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- PDB-6kve: Crystal structure of a GH28 endo-polygalacturonase from Talaromyc... -

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Basic information

Entry
Database: PDB / ID: 6kve
TitleCrystal structure of a GH28 endo-polygalacturonase from Talaromyces leycettanus JCM 12802
ComponentsEndo-polygalacturonase
KeywordsHYDROLASE / Thermophilic / Endo-polygalacturonase
Biological speciesTalaromyces leycettanus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.32 Å
AuthorsTu, T. / Hakulinen, N. / Yao, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31702145 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Structural Insights into the Mechanisms Underlying the Kinetic Stability of GH28 Endo-Polygalacturonase.
Authors: Tu, T. / Wang, Z. / Luo, Y. / Li, Y. / Su, X. / Wang, Y. / Zhang, J. / Rouvinen, J. / Yao, B. / Hakulinen, N. / Luo, H.
History
DepositionSep 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Endo-polygalacturonase


Theoretical massNumber of molelcules
Total (without water)35,2381
Polymers35,2381
Non-polymers00
Water8,521473
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint5 kcal/mol
Surface area12200 Å2
Unit cell
Length a, b, c (Å)44.175, 67.823, 87.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Endo-polygalacturonase


Mass: 35238.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces leycettanus (fungus) / Production host: Komagataella phaffii GS115 (fungus)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1 M citrate buffer (pH 4.8), 28% (w/v) polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→53.72 Å / Num. obs: 60589 / % possible obs: 95.83 % / Redundancy: 3.7 % / Biso Wilson estimate: 11.94 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.08757 / Rpim(I) all: 0.05173 / Rrim(I) all: 0.1027 / Net I/σ(I): 6.63
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.7499 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 5346 / CC1/2: 0.528 / Rpim(I) all: 0.4617 / Rrim(I) all: 0.8882 / % possible all: 84.93

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.32→53.72 Å / SU ML: 0.2158 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1827
RfactorNum. reflection% reflection
Rfree0.2197 2948 4.88 %
Rwork0.1596 --
obs0.1626 60352 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.17 Å2
Refinement stepCycle: LAST / Resolution: 1.32→53.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 25 473 2907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052584
X-RAY DIFFRACTIONf_angle_d0.77483556
X-RAY DIFFRACTIONf_chiral_restr0.085432
X-RAY DIFFRACTIONf_plane_restr0.0049462
X-RAY DIFFRACTIONf_dihedral_angle_d3.62961346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.340.35921280.27572218X-RAY DIFFRACTION78.28
1.34-1.360.30211150.26692550X-RAY DIFFRACTION90.89
1.36-1.390.37171260.26752750X-RAY DIFFRACTION96.67
1.39-1.420.34031180.26772749X-RAY DIFFRACTION97.32
1.42-1.440.34791410.25982753X-RAY DIFFRACTION97.61
1.44-1.480.32811600.23662724X-RAY DIFFRACTION97.17
1.48-1.510.28521510.21932763X-RAY DIFFRACTION98.75
1.51-1.550.31341460.19772701X-RAY DIFFRACTION95.76
1.55-1.590.28181210.21562774X-RAY DIFFRACTION97.87
1.59-1.640.34971400.20882804X-RAY DIFFRACTION98.4
1.64-1.690.25691270.22142819X-RAY DIFFRACTION99.03
1.69-1.750.28561480.21762776X-RAY DIFFRACTION98.75
1.75-1.820.27041220.19582749X-RAY DIFFRACTION95.92
1.82-1.90.2771450.17462795X-RAY DIFFRACTION98.62
1.9-20.2281490.16122837X-RAY DIFFRACTION98.87
2-2.130.2031310.13512823X-RAY DIFFRACTION98.7
2.13-2.290.17761590.11682737X-RAY DIFFRACTION96.57
2.29-2.520.16431700.11892774X-RAY DIFFRACTION96.71
2.52-2.890.18291670.12012779X-RAY DIFFRACTION97.1
2.89-3.640.17321550.11892733X-RAY DIFFRACTION93.4
Refinement TLS params.Method: refined / Origin x: 55.474 Å / Origin y: 7.3858 Å / Origin z: 98.65 Å
111213212223313233
T0.1268 Å20.0051 Å20.001 Å2-0.1089 Å20.0165 Å2--0.1142 Å2
L0.2867 °20.0858 °20.0423 °2-0.5296 °20.1136 °2--0.3353 °2
S-0.0066 Å °0.004 Å °-0.0016 Å °-0.014 Å °0.008 Å °0.0007 Å °-0.0061 Å °0.0044 Å °-0.0034 Å °
Refinement TLS groupSelection details: all

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