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- PDB-5l9c: Crystal structure of an endoglucanase from Penicillium verruculos... -

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Basic information

Entry
Database: PDB / ID: 5l9c
TitleCrystal structure of an endoglucanase from Penicillium verruculosum in complex with cellobiose
Componentsendoglucanase
KeywordsHYDROLASE / endohydrolysis / cellulose
Function / homology
Function and homology information


glucan catabolic process / cellulase / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
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 / cellulase
Similarity search - Component
Biological speciesTalaromyces verruculosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNemashkalov, V. / Vakhrusheva, A. / Tishchenko, S. / Gabdulkhakov, A. / Kravchenko, O. / Gusakov, A. / Sinisyn, A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Federation
CitationJournal: to be published
Title: Crystal structure of an endoglucanase from Penicillium verruculosum in complex with cellobiose
Authors: Nemashkalov, V. / Vakhrusheva, A. / Tishchenko, S. / Gabdulkhakov, A. / Kravchenko, O. / Gusakov, A. / Sinisyn, A.
History
DepositionJun 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
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 / 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_close_contact / struct_asym / struct_conn / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: endoglucanase
B: endoglucanase
C: endoglucanase
D: endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,03717
Polymers138,5834
Non-polymers4,45413
Water28,4461579
1
A: endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7554
Polymers34,6461
Non-polymers1,1093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7554
Polymers34,6461
Non-polymers1,1093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7735
Polymers34,6461
Non-polymers1,1274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7554
Polymers34,6461
Non-polymers1,1093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.330, 73.230, 91.150
Angle α, β, γ (deg.)87.23, 94.17, 100.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
endoglucanase


Mass: 34645.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces verruculosus (fungus) / Production host: Talaromyces verruculosus (fungus) / References: UniProt: A0A1U7Q1U3*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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.: 8
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1579 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycole 6000, 50 mM bis-tris propane pH 7.0, 7% 2 methyl-2,4,-pentanediol, 5% 2 methyl-2 propanal, 6% PEG 5000, cellobiose

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.78→48.4 Å / Num. obs: 107169 / % possible obs: 90 % / Redundancy: 1.83 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 6.1
Reflection shellResolution: 1.78→1.83 Å / Rmerge(I) obs: 0.498

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I6S

5i6s


Resolution: 1.85→48.398 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.19
RfactorNum. reflection% reflection
Rfree0.2731 5057 5 %
Rwork0.2264 --
obs0.2288 101178 94.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→48.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9460 0 296 1579 11335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610056
X-RAY DIFFRACTIONf_angle_d0.65913755
X-RAY DIFFRACTIONf_dihedral_angle_d11.7923499
X-RAY DIFFRACTIONf_chiral_restr0.0451531
X-RAY DIFFRACTIONf_plane_restr0.0041745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.32921540.27732957X-RAY DIFFRACTION86
1.871-1.8930.35291650.28673138X-RAY DIFFRACTION94
1.893-1.91610.34341680.28193186X-RAY DIFFRACTION94
1.9161-1.94040.34891660.27473140X-RAY DIFFRACTION94
1.9404-1.96590.32681700.27063239X-RAY DIFFRACTION95
1.9659-1.99280.32841680.2633198X-RAY DIFFRACTION95
1.9928-2.02130.35861690.25923208X-RAY DIFFRACTION95
2.0213-2.05150.29641680.25673177X-RAY DIFFRACTION94
2.0515-2.08350.29241660.25283157X-RAY DIFFRACTION94
2.0835-2.11770.32561690.24753207X-RAY DIFFRACTION94
2.1177-2.15420.27531680.25193195X-RAY DIFFRACTION95
2.1542-2.19340.30981640.2483124X-RAY DIFFRACTION94
2.1934-2.23560.3311720.24873270X-RAY DIFFRACTION95
2.2356-2.28120.30771670.24963179X-RAY DIFFRACTION95
2.2812-2.33080.31691680.2433195X-RAY DIFFRACTION95
2.3308-2.3850.29211690.2393212X-RAY DIFFRACTION95
2.385-2.44470.30671720.24463258X-RAY DIFFRACTION96
2.4447-2.51080.29151690.23093217X-RAY DIFFRACTION96
2.5108-2.58460.29311710.23543256X-RAY DIFFRACTION96
2.5846-2.66810.29261690.23043203X-RAY DIFFRACTION95
2.6681-2.76340.28891720.23173260X-RAY DIFFRACTION96
2.7634-2.8740.25911690.22343220X-RAY DIFFRACTION96
2.874-3.00480.2681700.22853233X-RAY DIFFRACTION96
3.0048-3.16320.25931720.21373257X-RAY DIFFRACTION96
3.1632-3.36140.24431680.21243221X-RAY DIFFRACTION96
3.3614-3.62080.24671710.19883249X-RAY DIFFRACTION96
3.6208-3.9850.21321720.18023259X-RAY DIFFRACTION96
3.985-4.56130.17371720.16663257X-RAY DIFFRACTION96
4.5613-5.74530.2321670.19633174X-RAY DIFFRACTION95
5.7453-48.41450.22051720.21543275X-RAY DIFFRACTION96

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