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- PDB-6t9f: CRYSTAL STRUCTURE OF EN ENDOGLUCANASE S308P FROM PENICILLIUM VERR... -

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Basic information

Entry
Database: PDB / ID: 6t9f
TitleCRYSTAL STRUCTURE OF EN ENDOGLUCANASE S308P 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: 2.24847339752 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 EN ENDOGLUCANASE S308P 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 23, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)139,9158
Polymers138,6234
Non-polymers1,2914
Water1,29772
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0802
Polymers34,6561
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8772
Polymers34,6561
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0802
Polymers34,6561
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8772
Polymers34,6561
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.358, 77.391, 90.923
Angle α, β, γ (deg.)81.807, 76.690, 75.864
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Endoglucanase


Mass: 34655.840 Da / Num. of mol.: 4 / Mutation: S308P
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: 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 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: sodium formate, PIPES pH 7.0, ammonium acetate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.24→59.75 Å / Num. obs: 198022 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.5443636046 Å2 / CC1/2: 0.992 / Net I/σ(I): 5.93
Reflection shellResolution: 2.24→2.38 Å / Num. unique obs: 8958 / CC1/2: 0.687

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Processing

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

5i6s


Resolution: 2.24847339752→59.75 Å / SU ML: 0.36997125315 / Cross valid method: FREE R-VALUE / σ(F): 1.95835266787 / Phase error: 32.0032317018
RfactorNum. reflection% reflection
Rfree0.256007360772 2808 4.97960631318 %
Rwork0.217910402858 --
obs0.219809562325 56390 97.7177812051 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.5060772505 Å2
Refinement stepCycle: LAST / Resolution: 2.24847339752→59.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9473 0 84 72 9629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008660598878049837
X-RAY DIFFRACTIONf_angle_d0.99903817592813462
X-RAY DIFFRACTIONf_chiral_restr0.05584277393631448
X-RAY DIFFRACTIONf_plane_restr0.007615372819091751
X-RAY DIFFRACTIONf_dihedral_angle_d18.42527774963346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2485-2.28720.3918643614351190.352550X-RAY DIFFRACTION92.4168975069
2.2872-2.32880.3555869217241450.3284063022942679X-RAY DIFFRACTION97.2451790634
2.3288-2.37360.3700623492261410.2990785121272709X-RAY DIFFRACTION97.2364380757
2.3736-2.42210.365645126461440.2966726043072621X-RAY DIFFRACTION97.5308641975
2.4221-2.47470.3840346256891480.2880626632432650X-RAY DIFFRACTION97.5592747559
2.4747-2.53230.2793045350341450.2723153273742658X-RAY DIFFRACTION97.2926067338
2.5323-2.59560.3379699887561140.2744603496912732X-RAY DIFFRACTION97.7335164835
2.5956-2.66580.3277881571151430.2624925202252667X-RAY DIFFRACTION97.7391304348
2.6658-2.74430.3246276148811290.2574601322992662X-RAY DIFFRACTION97.7583187391
2.7443-2.83280.2913077241991110.2577087435292737X-RAY DIFFRACTION97.8357952594
2.8328-2.93410.2793996756381450.2596087046472681X-RAY DIFFRACTION98.2614742698
2.9341-3.05160.2927407199631290.2347906662842685X-RAY DIFFRACTION98.0146290491
3.0516-3.19040.2684096400431570.2296521764142697X-RAY DIFFRACTION98.4137931034
3.1904-3.35860.2818864119691740.2216869969372695X-RAY DIFFRACTION98.2534246575
3.3586-3.5690.2549968601591540.1930138380752632X-RAY DIFFRACTION98.0295566502
3.569-3.84460.2370139093441450.192056975522714X-RAY DIFFRACTION98.6542443064
3.8446-4.23140.1940610874981330.1574020665582698X-RAY DIFFRACTION98.4353268428
4.2314-4.84340.1849689338881590.1512589568162706X-RAY DIFFRACTION98.7931034483
4.8434-6.10120.1760066508731410.1832536061452695X-RAY DIFFRACTION98.780912574
6.1012-59.750.2195462436061320.1920130013782714X-RAY DIFFRACTION98.4434451747

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