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

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Basic information

Entry
Database: PDB / ID: 5fkt
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, GLY74A
KeywordsHYDROLASE / CELLVIBRIO JAPONICUS / XYLOGLUCAN SACCHARIFICATION / GLYCOSIDE HYDROLASE / CARBOHYDRATE BINDING MODULE
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: 1.52 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 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jan 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, GLY74A
B: ENDO-1,4-BETA-GLUCANASE/XYLOGLUCANASE, GLY74A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,68115
Polymers156,8852
Non-polymers79713
Water23,0051277
1
A: ENDO-1,4-BETA-GLUCANASE/XYLOGLUCANASE, GLY74A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8728
Polymers78,4421
Non-polymers4297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-1,4-BETA-GLUCANASE/XYLOGLUCANASE, GLY74A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8107
Polymers78,4421
Non-polymers3676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.120, 94.290, 105.560
Angle α, β, γ (deg.)90.00, 103.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 78442.336 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 34-765 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Strain: UEDA107 / Plasmid: PET28A / 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, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- ...References: UniProt: B3PKK9, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, xyloglucan-specific endo-beta-1,4-glucanase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1277 / 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: 2.61 Å3/Da / Density % sol: 52.95 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM ACETATE (PH 5.0), 0.6 M SODIUM FORMATE, 8 % W/V 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 / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.52→69.48 Å / Num. obs: 245787 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.7
Reflection shellResolution: 1.52→1.56 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FKR

5fkr


Resolution: 1.52→69.48 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.429 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES, REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19384 12120 4.9 %RANDOM
Rwork0.16726 ---
obs0.16858 233635 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.946 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.38 Å2
2---0.09 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.52→69.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11083 0 40 1277 12400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211477
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210260
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.91715688
X-RAY DIFFRACTIONr_angle_other_deg1.083323539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2351478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04823.808499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.164151573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7871562
X-RAY DIFFRACTIONr_chiral_restr0.1280.21662
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02113447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022815
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_it1.1681.1955870
X-RAY DIFFRACTIONr_mcbond_other1.1591.1945869
X-RAY DIFFRACTIONr_mcangle_it1.6721.797338
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7691.3045607
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 883 -
Rwork0.257 17235 -
obs--99.87 %

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