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- PDB-2zun: Functional Analysis of Hyperthermophilic Endocellulase from the A... -

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Basic information

Entry
Database: PDB / ID: 2zun
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


cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / 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: 2 Å
AuthorsKim, H.-W. / Ishikawa, K.
CitationJournal: To be Published
Title: Functional Analysis of Hyperthermophilic Endocellulase from the Archaeon Pyrococcus horikoshii
Authors: Kim, H.-W. / Ishikawa, K.
History
DepositionOct 21, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / 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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)158,20312
Polymers155,8653
Non-polymers2,3399
Water8,755486
1
A: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9246
Polymers51,9551
Non-polymers9705
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)52,6393
Polymers51,9551
Non-polymers6852
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)52,6393
Polymers51,9551
Non-polymers6852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.157, 58.404, 138.332
Angle α, β, γ (deg.)90.00, 109.22, 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: 51954.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: EGPh / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / 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.: 6
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
Has protein modificationY
Sequence detailsTHERE IS CONFLICT BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. IN THIS ENTRY, ...THERE IS CONFLICT BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. IN THIS ENTRY, 289TH RESIDUE IS OBVIOUSLY LYS BASED ON THE ELECTRON DENSITY.

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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: 1.98 Å3/Da / Density % sol: 38.01 %
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
DetectorType: Bruker DIP-6040 / Detector: CCD
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
NameVersionClassification
REFMAC5.4.0077refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
CNS1.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZUM

2zum


Resolution: 2→48.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.385 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3974 4.8 %RANDOM
Rwork0.216 74687 --
obs-78661 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK / Bsol: 73.825 Å2
Displacement parametersBiso max: 84.75 Å2 / Biso mean: 37.085 Å2 / Biso min: 9.12 Å2
Baniso -1Baniso -2Baniso -3
1-10.816 Å20 Å29.363 Å2
2---5.019 Å20 Å2
3----5.797 Å2
Refinement stepCycle: LAST / Resolution: 2→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9238 0 151 486 9875
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2921.5
X-RAY DIFFRACTIONc_scbond_it1.8192
X-RAY DIFFRACTIONc_mcangle_it1.9632
X-RAY DIFFRACTIONc_scangle_it2.5462.5
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 288 -
Rwork0.275 5430 -
obs--94.02 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4cbi.param

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