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

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Basic information

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


glucan catabolic process / cellulase / cellulase activity / beta-glucosidase activity / cell surface / extracellular region
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: 1.9 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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.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 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)91,42811
Polymers88,7922
Non-polymers2,6369
Water1,76598
1
A: Cellulase, putative, cel5D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8136
Polymers44,3961
Non-polymers1,4175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulase, putative, cel5D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6155
Polymers44,3961
Non-polymers1,2194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.343, 95.830, 157.208
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 / Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Strain: Ueda107 / Gene: cel5D, CJA_3010 / 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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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D- ...beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1092.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-1-1-1-2-2-3/a4-b1_b4-c1_b6-f1_c4-d1_c6-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D- ...beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 930.808 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-1-2-2/a4-b1_b4-c1_b6-f1_c4-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 105 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5 / Details: ammonium sulphate, 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: 1.9→81.83 Å / Num. obs: 66811 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.6 % / Num. unique obs: 4194 / CC1/2: 0.813 / Rpim(I) all: 0.592 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OYC.PDB

5oyc


Resolution: 1.9→81.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.098 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.18
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THERE IS UNMODELLED DENSITY BETWEEN THE SIDE CHAINS OF GLN172 AND TYR173 IN BOTH CHAINS, AND NEAR O2 OF XYS 3.
RfactorNum. reflection% reflectionSelection details
Rfree0.29997 3299 4.9 %RANDOM
Rwork0.23415 ---
obs0.2374 63393 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.356 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--7.41 Å2-0 Å2
3----6.8 Å2
Refinement stepCycle: 1 / Resolution: 1.9→81.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 168 98 6091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.026161
X-RAY DIFFRACTIONr_bond_other_d0.0020.025329
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9548420
X-RAY DIFFRACTIONr_angle_other_deg1.143312355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6835.155776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29125.049307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96215.127944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7371528
X-RAY DIFFRACTIONr_chiral_restr0.1330.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026856
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021268
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_it5.0965.5492976
X-RAY DIFFRACTIONr_mcbond_other5.0945.5482975
X-RAY DIFFRACTIONr_mcangle_it6.6018.3133720
X-RAY DIFFRACTIONr_mcangle_other6.68.3143721
X-RAY DIFFRACTIONr_scbond_it5.0735.5393185
X-RAY DIFFRACTIONr_scbond_other5.0735.5393185
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6128.2694701
X-RAY DIFFRACTIONr_long_range_B_refined7.99563.8187096
X-RAY DIFFRACTIONr_long_range_B_other7.99763.8177096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 202 -
Rwork0.435 4594 -
obs--99.75 %

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