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

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Basic information

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


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / 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: 1.601 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: Atomic model / Data collection ...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 / 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 / _refine_hist.d_res_high / _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)68,9638
Polymers68,3992
Non-polymers5656
Water4,954275
1
A: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4824
Polymers34,1991
Non-polymers2823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4824
Polymers34,1991
Non-polymers2823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.866, 48.201, 77.798
Angle α, β, γ (deg.)90.000, 90.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Xylanase /


Mass: 34199.316 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: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2 / 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 1.97 Å3/Da / Density % sol: 37.56 %
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: 1.033 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: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 69577 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.54 % / Biso Wilson estimate: 21.057 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.112 / Χ2: 0.917 / Net I/σ(I): 11.54 / Num. measured all: 246951
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.6-1.70.6970.5892.553877411302109100.69396.5
1.7-1.810.830.423.763887810630104800.49198.6
1.81-1.960.9190.2745.7536541992598430.3299.2
1.96-2.150.9660.179.0933147911990680.19999.4
2.15-2.40.9810.11911.9828511832282680.14199.4
2.4-2.770.9880.0914.9524312731972750.10799.4
2.77-3.390.9950.05721.0119851620961470.06899
3.39-4.770.9980.03233.7317047487748390.03899.2
4.770.9990.02935.219890277327470.03499.1

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 1.601→40.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.244 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 3516 5.1 %RANDOM
Rwork0.1856 66061 --
obs0.1877 69577 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.89 Å2 / Biso mean: 14.034 Å2 / Biso min: 8.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å20.02 Å2
2--0.16 Å20 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 1.601→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 34 275 5149
Biso mean--13.55 21 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195016
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.9316846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0335604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87423.828256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59115748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6751536
X-RAY DIFFRACTIONr_chiral_restr0.0740.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213964
X-RAY DIFFRACTIONr_mcbond_it1.3311.2772422
X-RAY DIFFRACTIONr_mcangle_it1.7461.9183024
X-RAY DIFFRACTIONr_scbond_it1.8531.3922594
X-RAY DIFFRACTIONr_rigid_bond_restr0.97835016
X-RAY DIFFRACTIONr_sphericity_free24.714572
X-RAY DIFFRACTIONr_sphericity_bonded12.52355077
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 243 -
Rwork0.255 4610 -
all-4853 -
obs--94.58 %

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