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- PDB-5h4u: Crystal structure of cellulase from Antarctic springtail, Cryptop... -

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Basic information

Entry
Database: PDB / ID: 5h4u
TitleCrystal structure of cellulase from Antarctic springtail, Cryptopygus antarcticus
ComponentsEndo-beta-1,4-glucanase
KeywordsHYDROLASE / cold-active / Cellulase / Antarctic springtail / Cryptopygus antarcticus
Function / homology
Function and homology information


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 / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesCryptopygus antarcticus (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAn, Y.J. / Hong, S.K. / Cha, S.S.
CitationJournal: J. Agric. Food Chem. / Year: 2017
Title: Genetic and Structural Characterization of a Thermo-Tolerant, Cold-Active, and Acidic Endo-beta-1,4-glucanase from Antarctic Springtail, Cryptopygus antarcticus.
Authors: Song, J.M. / Hong, S.K. / An, Y.J. / Kang, M.H. / Hong, K.H. / Lee, Y.H. / Cha, S.S.
History
DepositionNov 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 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
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: Endo-beta-1,4-glucanase
B: Endo-beta-1,4-glucanase
C: Endo-beta-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)73,9223
Polymers73,9223
Non-polymers00
Water3,279182
1
A: Endo-beta-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)24,6411
Polymers24,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-beta-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)24,6411
Polymers24,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endo-beta-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)24,6411
Polymers24,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.714, 81.714, 89.352
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Endo-beta-1,4-glucanase


Mass: 24640.541 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptopygus antarcticus (arthropod) / Production host: Escherichia coli (E. coli) / References: UniProt: D3GDK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.2
Details: 20% PEG 8K, 0.1M phosphate-citrate pH 4.2, 0.2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 21047 / % possible obs: 97.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 13.31 Å2 / Net I/σ(I): 16.1
Reflection shellResolution: 2.6→2.69 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OA9

1oa9


Resolution: 2.6→40.857 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 2.19 / Phase error: 28.35
RfactorNum. reflection% reflection
Rfree0.2891 1985 9.66 %
Rwork0.219 --
obs0.2256 20549 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→40.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 0 182 4740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124684
X-RAY DIFFRACTIONf_angle_d1.3886371
X-RAY DIFFRACTIONf_dihedral_angle_d16.372767
X-RAY DIFFRACTIONf_chiral_restr0.076669
X-RAY DIFFRACTIONf_plane_restr0.008841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.587-2.65160.32481370.26631254X-RAY DIFFRACTION93
2.6516-2.72330.31251480.26151318X-RAY DIFFRACTION98
2.7233-2.80340.3021480.24411329X-RAY DIFFRACTION98
2.8034-2.89390.30971370.25261329X-RAY DIFFRACTION99
2.8939-2.99730.28741370.2241317X-RAY DIFFRACTION99
2.9973-3.11730.31361440.22971325X-RAY DIFFRACTION99
3.1173-3.25910.31911390.22251352X-RAY DIFFRACTION99
3.2591-3.43080.24971350.21711323X-RAY DIFFRACTION99
3.4308-3.64570.3011450.19731341X-RAY DIFFRACTION99
3.6457-3.92690.26941380.19491319X-RAY DIFFRACTION99
3.9269-4.32170.24511440.18881374X-RAY DIFFRACTION100
4.3217-4.94620.27821400.19821308X-RAY DIFFRACTION100
4.9462-6.22810.29341450.22281356X-RAY DIFFRACTION100
6.2281-40.86210.29711480.23011319X-RAY DIFFRACTION99

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