0.2 M sodium acetate, 28% PEG8000, 5% glycerol

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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: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.43→48.17 Å / Num. obs: 109499 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.14 % / Biso Wilson estimate: 23.61 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.071 / Χ2: 0.897 / Net I/σ(I): 12.15 / Num. measured all: 452924
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.43-1.520.7120.7891.665895517922168750.93494.2
1.52-1.630.8550.4732.886511416803167650.5599.8
1.63-1.760.9350.34.56308415636156140.34699.9
1.76-1.920.9780.1757.516060314405143930.299.9
1.92-2.150.9920.09813.175687513042130370.112100
2.15-2.480.9960.06519.495092611464114600.074100
2.48-3.040.9980.05123.0444076970497040.058100
3.04-4.290.9990.03436.6934470752575230.038100
4.290.9990.02843.8518821416241280.03299.2

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GZJ

1gzj


Resolution: 1.43→48.17 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.153 / WRfactor Rwork: 0.1154 / FOM work R set: 0.8731 / SU B: 2.403 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0585 / SU Rfree: 0.0568 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.173 2831 4.9 %RANDOM
Rwork0.1319 54738 --
obs0.1339 54738 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.38 Å2 / Biso mean: 20.226 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.37 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: final / Resolution: 1.43→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 46 256 2749
Biso mean--29.55 32.73 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022572
X-RAY DIFFRACTIONr_bond_other_d0.0010.022393
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9683496
X-RAY DIFFRACTIONr_angle_other_deg0.79935533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69724.587109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04615415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.032159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02588
X-RAY DIFFRACTIONr_mcbond_it2.0891.7281256
X-RAY DIFFRACTIONr_mcbond_other2.0561.7251255
X-RAY DIFFRACTIONr_mcangle_it2.7122.6061570
X-RAY DIFFRACTIONr_rigid_bond_restr3.13734965
X-RAY DIFFRACTIONr_sphericity_free30.838573
X-RAY DIFFRACTIONr_sphericity_bonded12.65655077
LS refinement shellResolution: 1.435→1.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 166 -
Rwork0.319 3676 -
all-3842 -
obs--90.78 %

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