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- PDB-6fao: Discovery and characterization of a thermostable GH6 endoglucanas... -

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Basic information

Entry
Database: PDB / ID: 6fao
TitleDiscovery and characterization of a thermostable GH6 endoglucanase from a compost metagenome
ComponentsGlycoside hydrolase family 6
KeywordsHYDROLASE / glycoside hydrolase family 6 / carbohydrate binding module family 2 / endoglucanase / lignocellulose
Function / homology1, 4-beta cellobiohydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsJensen, M.S. / Fredriksen, L. / MacKenzie, A.K. / Pope, P.B. / Chylenski, P. / Leiros, I. / Williamson, A.K. / Christopeit, T. / Ostby, H. / Vaaje-Kolstad, G. / Eijsink, V.G.H.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway221568 Norway
CitationJournal: PLoS ONE / Year: 2018
Title: Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome.
Authors: Jensen, M.S. / Fredriksen, L. / MacKenzie, A.K. / Pope, P.B. / Leiros, I. / Chylenski, P. / Williamson, A.K. / Christopeit, T. / Ostby, H. / Vaaje-Kolstad, G. / Eijsink, V.G.H.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0823
Polymers30,9231
Non-polymers1582
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-4 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.741, 78.683, 85.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycoside hydrolase family 6


Mass: 30923.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal Methionine (M) and C-terminal residues AHHHHHH are introduced by the expression vector pNIC. This structure represents the catalytic domain without signal peptide and C-terminal ...Details: N-terminal Methionine (M) and C-terminal residues AHHHHHH are introduced by the expression vector pNIC. This structure represents the catalytic domain without signal peptide and C-terminal CBM domain. The CBM2 and linker regions are excluded due to the flexibility (and reduced crystallisability) they impose
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: cellulase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailshttps://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=MetaGeneDetail&page=metaGeneDetail&data_ ...https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=MetaGeneDetail&page=metaGeneDetail&data_type=assembled&taxon_oid=2199352008&gene_oid=2200387098

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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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M (NH4)2SO4, 0.1 M BisTris pH 5.5, 1 % PEG 3350 / Temp details: RT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.88→57.91 Å / Num. obs: 27338 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 10 Å2 / Rpim(I) all: 0.064 / Net I/σ(I): 10.5
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 4.3 % / Num. unique obs: 1636 / Rpim(I) all: 0.534 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BOE

2boe


Resolution: 1.88→57.91 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.96 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 2182 8 %RANDOM
Rwork0.15829 ---
obs0.16191 25063 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-0 Å2
2---0.48 Å20 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.88→57.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 9 379 2477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192168
X-RAY DIFFRACTIONr_bond_other_d0.0040.021955
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9412968
X-RAY DIFFRACTIONr_angle_other_deg1.08934522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4875288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86623.84691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7451516
X-RAY DIFFRACTIONr_chiral_restr0.1080.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212511
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02437
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_it1.5491.571152
X-RAY DIFFRACTIONr_mcbond_other1.5471.5671151
X-RAY DIFFRACTIONr_mcangle_it2.2722.341440
X-RAY DIFFRACTIONr_mcangle_other2.2742.3431441
X-RAY DIFFRACTIONr_scbond_it2.0181.7241016
X-RAY DIFFRACTIONr_scbond_other2.0121.7171012
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0442.5071523
X-RAY DIFFRACTIONr_long_range_B_refined4.77920.6452629
X-RAY DIFFRACTIONr_long_range_B_other4.77820.6492630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.878→1.927 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 135 -
Rwork0.318 1749 -
obs--94.34 %

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