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- PDB-3ayr: GH5 endoglucanase EglA from a ruminal fungus -

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Basic information

Entry
Database: PDB / ID: 3ayr
TitleGH5 endoglucanase EglA from a ruminal fungus
ComponentsEndoglucanase
KeywordsHYDROLASE / Tim Barrel / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesPiromyces rhizinflatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTseng, C.-W. / Ko, T.-P. / Guo, R.-T. / Liu, J.-R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Substrate binding of a GH5 endoglucanase from the ruminal fungus Piromyces rhizinflata.
Authors: Tseng, C.-W. / Ko, T.-P. / Guo, R.-T. / Huang, J.-W. / Wang, H.-C. / Huang, C.-H. / Cheng, Y.-S. / Wang, A.H.-J. / Liu, J.-R.
History
DepositionMay 16, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)43,3771
Polymers43,3771
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Endoglucanase

A: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)86,7552
Polymers86,7552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area2470 Å2
ΔGint-14 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.396, 83.396, 225.085
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-586-

HOH

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Components

#1: Protein Endoglucanase


Mass: 43377.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piromyces rhizinflatus (fungus) / Gene: eglA / Plasmid: pET46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9URH5, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.5M sodium citrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2010 / Details: Rh Coated mirrors
RadiationMonochromator: LN2-Cooled, Fixed-Exit Si(111) Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 32241 / Num. obs: 31439 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 39.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 54.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 42.8 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 8.8 / Num. unique all: 1530 / % possible all: 97.1

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Processing

Software
NameVersionClassification
Blu-IceControl Softwaredata collection
CNSrefinement
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EDG

1edg


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.929 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21575 1594 5.1 %RANDOM
Rwork0.17042 ---
all0.173 32241 --
obs0.17269 29845 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.145 Å0.152 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 0 231 3202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223051
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1261.9214138
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1725365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26325.21167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17515508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4551513
X-RAY DIFFRACTIONr_chiral_restr0.1610.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212396
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4941.51818
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.41522926
X-RAY DIFFRACTIONr_scbond_it3.80731233
X-RAY DIFFRACTIONr_scangle_it5.6594.51212
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 133 -
Rwork0.166 2107 -
obs--97.52 %
Refinement TLS params.Method: refined / Origin x: -1.8444 Å / Origin y: 34.205 Å / Origin z: -1.886 Å
111213212223313233
T0.0135 Å2-0.0092 Å2-0.0047 Å2-0.3138 Å20.2077 Å2--0.1648 Å2
L1.8125 °2-0.5539 °20.3553 °2-1.0439 °2-0.2416 °2--1.5332 °2
S0.0503 Å °-0.4208 Å °-0.4331 Å °0.0128 Å °0.1255 Å °0.0804 Å °0.0035 Å °-0.3088 Å °-0.1759 Å °

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