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- PDB-6t9g: CRYSTAL STRUCTURE OF AN ENDOGLUCANASE D213A FROM PENICILLIUM VERR... -

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Basic information

Entry
Database: PDB / ID: 6t9g
TitleCRYSTAL STRUCTURE OF AN ENDOGLUCANASE D213A FROM PENICILLIUM VERRUCULOSUM
ComponentsEndoglucanase
KeywordsHYDROLASE / ENDOHYDROLYSIS / CELLULOSE
Function / homologyglucan catabolic process / cellulase / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / cellulase
Function and homology information
Biological speciesTalaromyces verruculosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29620665336 Å
AuthorsNemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A.
Funding support1items
OrganizationGrant numberCountry
Russian Science Foundation
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF AN ENDOGLUCANASE D213A FROM PENICILLIUM VERRUCULOSUM
Authors: Nemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A.
History
DepositionOct 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 1.2Oct 16, 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

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)140,1058
Polymers138,4074
Non-polymers1,6984
Water2,090116
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0262
Polymers34,6021
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0262
Polymers34,6021
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0262
Polymers34,6021
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0262
Polymers34,6021
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.437, 89.965, 91.587
Angle α, β, γ (deg.)90.000, 90.085, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Endoglucanase


Mass: 34601.793 Da / Num. of mol.: 4 / Mutation: D213A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces verruculosus (fungus) / Production host: Penicillium canescens (fungus) / References: UniProt: A0A1U7Q1U3
#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.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: PEG 3350,bis-tris pH 5,5, magnesium chloride

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.29620665336→44.9825 Å / Num. obs: 56494 / % possible obs: 96.6 % / Redundancy: 6.41 % / Biso Wilson estimate: 30.2086713733 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.51
Reflection shellResolution: 2.29620665336→2.43 Å / Num. unique obs: 7727 / CC1/2: 0.863

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I6S

5i6s


Resolution: 2.29620665336→44.9825 Å / SU ML: 0.333770843734 / Cross valid method: FREE R-VALUE / σ(F): 1.34352979153 / Phase error: 33.4529028914
RfactorNum. reflection% reflection
Rfree0.248071271556 2677 4.75606722809 %
Rwork0.211418507552 --
obs0.213151746088 56286 96.418109872 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.2834396943 Å2
Refinement stepCycle: LAST / Resolution: 2.29620665336→44.9825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9456 0 112 116 9684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008213449313429844
X-RAY DIFFRACTIONf_angle_d0.96530477063413470
X-RAY DIFFRACTIONf_chiral_restr0.05335962925551457
X-RAY DIFFRACTIONf_plane_restr0.006478684519951745
X-RAY DIFFRACTIONf_dihedral_angle_d17.78535741033340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29620665336-2.3380.3878523432521230.3997629091321918X-RAY DIFFRACTION67.8298438019
2.338-2.38290.4104463016821190.3439911693462424X-RAY DIFFRACTION83.186130193
2.3829-2.43160.3764360563331520.3407910292242779X-RAY DIFFRACTION95.4412243569
2.4316-2.48440.365105204491370.2955278434872849X-RAY DIFFRACTION98.0946123522
2.4844-2.54220.3197023361991610.2755476726532835X-RAY DIFFRACTION98.6499835364
2.5422-2.60580.3002099278091300.2615073666782924X-RAY DIFFRACTION98.6434108527
2.6058-2.67620.2582828307681340.260782624142892X-RAY DIFFRACTION98.7597911227
2.6762-2.7550.2828070451151610.2548506217962861X-RAY DIFFRACTION98.8227599738
2.755-2.84390.3373396156871520.2480406192042859X-RAY DIFFRACTION98.8834154351
2.8439-2.94550.3568393769951680.269788727752876X-RAY DIFFRACTION98.9275268118
2.9455-3.06340.3042752661921360.2425614747372908X-RAY DIFFRACTION99.1530944625
3.0634-3.20280.280634217574880.2226826065662975X-RAY DIFFRACTION99.577373212
3.2028-3.37160.2760538531061470.209191807522910X-RAY DIFFRACTION99.4146341463
3.3716-3.58280.2341175047631360.2078463779342910X-RAY DIFFRACTION99.4125326371
3.5828-3.85930.1841130470871750.1821634044022885X-RAY DIFFRACTION99.4152046784
3.8593-4.24740.1818099699121210.1473503984262954X-RAY DIFFRACTION99.7081712062
4.2474-4.86130.1721955399631400.1372203635362938X-RAY DIFFRACTION99.3223620523
4.8613-6.12230.1560156127291420.1581866699132960X-RAY DIFFRACTION99.6786632391
6.1223-44.98250.2007542252541550.1835554362972952X-RAY DIFFRACTION98.3850538315

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