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- PDB-5glx: Crystal structure of a glycoside hydrolase from Thielavia terrest... -

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Basic information

Entry
Database: PDB / ID: 5glx
TitleCrystal structure of a glycoside hydrolase from Thielavia terrestris NRRL 8126
ComponentsGlycoside hydrolase family 45 protein
KeywordsHYDROLASE / substrate binding / cellulase / inhibitor
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 45 / Glycosyl hydrolase family 45 / Glycosyl hydrolases family 45 active site. / RlpA-like domain / RlpA-like domain superfamily / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. ...Glycoside hydrolase, family 45 / Glycosyl hydrolase family 45 / Glycosyl hydrolases family 45 active site. / RlpA-like domain / RlpA-like domain superfamily / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesThielavia terrestris NRRL 8126 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsGao, J. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
CitationJournal: Enzyme Microb. Technol. / Year: 2017
Title: Characterization and crystal structure of a thermostable glycoside hydrolase family 45 1,4-beta-endoglucanase from Thielavia terrestris
Authors: Gao, J. / Huang, J.W. / Li, Q. / Liu, W.D. / Ko, T.P. / Zheng, Y.Y. / Xiao, X. / Kuo, C.J. / Chen, C.C. / Guo, R.T.
History
DepositionJul 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 45 protein


Theoretical massNumber of molelcules
Total (without water)22,7531
Polymers22,7531
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8990 Å2
Unit cell
Length a, b, c (Å)36.283, 58.868, 38.380
Angle α, β, γ (deg.)90.000, 115.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycoside hydrolase family 45 protein


Mass: 22752.932 Da / Num. of mol.: 1 / Fragment: UNP residues 22-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia terrestris NRRL 8126 / Strain: NRRL 8126 / Gene: THITE_2110957 / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: G2QVH7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.63 Å3/Da / Density % sol: 24.66 % / Mosaicity: 0.741 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MgCl2, Tris-Cl, PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→25 Å / Num. obs: 27662 / % possible obs: 99.4 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.068 / Net I/av σ(I): 17.673 / Net I/σ(I): 22.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.42-1.474.90.1810.974199.1
1.47-1.535.20.1470.9831100
1.53-1.65.20.1160.988199.9
1.6-1.685.30.1010.991199.9
1.68-1.795.30.0930.991199.9
1.79-1.935.30.0820.993199.8
1.93-2.125.20.0750.993199.9
2.12-2.435.20.0750.994199.9
2.43-3.065.20.0740.994199.6
3.062-2550.0550.996195.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OA7

1oa7


Resolution: 1.42→25 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.856 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1608 1380 5 %RANDOM
Rwork0.1332 ---
obs0.1346 26261 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.22 Å2 / Biso mean: 16.655 Å2 / Biso min: 8.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.02 Å2
2---0.19 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.42→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 0 145 1738
Biso mean---25.06 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021646
X-RAY DIFFRACTIONr_bond_other_d00.021393
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9152245
X-RAY DIFFRACTIONr_angle_other_deg0.79233220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86724.7374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21815214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.736156
X-RAY DIFFRACTIONr_chiral_restr0.1070.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02411
X-RAY DIFFRACTIONr_mcbond_it1.7891.469867
X-RAY DIFFRACTIONr_mcbond_other1.7731.466866
X-RAY DIFFRACTIONr_mcangle_it2.6442.2031082
LS refinement shellResolution: 1.417→1.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 102 -
Rwork0.164 1901 -
all-2003 -
obs--97.9 %

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