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- PDB-5fkr: Unraveling the first step of xyloglucan degradation by the soil s... -

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Basic information

Entry
Database: PDB / ID: 5fkr
TitleUnraveling the first step of xyloglucan degradation by the soil saprophyte Cellvibrio japonicus through the functional and structural characterization of a potent GH74 endo-xyloglucanase
ComponentsENDO-1,4-BETA-GLUCANASE/XYLOGLUCANASE, PUTATIVE, GLY74A
KeywordsHYDROLASE / CELLVIBRIO JAPONICUS / XYLOGLUCAN SACCHARIFICATION / GLYCOSIDE HYDROLASE / CARBOHYDRATE BINDING MODULE / GREEN FLUORESCENT PROTEIN
Function / homology
Function and homology information


xyloglucan metabolic process / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Carbohydrate binding module family 10 / CBM10 superfamily / : / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain ...Carbohydrate binding module family 10 / CBM10 superfamily / : / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / : / Endo-1,4-beta-glucanase/xyloglucanase, putative, gly74A
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsAttia, M. / Stepper, J. / Davies, G.J. / Brumer, H.
CitationJournal: FEBS J. / Year: 2016
Title: Functional and Structural Characterization of a Potent Gh74 Endo-Xyloglucanase from the Soil Saprophyte Cellvibrio Japonicus Unravels the First Step of Xyloglucan Degradation.
Authors: Attia, M. / Stepper, J. / Davies, G.J. / Brumer, H.
History
DepositionOct 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-1,4-BETA-GLUCANASE/XYLOGLUCANASE, PUTATIVE, GLY74A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4654
Polymers78,2841
Non-polymers1813
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.890, 131.910, 73.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ENDO-1,4-BETA-GLUCANASE/XYLOGLUCANASE, PUTATIVE, GLY74A / GH74 ENDO-XYLOGLUCANASE


Mass: 78284.070 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 35-765
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Strain: UEDA107 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B3PKK9, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, xyloglucan-specific endo-beta-1,4-glucanase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.72 Å3/Da / Density % sol: 54.79 % / Description: NONE
Crystal growDetails: 0.1 M TRIS (PH 7.8), 0.3 M POTASSIUM BROMIDE, 8 % PGA-LM

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.28→73.17 Å / Num. obs: 39506 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.4
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LGN

4lgn


Resolution: 2.28→73.17 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.602 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26836 1948 4.9 %RANDOM
Rwork0.20969 ---
obs0.21265 37512 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.639 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20 Å20 Å2
2--6.14 Å20 Å2
3----4.25 Å2
Refinement stepCycle: LAST / Resolution: 2.28→73.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5538 0 6 156 5700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.025702
X-RAY DIFFRACTIONr_bond_other_d0.0020.025086
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9167795
X-RAY DIFFRACTIONr_angle_other_deg1.023311665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5945730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78523.815249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81315781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.651531
X-RAY DIFFRACTIONr_chiral_restr0.0950.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216682
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021399
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_it1.842.8532923
X-RAY DIFFRACTIONr_mcbond_other1.842.8522922
X-RAY DIFFRACTIONr_mcangle_it2.8054.2713652
X-RAY DIFFRACTIONr_mcangle_other2.8054.2723653
X-RAY DIFFRACTIONr_scbond_it1.8042.9472779
X-RAY DIFFRACTIONr_scbond_other1.8042.9472779
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.754.3764144
X-RAY DIFFRACTIONr_long_range_B_refined4.29422.9316425
X-RAY DIFFRACTIONr_long_range_B_other4.26522.9436406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 141 -
Rwork0.302 2718 -
obs--99.65 %

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