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- PDB-5gm9: Crystal structure of a glycoside hydrolase in complex with cellobiose -

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Basic information

Entry
Database: PDB / ID: 5gm9
TitleCrystal structure of a glycoside hydrolase in complex with cellobiose
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
beta-cellobiose / alpha-cellobiose / Cellulase
Similarity search - Component
Biological speciesThielavia terrestris NRRL 8126 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0033
Polymers22,3181
Non-polymers6852
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint1 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.337, 54.315, 84.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycoside hydrolase family 45 protein


Mass: 22318.486 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 (fungus)
Strain: NRRL 8126 / Gene: THITE_2110957 / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: G2QVH7
#2: Polysaccharide beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.39 Å3/Da / Density % sol: 48.58 % / Mosaicity: 0.329 °
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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 16, 2016
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→25 Å / Num. obs: 46675 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.035 / Net I/av σ(I): 57.314 / Net I/σ(I): 27.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.36-1.4110.70.1040.996199.7
1.41-1.4610.70.0840.9981100
1.46-1.5310.80.070.9971100
1.53-1.6110.80.0570.9981100
1.61-1.7110.90.0560.9981100
1.71-1.8510.90.0520.9981100
1.85-2.0310.90.0370.9991100
2.03-2.3310.90.0370.9991100
2.33-2.9310.90.0320.9991100
2.931-2510.20.0280.999199.3

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Processing

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

1oa7


Resolution: 1.36→25 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.587 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.046
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1643 2302 4.9 %RANDOM
Rwork0.1414 ---
obs0.1426 44309 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.75 Å2 / Biso mean: 15.275 Å2 / Biso min: 8.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0 Å2
2---0.06 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.36→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 46 237 1845
Biso mean--20.38 26.86 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021662
X-RAY DIFFRACTIONr_bond_other_d0.0010.021399
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9492272
X-RAY DIFFRACTIONr_angle_other_deg0.84333246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3035212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76824.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.9715210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.651156
X-RAY DIFFRACTIONr_chiral_restr0.3130.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02402
X-RAY DIFFRACTIONr_mcbond_it1.5271.301851
X-RAY DIFFRACTIONr_mcbond_other1.5181.296850
X-RAY DIFFRACTIONr_mcangle_it2.0981.9511062
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 156 -
Rwork0.155 3172 -
all-3328 -
obs--98.26 %

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