[English] 日本語
Yorodumi
- PDB-2x05: Inhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x05
TitleInhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamine- configured castanospermine and an amino-australine analogue
ComponentsEXO-BETA-D-GLUCOSAMINIDASE
KeywordsHYDROLASE / EXO-BETA-D-GLUCOSAMINIDASE / GLYCOSIDE HYDROLASE / GH2 / CSXA / GLYCOSIDASE
Function / homology
Function and homology information


exo-1,4-beta-D-glucosaminidase / exo-1,4-beta-D-glucosaminidase activity / chitin catabolic process / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region
Similarity search - Function
Exo-beta-D-glucosaminidase, Ig-fold domain / Exo-beta-D-glucosaminidase/Endo-beta-mannosidase / Exo-beta-D-glucosaminidase Ig-fold domain / : / Glycosyl hydrolase 2 galactose-binding domain-like / Carbohydrate binding module (family 35) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich ...Exo-beta-D-glucosaminidase, Ig-fold domain / Exo-beta-D-glucosaminidase/Endo-beta-mannosidase / Exo-beta-D-glucosaminidase Ig-fold domain / : / Glycosyl hydrolase 2 galactose-binding domain-like / Carbohydrate binding module (family 35) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / AMINO-CASTANOSPERMINE / Exo-beta-D-glucosaminidase
Similarity search - Component
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPluvinage, B. / Ghinet, M.G. / Brzezinski, R. / Boraston, A.B. / Stubbs, K.A.
CitationJournal: Org.Biomol.Chem. / Year: 2009
Title: Inhibition of the Exo-Beta-D-Glucosaminidase Csxa by a Glucosamine-Configured Castanospermine and an Amino-Australine Analogue.
Authors: Pluvinage, B. / Ghinet, M.G. / Brzezinski, R. / Boraston, A.B. / Stubbs, K.A.
History
DepositionDec 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_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.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXO-BETA-D-GLUCOSAMINIDASE
B: EXO-BETA-D-GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,78023
Polymers221,2682
Non-polymers2,51221
Water21,7081205
1
A: EXO-BETA-D-GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,83411
Polymers110,6341
Non-polymers1,20010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EXO-BETA-D-GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,94612
Polymers110,6341
Non-polymers1,31211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.120, 121.800, 91.560
Angle α, β, γ (deg.)90.00, 90.51, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein EXO-BETA-D-GLUCOSAMINIDASE


Mass: 110633.797 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-1032
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Plasmid: PFD666 / Production host: STREPTOMYCES LIVIDANS (bacteria) / Strain (production host): TK24 / References: UniProt: Q56F26, exo-1,4-beta-D-glucosaminidase
#2: Chemical ChemComp-X05 / AMINO-CASTANOSPERMINE / (1S,6S,7R,8R,8AR)-6-AMINOOCTAHYDROINDOLIZINE-1,7,8-TRIOL


Mass: 188.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16N2O3
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1205 / 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: 2.1 Å3/Da / Density % sol: 43.32 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-3 / Wavelength: 0.97946
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 83030 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
CCP4SCALEdata scaling
MERGEINTENSITIESdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VZS

2vzs


Resolution: 2.3→43.79 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.882 / SU B: 7.232 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24816 4151 5 %RANDOM
Rwork0.18401 ---
obs0.18723 78855 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20.3 Å2
2--0.28 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13034 0 45 1205 14284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213408
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9418307
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51451708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3524.301579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.314152054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0291570
X-RAY DIFFRACTIONr_chiral_restr0.0910.22019
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110334
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.511.58473
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.943213641
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51634935
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3464.54663
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 313 -
Rwork0.235 5823 -
obs--99.84 %

+
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