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- PDB-6gl2: Structure of ZgEngAGH5_4 wild type at 1.2 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6gl2
TitleStructure of ZgEngAGH5_4 wild type at 1.2 Angstrom resolution
ComponentsEndoglucanase, family GH5
KeywordsHYDROLASE / Glycoside hydrolase / GH5 / Mixed linked glucan / Zobellia galactanivorans
Function / homology
Function and homology information


cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region / metal ion binding
Similarity search - Function
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Endoglucanase, family GH5
Similarity search - Component
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsDorival, J. / Ruppert, S. / Gunnoo, M. / Orlowski, A. / Chapelais, M. / Dabin, J. / Labourel, A. / Thompson, D. / Michel, G. / Czjzek, M. / Genicot, S.
CitationJournal: Biochem. J. / Year: 2018
Title: The laterally acquired GH5ZgEngAGH5_4from the marine bacteriumZobellia galactanivoransis dedicated to hemicellulose hydrolysis.
Authors: Dorival, J. / Ruppert, S. / Gunnoo, M. / Orlowski, A. / Chapelais-Baron, M. / Dabin, J. / Labourel, A. / Thompson, D. / Michel, G. / Czjzek, M. / Genicot, S.
History
DepositionMay 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 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.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase, family GH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5773
Polymers38,4391
Non-polymers1382
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint5 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.490, 48.460, 59.260
Angle α, β, γ (deg.)90.00, 104.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endoglucanase, family GH5


Mass: 38438.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: engA, zobellia_208 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0L8Z3, cellulase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 14% PEG 6000, 200 mM CaCl2, 100 mM M sodium acetate buffer at pH 5.0
PH range: none

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.18→57.41 Å / Num. obs: 99084 / % possible obs: 98 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.16 / Net I/σ(I): 10.4
Reflection shellResolution: 1.18→1.24 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 14405 / CC1/2: 0.43 / Rrim(I) all: 0.74 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NDZ

3ndz


Resolution: 1.96→57.41 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.741 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.045 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 4956 5 %RANDOM
Rwork0.17207 ---
obs0.17348 94103 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.635 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.32 Å2
2--0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.96→57.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 10 457 3107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022843
X-RAY DIFFRACTIONr_bond_other_d0.0020.021890
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.9283883
X-RAY DIFFRACTIONr_angle_other_deg1.17134612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20824.966145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83815471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4561514
X-RAY DIFFRACTIONr_chiral_restr0.1560.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.176→1.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 372 -
Rwork0.373 6779 -
obs--97.95 %

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