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- PDB-5m2d: CRYSTAL STRUCTURE 4Ac Endoglucanase-like protein from Acremonium ... -

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Basic information

Entry
Database: PDB / ID: 5m2d
TitleCRYSTAL STRUCTURE 4Ac Endoglucanase-like protein from Acremonium chrysogenum
ComponentsEndoglucanase-like protein
KeywordsHYDROLASE / Endoglucanase-like protein / ALPHA/BETA BARREL
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endoglucanase-like protein
Similarity search - Component
Biological speciesAcremonium chrysogenum ATCC 11550 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.097 Å
AuthorsGabdulkhakov, A. / Tishchenko, S.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE 4Ac Endoglucanase-like protein from Acremonium chrysogenum
Authors: Gabdulkhakov, A. / Tishchenko, S. / Lisov, A.
History
DepositionOct 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 2.0Oct 16, 2019Group: Atomic model / Data collection / Category: atom_site / reflns_shell / Item: _atom_site.occupancy
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Endoglucanase-like protein
B: Endoglucanase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6364
Polymers51,4522
Non-polymers1842
Water2,576143
1
A: Endoglucanase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8182
Polymers25,7261
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8182
Polymers25,7261
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.889, 49.255, 117.552
Angle α, β, γ (deg.)90.00, 93.03, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-478-

HOH

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Components

#1: Protein Endoglucanase-like protein


Mass: 25726.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acremonium chrysogenum ATCC 11550 (fungus)
Gene: ACRE_041060 / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: A0A086T6R4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.2 M Sodium malonate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.09→42 Å / Num. obs: 23601 / % possible obs: 95.2 % / Redundancy: 3.67 % / Net I/σ(I): 7.15

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.097→40.793 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.17 / Phase error: 21.62
RfactorNum. reflection% reflection
Rfree0.2142 2215 4.83 %
Rwork0.1896 --
obs0.1909 23601 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.097→40.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 12 143 3609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083600
X-RAY DIFFRACTIONf_angle_d0.8534914
X-RAY DIFFRACTIONf_dihedral_angle_d14.441230
X-RAY DIFFRACTIONf_chiral_restr0.056480
X-RAY DIFFRACTIONf_plane_restr0.006659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0973-2.14290.26271120.22972065X-RAY DIFFRACTION72
2.1429-2.19270.2791190.23692312X-RAY DIFFRACTION83
2.1927-2.24750.26111710.23662632X-RAY DIFFRACTION93
2.2475-2.30830.32961300.22852811X-RAY DIFFRACTION100
2.3083-2.37620.22581180.22712880X-RAY DIFFRACTION99
2.3762-2.45290.23411170.22222881X-RAY DIFFRACTION99
2.4529-2.54060.21191200.2072789X-RAY DIFFRACTION99
2.5406-2.64230.25581310.20522797X-RAY DIFFRACTION98
2.6423-2.76250.24971250.20152896X-RAY DIFFRACTION100
2.7625-2.90810.26251490.20482788X-RAY DIFFRACTION99
2.9081-3.09020.21051220.20142877X-RAY DIFFRACTION99
3.0902-3.32870.17991340.1742764X-RAY DIFFRACTION98
3.3287-3.66350.20342250.16232744X-RAY DIFFRACTION99
3.6635-4.19320.17831460.15042785X-RAY DIFFRACTION98
4.1932-5.28120.13551740.1382782X-RAY DIFFRACTION99
5.2812-40.80050.20451220.17252814X-RAY DIFFRACTION98

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