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- PDB-6haa: Structure of a covalent complex of endo-Xyloglucanase from Cellvi... -

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Basic information

Entry
Database: PDB / ID: 6haa
TitleStructure of a covalent complex of endo-Xyloglucanase from Cellvibrio japonicus after reacting with XXXG(2F)-beta-DNP
ComponentsCellulase, putative, cel5D
KeywordsHYDROLASE / Glycoside hydrolase / xyloglucan / covalent inhibitor
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
TRIETHYLENE GLYCOL / Cellulase, putative, cel5D
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOffen, W. / Davies, G.J.
CitationJournal: Org. Biomol. Chem. / Year: 2018
Title: Synthesis and application of a highly branched, mechanism-based 2-deoxy-2-fluoro-oligosaccharide inhibitor of endo-xyloglucanases.
Authors: Jain, N. / Attia, M.A. / Offen, W.A. / Davies, G.J. / Brumer, H.
History
DepositionAug 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity.pdbx_ec / _struct.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)92,07214
Polymers88,6762
Non-polymers3,39512
Water6,431357
1
A: Cellulase, putative, cel5D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0478
Polymers44,3381
Non-polymers1,7097
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulase, putative, cel5D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0256
Polymers44,3381
Non-polymers1,6875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.058, 97.206, 156.677
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: 44338.148 Da / Num. of mol.: 2 / Mutation: E255A
Source method: isolated from a genetically manipulated source
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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Sugars , 2 types, 2 molecules

#2: 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)-2-deoxy-2-fluoro-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 932.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,6,5/[a2122h-1a_1-5_2*F][a2122h-1b_1-5][a212h-1a_1-5]/1-2-2-2-3-3/a4-b1_b4-c1_b6-f1_c4-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp2fluoro]{[(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
#3: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-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)-2-deoxy-2-fluoro-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1064.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,7,6/[a2122h-1a_1-5_2*F][a2122h-1b_1-5][a212h-1a_1-5]/1-2-2-2-3-3-3/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp2fluoro]{[(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]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 367 molecules

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


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14O4
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: ammonium sulphate, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.7→33.25 Å / Num. obs: 94971 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.998 / Net I/σ(I): 12.3
Reflection shellResolution: 1.7→1.73 Å / CC1/2: 0.777

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OYC.PDB

5oyc


Resolution: 1.7→33.25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.148 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.127
Details: THERE IS UNMODELLED DENSITY NEAR THE SIDE CHAINS OF GLN172 AND TYR173 IN BOTH MOLECULES, AND NEAR TO O6 OF THE TERMINAL BGC OF THE LIGAND IN MOLECULE A.
RfactorNum. reflection% reflectionSelection details
Rfree0.27134 4597 4.9 %RANDOM
Rwork0.2176 ---
obs0.22023 89231 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.445 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--2.12 Å2-0 Å2
3----2.74 Å2
Refinement stepCycle: 1 / Resolution: 1.7→33.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5816 0 221 357 6394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.026248
X-RAY DIFFRACTIONr_bond_other_d0.0020.025447
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.9598517
X-RAY DIFFRACTIONr_angle_other_deg1.118312643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7665770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18924.935308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91215.053935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4041529
X-RAY DIFFRACTIONr_chiral_restr0.120.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026903
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021282
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_it3.7813.9092988
X-RAY DIFFRACTIONr_mcbond_other3.7783.9092987
X-RAY DIFFRACTIONr_mcangle_it4.5785.8593739
X-RAY DIFFRACTIONr_mcangle_other4.5775.863740
X-RAY DIFFRACTIONr_scbond_it3.7323.9943260
X-RAY DIFFRACTIONr_scbond_other3.733.9943260
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8625.934778
X-RAY DIFFRACTIONr_long_range_B_refined6.04545.0937063
X-RAY DIFFRACTIONr_long_range_B_other6.04645.0997064
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 350 -
Rwork0.356 6513 -
obs--100 %

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