[English] 日本語
Yorodumi
- PDB-5m1z: STRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A FROM FUSARIUM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m1z
TitleSTRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A FROM FUSARIUM GRAMINEARUM IN COMPLEX WITH AN hydroximolactone INHIBITOR
ComponentsExo-1,5-alpha-L-arabinofuranobiosidase
KeywordsHYDROLASE / arabinofuramisodase / inhibitor / complex
Function / homologynon-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / Neuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta / metal ion binding / : / Exo-1,5-alpha-L-arabinofuranobiosidase
Function and homology information
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVarrot, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research CouncilAPP1073250 Australia
CitationJournal: Chembiochem / Year: 2017
Title: Exploiting sp(2) -Hybridisation in the Development of Potent 1,5-alpha-l-Arabinanase Inhibitors.
Authors: Coyle, T. / Debowski, A.W. / Varrot, A. / Stubbs, K.A.
History
DepositionOct 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _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_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,27113
Polymers41,1211
Non-polymers1,14912
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-83 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.222, 105.222, 140.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-510-

MN

21A-602-

HOH

31A-789-

HOH

41A-839-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Exo-1,5-alpha-L-arabinofuranobiosidase


Mass: 41121.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE DEPOSITED SEQUENCE IS FROM THE MATURE PROTEIN. OUR NUMBERING INCLUDE THE PEPTIDE SIGNAL AND IS SWITCHED BY 16 AMINO ACIDs
Source: (gene. exp.) Gibberella zeae (fungus) / Gene: arb93a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B8ZY56, non-reducing end alpha-L-arabinofuranosidase
#2: Polysaccharide alpha-L-arabinofuranose-(1-5)-(Z)-L-Arabinonhydroximo-1,4-lactone


Type: oligosaccharide / Mass: 295.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[A211h_1-4_1*=NO][a211h-1a_1-4]/1-2/a5-b1WURCSPDB2Glycan 1.1.0
[][<O1>]{[(1+1)][a-L-Araf1N]{[(5+1)][a-L-Araf]{}}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 289 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.38 Å3/Da / Density % sol: 48.29 % / Description: diamond
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 40% peg550MME 0.1M mes 6.5 0.2M MnSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.12713 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2→35.06 Å / Num. obs: 26709 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimless0.3.6data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YDT

2ydt


Resolution: 2→35.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.556 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1402 5.3 %RANDOM
Rwork0.146 ---
obs0.148 25290 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2→35.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 59 278 3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022976
X-RAY DIFFRACTIONr_bond_other_d0.0020.022681
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9714068
X-RAY DIFFRACTIONr_angle_other_deg0.99436209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1055360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39224.24125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12915442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4071511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02658
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4841.8691440
X-RAY DIFFRACTIONr_mcbond_other1.4711.8671439
X-RAY DIFFRACTIONr_mcangle_it2.2422.7921800
X-RAY DIFFRACTIONr_mcangle_other2.2442.7941801
X-RAY DIFFRACTIONr_scbond_it2.1522.1091536
X-RAY DIFFRACTIONr_scbond_other2.1522.1091536
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2843.0682269
X-RAY DIFFRACTIONr_long_range_B_refined4.96122.6243368
X-RAY DIFFRACTIONr_long_range_B_other4.85222.4223329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 93 -
Rwork0.183 1849 -
obs--99.69 %

+
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