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

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Basic information

Entry
Database: PDB / ID: 4pmx
TitleCrystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri in the native form
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
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.304 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 1.3Nov 7, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4692
Polymers34,4291
Non-polymers401
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-11 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.463, 71.834, 83.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Xylanase


Mass: 34428.547 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria) / References: UniProt: Q8PET6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
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: 1.03 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: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 69082 / % possible obs: 94.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.04 / Χ2: 1.048 / Net I/av σ(I): 20.845 / Net I/σ(I): 13.5 / Num. measured all: 200829
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.3-1.3230.56134421.07195.5
1.32-1.3530.50634671.07596.6
1.35-1.372.90.43634711.06895.8
1.37-1.42.90.38734741.06395.5
1.4-1.432.90.33234551.04996
1.43-1.462.90.26934391.03295.3
1.46-1.52.80.2234291.0394.8
1.5-1.542.80.20434401.07794.8
1.54-1.592.70.16134111.05493.5
1.59-1.642.70.13333721.08292.9
1.64-1.72.70.11933411.0392.4
1.7-1.762.70.09333291.07891.6
1.76-1.842.80.07533291.00491.4
1.84-1.942.80.06333001.05790.2
1.94-2.062.80.05732491.02889.2
2.06-2.222.70.05133391.01790.6
2.22-2.452.80.04334721.02894
2.45-2.83.20.02836711.10599.2
2.8-3.533.50.0237531.01399.9
3.53-503.40.01638991.00599

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.304→41.95 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.683 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1743 1873 2.7 %RANDOM
Rwork0.1322 67014 --
obs0.1333 68887 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.69 Å2 / Biso mean: 14.16 Å2 / Biso min: 6.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20 Å2
2--0.06 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.304→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 1 323 2760
Biso mean--12.74 26.63 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192531
X-RAY DIFFRACTIONr_bond_other_d0.0010.022329
X-RAY DIFFRACTIONr_angle_refined_deg2.021.9253448
X-RAY DIFFRACTIONr_angle_other_deg0.99135328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9485307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68223.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72415381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0211520
X-RAY DIFFRACTIONr_chiral_restr0.1410.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02639
X-RAY DIFFRACTIONr_mcbond_it2.3571.1441227
X-RAY DIFFRACTIONr_mcbond_other2.2431.141224
X-RAY DIFFRACTIONr_mcangle_it2.6881.7181530
X-RAY DIFFRACTIONr_rigid_bond_restr5.93534860
X-RAY DIFFRACTIONr_sphericity_free35.407574
X-RAY DIFFRACTIONr_sphericity_bonded10.62555030
LS refinement shellResolution: 1.304→1.337 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 110 -
Rwork0.231 4082 -
all-4192 -
obs--78.06 %

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