[English] 日本語
Yorodumi
- PDB-1kcd: Endopolygalacturonase I from Stereum purpureum complexed with two... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kcd
TitleEndopolygalacturonase I from Stereum purpureum complexed with two galacturonate at 1.15 A resolution.
ComponentsENDOPOLYGALACTURONASEPolygalacturonase
KeywordsHYDROLASE / BETA HELICAL STRUCTURE / GLYCOSIDE HYDROLASE / SILVER-LEAF INDUCING SUBSTANCE
Function / homology
Function and homology information


endo-polygalacturonase / polygalacturonase activity / pectin catabolic process / cell wall organization
Similarity search - Function
Polygalacturonase active site. / Glycoside hydrolase, family 28 / Glycosyl hydrolases family 28 / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
beta-D-galactofuranuronic acid / beta-D-galactopyranuronic acid / endo-polygalacturonase
Similarity search - Component
Biological speciesChondrostereum purpureum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsShimizu, T. / Nakatsu, T. / Miyairi, K. / Okuno, T. / Kato, H.
Citation
Journal: Biochemistry / Year: 2002
Title: Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
Authors: Shimizu, T. / Nakatsu, T. / Miyairi, K. / Okuno, T. / Kato, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray study of endopolygalacturonase from the pathogenic fungus Stereum purpureum
Authors: Shimizu, T. / Nakatsu, T. / Miyairi, K. / Okuno, T. / Kato, H.
#2: Journal: Eur.J.Biochem. / Year: 2000
Title: Determination of glycosylation sites, disulfide bridges, and the C-terminus of Stereum purpureum mature endopolygalacturonase I by electrospray ionization mass spectrometry
Authors: Shimizu, T. / Miyairi, K. / Okuno, T.
#3: Journal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 1998
Title: Isolation, characterization, and sugar chain structure of endoPG Ia, Ib and Ic from Stereum purpureum
Authors: Hasui, Y. / Fukui, Y. / Kikuchi, J. / Kato, N. / Miyairi, K. / Okuno, T.
History
DepositionNov 8, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 24, 2011Group: Non-polymer description
Revision 1.4Oct 14, 2015Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.0Nov 15, 2023Group: Atomic model / Category: atom_site / Item: _atom_site.occupancy

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOPOLYGALACTURONASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5196
Polymers34,6521
Non-polymers8665
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.500, 52.070, 37.230
Angle α, β, γ (deg.)72.39, 69.50, 70.54
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein ENDOPOLYGALACTURONASE / Polygalacturonase


Mass: 34652.363 Da / Num. of mol.: 1 / Fragment: residues 1-335 / Source method: isolated from a natural source / Source: (natural) Chondrostereum purpureum (fungus) / Strain: ASP-4B / References: UniProt: P79074, endo-polygalacturonase

-
Sugars , 3 types, 4 molecules

#2: Sugar ChemComp-GTK / beta-D-galactofuranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid / D-Galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalfAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactofuranuronic acidCOMMON NAMEGMML 1.0
b-D-GalfAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid / D-Galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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

-
Non-polymers , 2 types, 521 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.66 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Shimizu, T., (2001) Acta Crystallogr., Sect.D, 57, 1171.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium acetate1droppH5.0
210 mg/mlprotein1drop
350 mMsodium acetate1reservoirpH5.0
40.2 M1reservoirNaCl
512-17.5 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.6 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 1.15→12.1 Å / Num. all: 104270 / Num. obs: 104270 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 5.6 Å2 / Rsym value: 0.071 / Net I/σ(I): 6.5
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 15075 / Rsym value: 0.251 / % possible all: 96.2
Reflection
*PLUS
Num. measured all: 230114 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 96.2 % / Rmerge(I) obs: 0.251

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K5C

1k5c


Resolution: 1.15→10 Å / Num. parameters: 27121 / Num. restraintsaints: 32146 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1635 5171 4.96 %RANDOM
Rwork0.1257 ---
obs0.1276 104207 92.6 %-
all-99036 --
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2925.52
Refinement stepCycle: LAST / Resolution: 1.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 55 520 2986
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0331
X-RAY DIFFRACTIONs_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.072
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor all: 0.135 / Rfactor obs: 0.126 / Rfactor Rfree: 0.164 / Rfactor Rwork: 0.126
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.033
X-RAY DIFFRACTIONs_chiral_restr0.09

+
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