[English] 日本語
Yorodumi
- PDB-1k7c: Rhamnogalacturonan acetylesterase with seven N-linked carbohydrat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k7c
TitleRhamnogalacturonan acetylesterase with seven N-linked carbohydrate residues distributed at two N-glycosylation sites refined at 1.12 A resolution
Componentsrhamnogalacturonan acetylesterase
KeywordsHYDROLASE / N-linked glycosylation / SGNH-hydrolase
Function / homology
Function and homology information


rhamnogalacturonan acetylesterase / hydrolase activity, acting on ester bonds
Similarity search - Function
Rhamnogalacturonan acetylesterase RhgT-like / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Rhamnogalacturonan acetylesterase
Similarity search - Component
Biological speciesAspergillus aculeatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.12 Å
AuthorsMolgaard, A. / Larsen, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: A branched N-linked glycan at atomic resolution in the 1.12 A structure of rhamnogalacturonan acetylesterase.
Authors: Molgaard, A. / Larsen, S.
#1: Journal: To be Published
Title: Rhamnogalacturonan acetylesterase, a member of the SGNH-hydrolase family.
Authors: Molgaard, A.
#2: Journal: Structure / Year: 2000
Title: Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases.
Authors: Molgaard, A. / Kauppinen, S. / Larsen, S.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray diffraction studies of the heterogeneously glycosylated enzyme rhamnogalacturonan acetylesterase from Aspergillus aculeatus.
Authors: Molgaard, A. / Petersen, J.F.W. / Kauppinen, S. / Dalboge, H. / Johnsen, A.H. / Poulsen, J.-C.N. / Larsen, S.
#4: Journal: J.Biol.Chem. / Year: 1995
Title: Molecular cloning and characterization of a rhamnogalacturonan acetylesterase from Aspergillus aculeatus.
Authors: Kauppinen, S. / Christgau, S. / Kofod, L.V. / Halkier, T. / Dorreich, K. / Dalboge, H.
History
DepositionOct 19, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / software / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
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 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: rhamnogalacturonan acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3017
Polymers24,6231
Non-polymers1,6786
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.170, 56.920, 71.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein rhamnogalacturonan acetylesterase


Mass: 24622.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus aculeatus (mold) / Plasmid: PHD464 / Production host: Aspergillus oryzae (mold) / Strain (production host): A1560 / References: GenBank: 1004217, UniProt: Q00017*PLUS
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}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.: 1
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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Li2SO4, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: Molgaard, A., (1998) Acta Crystallogr., Sect.D, 54, 1026.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.4 M1reservoiror 1.4M (NH4)2SO4Li2SO4
20.1 Msodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1024 / Wavelength: 1.1024 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1024 Å / Relative weight: 1
ReflectionResolution: 1.12→38 Å / Num. all: 644629 / Num. obs: 644629 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.12→1.14 Å / Rmerge(I) obs: 0.37 / % possible all: 82.1
Reflection
*PLUS
Num. obs: 80624 / Num. measured all: 644629 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 82.1 % / Rmerge(I) obs: 0.37

-
Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MIR
Starting model: 1DEO

1deo


Resolution: 1.12→40 Å / Num. parameters: 19970 / Num. restraintsaints: 24756 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1344 4019 5 %RANDOM
Rwork0.1033 ---
all0.1095 80568 --
obs0.1045 71116 97.8 %-
Refine analyzeNum. disordered residues: 16 / Occupancy sum hydrogen: 1706 / Occupancy sum non hydrogen: 2123.96
Refinement stepCycle: LAST / Resolution: 1.12→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 106 329 2170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0.024
X-RAY DIFFRACTIONs_from_restr_planes0.0264
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.106
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.195
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.022
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.103
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 38 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.11 / Rfactor obs: 0.103 / Rfactor Rfree: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.026
X-RAY DIFFRACTIONs_chiral_restr0.079

+
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