[English] 日本語
Yorodumi
- PDB-6kvh: The mutant crystal structure of endo-polygalacturonase (T284A) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kvh
TitleThe mutant crystal structure of endo-polygalacturonase (T284A) from Talaromyces leycettanus JCM 12802
Componentsendo-polygalacturonase
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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein endo-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


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more