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- PDB-3axx: Functional analysis of hyperthermophilic endocellulase from the A... -

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Basic information

Entry
Database: PDB / ID: 3axx
TitleFunctional analysis of hyperthermophilic endocellulase from the Archaeon Pyrococcus horikoshii
Components458aa long hypothetical endo-1,4-beta-glucanase
KeywordsHYDROLASE / TIM barrel
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
CGP-CTERM domain / 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
beta-cellobiose / PHOSPHATE ION / 458aa long hypothetical endo-1,4-beta-glucanase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, H.-W. / Ishikawa, K.
Citation
Journal: Biochem.J. / Year: 2011
Title: Functional analysis of hyperthermophilic endocellulase from Pyrococcus horikoshii by crystallographic snapshots
Authors: Kim, H.-W. / Ishikawa, K.
#1: Journal: Proteins / Year: 2010
Title: Structure of hyperthermophilic endocellulase from Pyrococcus horikoshii
Authors: Kim, H.W. / Ishikawa, K.
History
DepositionApr 18, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Refinement description / Category: software
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 / pdbx_struct_assembly_gen / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: 458aa long hypothetical endo-1,4-beta-glucanase
B: 458aa long hypothetical endo-1,4-beta-glucanase
C: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,2609
Polymers155,9493
Non-polymers1,3126
Water8,755486
1
A: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6105
Polymers51,9831
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3252
Polymers51,9831
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3252
Polymers51,9831
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.467, 58.491, 138.504
Angle α, β, γ (deg.)90.00, 109.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 458aa long hypothetical endo-1,4-beta-glucanase / Family 5 endoglucanase


Mass: 51982.879 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: EGPh, PH1171 / Plasmid: pET11a / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): BL21(DE3) / References: UniProt: O58925, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 3
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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 1.99 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5M ammonium phosphate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorDetector: IMAGE PLATE / Date: Mar 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 97064 / Num. obs: 94740 / % possible obs: 97.6 % / Redundancy: 3.5 %

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZUM

2zum


Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.241 4609 4.7 %
Rwork0.2283 --
obs-91847 94.6 %
Solvent computationBsol: 74.2861 Å2
Displacement parametersBiso max: 83.52 Å2 / Biso mean: 36.6026 Å2 / Biso min: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1-10.744 Å20 Å29.296 Å2
2---4.951 Å20 Å2
3----5.793 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9244 0 84 486 9814
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2321.5
X-RAY DIFFRACTIONc_scbond_it1.7042
X-RAY DIFFRACTIONc_mcangle_it1.9142
X-RAY DIFFRACTIONc_scangle_it2.3982.5
LS refinement shellResolution: 1.9→2.02 Å /
Rfactor% reflection
Rfree0.362 -
Rwork0.354 -
obs-85.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4cbi.param
X-RAY DIFFRACTION5cis_peptide.param

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