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- PDB-5hos: Crystal structure of the endo-beta-1,4-glucanase Xac0029 from Xan... -

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Basic information

Entry
Database: PDB / ID: 5hos
TitleCrystal structure of the endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri
ComponentsCellulase
KeywordsHYDROLASE / endo-beta-1 / 4-glucanase
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
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 the endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri
Authors: Paiva, J.H. / Murakami, M.T.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)37,6572
Polymers37,5611
Non-polymers961
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.604, 85.604, 84.423
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cellulase /


Mass: 37561.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: egl, XAC0029 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8PRD4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG4000 0.2 M ammonium sulfate 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4587 Å / Relative weight: 1
ReflectionResolution: 1.6→42.8 Å / Num. obs: 47130 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.06 % / Biso Wilson estimate: 29.143 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.14
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.70.9061.28199.1
1.7-1.820.4292.751100
1.82-1.960.2515.661100
1.96-2.150.14811.261100
2.15-2.40.11517.741100
2.4-2.770.08323.771100
2.77-3.390.05733.29199.9
3.39-4.780.04742.291100
4.780.04144.36199.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W7U

4w7u


Resolution: 1.6→42.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.385 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.081
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 2381 5.1 %RANDOM
Rwork0.1662 ---
obs0.1682 44754 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.92 Å2 / Biso mean: 23.898 Å2 / Biso min: 12.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-0.56 Å2-0 Å2
2---1.12 Å20 Å2
3---3.62 Å2
Refinement stepCycle: final / Resolution: 1.6→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 5 198 2658
Biso mean--33.54 32.54 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192546
X-RAY DIFFRACTIONr_bond_other_d0.0020.022376
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.933470
X-RAY DIFFRACTIONr_angle_other_deg0.95135432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90122.982114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7515394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6881520
X-RAY DIFFRACTIONr_chiral_restr0.080.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212938
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
X-RAY DIFFRACTIONr_mcbond_it1.6052.1951270
X-RAY DIFFRACTIONr_mcbond_other1.5862.1931269
X-RAY DIFFRACTIONr_mcangle_it2.1273.2921588
X-RAY DIFFRACTIONr_rigid_bond_restr1.16934921
X-RAY DIFFRACTIONr_sphericity_free22.833571
X-RAY DIFFRACTIONr_sphericity_bonded8.70854982
LS refinement shellResolution: 1.604→1.646 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 128 -
Rwork0.341 3275 -
all-3403 -
obs--98.41 %

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