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- PDB-5oyc: GH5 endo-xyloglucanase from Cellvibrio japonicus -

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Basic information

Entry
Database: PDB / ID: 5oyc
TitleGH5 endo-xyloglucanase from Cellvibrio japonicus
ComponentsCellulase, putative, cel5D
KeywordsHYDROLASE / endo-xyloglucanase
Function / homology
Function and homology information


organic substance metabolic process / cellulase / cellulase activity
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Cellulase, putative, cel5D
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAttia, M. / Nelson, C.E. / Offen, W.A. / Jain, N. / Gardner, J.G. / Davies, G.J. / Brumer, H.
CitationJournal: Biotechnol Biofuels / Year: 2018
Title: In vitro and in vivo characterization of threeCellvibrio japonicusglycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions.
Authors: Attia, M.A. / Nelson, C.E. / Offen, W.A. / Jain, N. / Davies, G.J. / Gardner, J.G. / Brumer, H.
History
DepositionSep 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Cellulase, putative, cel5D
B: Cellulase, putative, cel5D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,95331
Polymers88,7922
Non-polymers3,16129
Water10,575587
1
A: Cellulase, putative, cel5D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,70014
Polymers44,3961
Non-polymers1,30313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulase, putative, cel5D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,25317
Polymers44,3961
Non-polymers1,85716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.004, 96.434, 158.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cellulase, putative, cel5D /


Mass: 44396.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminally his-tagged catalytic domain of putative cellulase Cel5D
Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Strain: Ueda107 / Gene: cel5D, CJA_3010 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: B3PD52, xyloglucan-specific endo-beta-1,4-glucanase

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Non-polymers , 6 types, 616 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H38O10 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 48.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5 / Details: ammonium sulfate, MES buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→82.45 Å / Num. obs: 112339 / % possible obs: 100 % / Redundancy: 7.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5530 / CC1/2: 0.699 / Rpim(I) all: 0.695 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZMR.PDB

3zmr


Resolution: 1.6→82.45 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.13 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.083
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THERE IS UNMODELLED DENSITY BETWEEN SOME SIDE CHAINS AS FOLLOWS:ASN132 ARG334 AND TRP143 IN BOTH MOL, GLN172 AND TYR173 IN BOTH MOL, AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THERE IS UNMODELLED DENSITY BETWEEN SOME SIDE CHAINS AS FOLLOWS:ASN132 ARG334 AND TRP143 IN BOTH MOL, GLN172 AND TYR173 IN BOTH MOL, AND BETWEEN TYR328 OF BOTH MOL.
RfactorNum. reflection% reflectionSelection details
Rfree0.20386 5553 4.9 %RANDOM
Rwork0.13717 ---
obs0.14046 106661 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.972 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0 Å2
2--1.81 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: 1 / Resolution: 1.6→82.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5885 0 200 587 6672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.026257
X-RAY DIFFRACTIONr_bond_other_d0.0020.025501
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9458472
X-RAY DIFFRACTIONr_angle_other_deg1.044312781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93425.189318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26415955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7941528
X-RAY DIFFRACTIONr_chiral_restr0.1050.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026971
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021281
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3153.2683003
X-RAY DIFFRACTIONr_mcbond_other4.2913.2673002
X-RAY DIFFRACTIONr_mcangle_it4.954.9113759
X-RAY DIFFRACTIONr_mcangle_other4.9534.9113760
X-RAY DIFFRACTIONr_scbond_it5.0343.5443254
X-RAY DIFFRACTIONr_scbond_other5.0333.5453255
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7255.2164714
X-RAY DIFFRACTIONr_long_range_B_refined5.78739.6777281
X-RAY DIFFRACTIONr_long_range_B_other5.78739.6827282
X-RAY DIFFRACTIONr_rigid_bond_restr3.828311756
X-RAY DIFFRACTIONr_sphericity_free31.1465353
X-RAY DIFFRACTIONr_sphericity_bonded15.605511869
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 422 -
Rwork0.297 7753 -
obs--99.83 %

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