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- PDB-6kvh: The mutant crystal structure of endo-polygalacturonase (T284A) fr... -

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Basic information

Entry
Database: PDB / ID: 6kvh
TitleThe mutant crystal structure of endo-polygalacturonase (T284A) from Talaromyces leycettanus JCM 12802
Componentsendo-polygalacturonasePolygalacturonase
KeywordsHYDROLASE / endo-polygalacturonase
Function / homologyalpha-D-mannopyranose
Function and homology information
Biological speciesTalaromyces leycettanus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsTu, T. / Wang, Z. / Luo, H. / 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 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: endo-polygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6103
Polymers35,2081
Non-polymers4012
Water7,062392
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint5 kcal/mol
Surface area12080 Å2
Unit cell
Length a, b, c (Å)44.361, 68.562, 88.276
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 / Polygalacturonase


Mass: 35208.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces leycettanus (fungus) / Strain: JCM 12802 / Production host: Komagataella phaffii GS115 (fungus)
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M citric acid (pH 3.5), 25% (w/v) polyethylene glycol 3350

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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: 1.198→25.93 Å / Num. obs: 80946 / % possible obs: 94.95 % / Redundancy: 1.3 % / Biso Wilson estimate: 15.24 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01 / Rpim(I) all: 0.01 / Rrim(I) all: 0.01146 / Net I/σ(I): 15.72
Reflection shellResolution: 1.198→1.241 Å / Redundancy: 1 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 3.94 / Num. unique obs: 6194 / CC1/2: 1 / Rpim(I) all: 0.01 / Rrim(I) all: 0.01 / % possible all: 73.61

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KVE

6kve


Resolution: 1.2→25.93 Å / SU ML: 0.0843 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.5573
RfactorNum. reflection% reflection
Rfree0.1497 4108 5.08 %
Rwork0.1239 --
obs0.1253 80926 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.12 Å2
Refinement stepCycle: LAST / Resolution: 1.2→25.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 25 392 2823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00442682
X-RAY DIFFRACTIONf_angle_d0.79553708
X-RAY DIFFRACTIONf_chiral_restr0.0871443
X-RAY DIFFRACTIONf_plane_restr0.0053491
X-RAY DIFFRACTIONf_dihedral_angle_d3.21281809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.208990.12391749X-RAY DIFFRACTION64.77
1.21-1.230.15991120.12392087X-RAY DIFFRACTION74.77
1.23-1.240.16191230.12392241X-RAY DIFFRACTION82.03
1.24-1.260.16731110.12392424X-RAY DIFFRACTION87.53
1.26-1.280.16951270.12392562X-RAY DIFFRACTION91.71
1.28-1.290.171490.12392594X-RAY DIFFRACTION94.62
1.29-1.310.18311410.12392591X-RAY DIFFRACTION94.66
1.31-1.330.16751470.12392664X-RAY DIFFRACTION95.94
1.33-1.360.1591550.12392637X-RAY DIFFRACTION96.34
1.36-1.380.17081440.12282643X-RAY DIFFRACTION95.77
1.38-1.40.13531310.11322690X-RAY DIFFRACTION97.31
1.4-1.430.1631410.11212714X-RAY DIFFRACTION96.45
1.43-1.460.14011450.11072677X-RAY DIFFRACTION98.19
1.46-1.490.13631530.11012718X-RAY DIFFRACTION97.82
1.49-1.530.14031430.11472679X-RAY DIFFRACTION96.94
1.53-1.570.13711640.10282734X-RAY DIFFRACTION98.87
1.57-1.610.14151490.10572711X-RAY DIFFRACTION98.21
1.61-1.660.13281350.10592731X-RAY DIFFRACTION97.98
1.66-1.710.14171420.11462752X-RAY DIFFRACTION98.34
1.71-1.770.15171220.12342806X-RAY DIFFRACTION99.05
1.77-1.840.13821480.12212744X-RAY DIFFRACTION99.04
1.84-1.920.14491550.1222765X-RAY DIFFRACTION98.85
1.92-2.030.15721340.11962783X-RAY DIFFRACTION99.05
2.03-2.150.14351440.11982807X-RAY DIFFRACTION99.53
2.15-2.320.15531500.1222801X-RAY DIFFRACTION99.63
2.32-2.550.14681490.13222824X-RAY DIFFRACTION99.56
2.55-2.920.14151360.12842855X-RAY DIFFRACTION99.73
2.92-3.680.15081970.11942838X-RAY DIFFRACTION99.97
3.68-100.15471620.13192997X-RAY DIFFRACTION99.65
Refinement TLS params.Method: refined / Origin x: 55.6251 Å / Origin y: 7.6311 Å / Origin z: 98.9514 Å
111213212223313233
T0.1781 Å20.0052 Å20.0016 Å2-0.1687 Å20.0101 Å2--0.0839 Å2
L0.3324 °20.0316 °2-0.0205 °2-0.4502 °20.0425 °2--0.3717 °2
S-0.0082 Å °0.0082 Å °0.0065 Å °0.0208 Å °0.0123 Å °0.0031 Å °-0.0137 Å °0.0046 Å °-0.0099 Å °
Refinement TLS groupSelection details: all

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