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- PDB-4pn2: Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthom... -

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Basic information

Entry
Database: PDB / ID: 4pn2
TitleCrystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri complexed with xylotriose
ComponentsXylanase
KeywordsHYDROLASE / xylanase
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-xylopyranose / Beta-xylanase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.42 Å
AuthorsSantos, C.R. / Martins, V.P.M. / Zanphorlin, L.M. / Ruller, R. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/13309-0 Brazil
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Molecular mechanisms associated with xylan degradation by xanthomonas plant pathogens.
Authors: Santos, C.R. / Hoffmam, Z.B. / de Matos Martins, V.P. / Zanphorlin, L.M. / de Paula Assis, L.H. / Honorato, R.V. / Lopes de Oliveira, P.S. / Ruller, R. / Murakami, M.T.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references / Structure summary
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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
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: Xylanase
B: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,63610
Polymers68,6552
Non-polymers9818
Water10,178565
1
A: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8185
Polymers34,3271
Non-polymers4904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8185
Polymers34,3271
Non-polymers4904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.284, 83.199, 72.050
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Xylanase


Mass: 34327.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: xynB, XAC4254 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PET6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Polyethylene glycol 8,000 / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 104039 / % possible obs: 95.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.087 / Χ2: 1.042 / Net I/av σ(I): 15.996 / Net I/σ(I): 10.7 / Num. measured all: 495131
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.42-1.444.50.55650911.05693.6
1.44-1.474.70.4750641.05394.1
1.47-1.54.80.42850761.05593.5
1.5-1.534.80.38851061.06593.6
1.53-1.564.90.35751051.06793.8
1.56-1.64.90.30750541.03393.4
1.6-1.6450.27550481.06492.8
1.64-1.6850.24950221.07393.3
1.68-1.7350.21551101.04993.7
1.73-1.794.90.19251771.04494.3
1.79-1.854.80.17851891.04395.6
1.85-1.934.70.15752371.04196.4
1.93-2.014.70.13752591.08296.8
2.01-2.124.60.1252691.00497
2.12-2.254.60.10652841.01896.9
2.25-2.434.40.09953351.01597.6
2.43-2.674.30.0953321.01797.5
2.67-3.064.50.07853491.01998
3.06-3.854.90.06454221.05198.6
3.85-505.20.05255100.99498.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 1.42→27.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.747 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 5226 5 %RANDOM
Rwork0.1825 99515 --
obs0.1854 99515 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.49 Å2 / Biso mean: 18.012 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å20.17 Å2
2--0.19 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: final / Resolution: 1.42→27.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 58 565 5481
Biso mean--23.77 27.18 -
Num. residues----610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195079
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9386936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36323.828256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31615758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1481536
X-RAY DIFFRACTIONr_chiral_restr0.1260.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213992
X-RAY DIFFRACTIONr_mcbond_it2.3941.5262444
X-RAY DIFFRACTIONr_mcangle_it2.9122.3023053
X-RAY DIFFRACTIONr_scbond_it3.4581.7542635
X-RAY DIFFRACTIONr_rigid_bond_restr6.92735079
X-RAY DIFFRACTIONr_sphericity_free26.1135144
X-RAY DIFFRACTIONr_sphericity_bonded13.36655353
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 356 -
Rwork0.26 6903 -
all-7259 -
obs--87.18 %

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