[English] 日本語
Yorodumi
- PDB-2ydp: Structure of the E242A mutant of the alpha-l-arabinofuranosidase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ydp
TitleStructure of the E242A mutant of the alpha-l-arabinofuranosidase arb93a from fusarium graminearum in complex with an iminosugar inhibitor
ComponentsEXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE
KeywordsHYDROLASE / GLYCOSYL HYDROLASE
Function / homology
Function and homology information


non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / metabolic process / metal ion binding
Similarity search - Function
Neuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
alpha-L-arabinofuranose / 1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL / Exo-1,5-alpha-L-arabinofuranobiosidase
Similarity search - Component
Biological speciesGIBBERELLA ZEAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGoddard-Borger, E.D. / Carapito, R. / Jeltsch, J.M. / Phalip, V. / Stick, R.V. / Varrot, A.
CitationJournal: Chem.Commun.(Camb.) / Year: 2011
Title: Alpha-L-Arabinofuranosylated Pyrrolidines as Arabinanase Inhibitors.
Authors: Goddard-Borger, E.D. / Carapito, R. / Jeltsch, J. / Phalip, V. / Stick, R.V. / Varrot, A.
History
DepositionMar 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references / Refinement description / Version format compliance
Revision 1.2Apr 1, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE
B: EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE
C: EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,16012
Polymers123,1903
Non-polymers9709
Water17,366964
1
A: EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3874
Polymers41,0631
Non-polymers3233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3874
Polymers41,0631
Non-polymers3233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3874
Polymers41,0631
Non-polymers3233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.930, 57.800, 91.600
Angle α, β, γ (deg.)90.14, 93.55, 114.50
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE / ALPHA-L-ARABINOFURANOSIDASE


Mass: 41063.324 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GIBBERELLA ZEAE (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B8ZY56, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-EDG / 1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL


Mass: 133.146 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11NO3
#3: Sugar ChemComp-AHR / alpha-L-arabinofuranose / alpha-L-arabinose / L-arabinose / arabinose / Arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArafaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinofuranoseCOMMON NAMEGMML 1.0
a-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 964 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 226 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 226 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 226 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 226 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 226 TO ALA
Sequence detailsTHE SEQUENCE CORRESPONDS TO THE MATURE PROTEIN ONLY. NUMBERING IS THEREFORE SHIFTED BY 16 AMINO ACIDS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.64 % / Description: NONE
Crystal growpH: 6.5
Details: 20% PEG 8000, 100 MM SODIUM CACODYLATE PH 6.5, 200 MM LISO4, 20% GLYCEROL AS CYOPROTECTANT.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.981
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 1.85→35.47 Å / Num. obs: 86184 / % possible obs: 95.2 % / Observed criterion σ(I): 1.8 / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.5
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.8 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W5N

2w5n


Resolution: 1.85→33.97 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.631 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4325 5 %RANDOM
Rwork0.171 ---
obs0.174 81852 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-1.25 Å2-0.26 Å2
2--0.28 Å2-0.5 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8550 0 57 964 9571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228916
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.96612181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98451084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62624.24375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.166151391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3871533
X-RAY DIFFRACTIONr_chiral_restr0.1010.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0226855
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.24218
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.26024
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2872
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.761.55422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3128824
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.04733494
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1694.53356
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 311 -
Rwork0.255 6060 -
obs--95.1 %

+
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