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- PDB-6tpc: Crystal structure of Endoglucanase N194A from Penicillium verruculosum -

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Basic information

Entry
Database: PDB / ID: 6tpc
TitleCrystal structure of Endoglucanase N194A 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 / PHOSPHATE ION / cellulase
Function and homology information
Biological speciesTalaromyces verruculosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52218948487 Å
AuthorsNemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation Russian Federation
CitationJournal: To Be Published
Title: Crystal structure of Endoglucanase N194A from Penicillium verruculosum
Authors: Nemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A.
History
DepositionDec 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: 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 1.2Nov 6, 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
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2456
Polymers69,2062
Non-polymers1,0404
Water7,386410
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1233
Polymers34,6031
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1223
Polymers34,6031
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.372, 82.551, 90.935
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-714-

HOH

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Components

#1: Protein Endoglucanase


Mass: 34602.781 Da / Num. of mol.: 2 / Mutation: N194A
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.: 2
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: PEG 6000, Bis-Tris-Propan,20% PEG 6000, MPD, tert-butano

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.522→48.652 Å / Num. obs: 90739 / % possible obs: 97.4 % / Redundancy: 7.56 % / Biso Wilson estimate: 16.1128787453 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.24
Reflection shellResolution: 1.522→1.61 Å / Num. unique obs: 14123 / CC1/2: 0.861

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Processing

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

5i6s


Resolution: 1.52218948487→48.6515593423 Å / SU ML: 0.193301673141 / Cross valid method: FREE R-VALUE / σ(F): 1.32584533157 / Phase error: 28.8661653177
RfactorNum. reflection% reflection
Rfree0.221846673182 4722 5.21848683774 %
Rwork0.175230683744 --
obs0.177624471113 90486 97.0921498777 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.6305504444 Å2
Refinement stepCycle: LAST / Resolution: 1.52218948487→48.6515593423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 66 410 5212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005126361193794992
X-RAY DIFFRACTIONf_angle_d0.8665930482026843
X-RAY DIFFRACTIONf_chiral_restr0.0502889950893739
X-RAY DIFFRACTIONf_plane_restr0.00551675044625889
X-RAY DIFFRACTIONf_dihedral_angle_d17.13707010751699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5222-1.53950.3991390235761200.3438651536972650X-RAY DIFFRACTION89.8475510866
1.5395-1.55760.3703006510691610.3053382115122788X-RAY DIFFRACTION95.3135100194
1.5576-1.57660.3274590313041510.2786460406672764X-RAY DIFFRACTION95.4173486088
1.5766-1.59660.3032487048721770.2641024060352762X-RAY DIFFRACTION95.6705729167
1.5966-1.61760.3227384262711550.2454051987692790X-RAY DIFFRACTION96.2103887618
1.6176-1.63970.3269542374981350.2395272878582781X-RAY DIFFRACTION95.2007835455
1.6397-1.66320.2811734315421640.2243350389542790X-RAY DIFFRACTION96.409921671
1.6632-1.6880.2757790879551500.2114863035772827X-RAY DIFFRACTION96.1873990307
1.688-1.71440.2580296019211510.2130061631592780X-RAY DIFFRACTION95.6592689295
1.7144-1.74250.2623377078131730.2052367154992784X-RAY DIFFRACTION96.4134333225
1.7425-1.77250.2814831941651630.1999704014842806X-RAY DIFFRACTION96.7100977199
1.7725-1.80470.2677818879111430.1875459493972834X-RAY DIFFRACTION96.4991896272
1.8047-1.83950.2559072286991330.1857799476092865X-RAY DIFFRACTION96.5228589826
1.8395-1.8770.2370058706711490.1652621463822837X-RAY DIFFRACTION97.1372804164
1.877-1.91780.2306013079271730.1558543231492821X-RAY DIFFRACTION97.4292222584
1.9178-1.96240.1991920743861470.1565230752872X-RAY DIFFRACTION97.2929423139
1.9624-2.01150.2200197717631840.1586119648092839X-RAY DIFFRACTION97.6105908944
2.0115-2.06590.2217617478741550.1675490446952864X-RAY DIFFRACTION97.639068564
2.0659-2.12670.1984771240111650.1662572282892866X-RAY DIFFRACTION97.9005167959
2.1267-2.19530.24217070491850.1699840390772830X-RAY DIFFRACTION97.8896103896
2.1953-2.27380.2067099269641520.1591690726242900X-RAY DIFFRACTION98.2298036691
2.2738-2.36480.2113234679661570.1543396440622893X-RAY DIFFRACTION97.9447655748
2.3648-2.47250.2090986783311910.1597168707982874X-RAY DIFFRACTION98.934796643
2.4725-2.60280.2328688383451570.1605212582192923X-RAY DIFFRACTION98.5284708893
2.6028-2.76590.1890965543841580.1628375227332947X-RAY DIFFRACTION98.7281399046
2.7659-2.97940.2386593280521490.1760577914652948X-RAY DIFFRACTION98.945686901
2.9794-3.27920.2422111927881420.1790146356732979X-RAY DIFFRACTION99.2368839428
3.2792-3.75350.208390863951620.1742699082062982X-RAY DIFFRACTION99.1172761665
3.7535-4.72840.1760560849371830.1440182150742998X-RAY DIFFRACTION99.1274540355
4.7284-48.65150.1521106601851370.1663600235843170X-RAY DIFFRACTION98.7458942968

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