[English] 日本語
Yorodumi
- PDB-4ayr: Structure of The GH47 processing alpha-1,2-mannosidase from Caulo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ayr
TitleStructure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with noeuromycin
ComponentsMANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE
KeywordsHYDROLASE / GH47 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE / GLYCOSIDASE INHIBITION
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum mannose trimming / carbohydrate metabolic process / calcium ion binding / membrane
Similarity search - Function
ER degradation-enhancing alpha-mannosidase-like protein 1/2/3 / Glycoside hydrolase family 47 / Seven-hairpin glycosidases / Glycosyl hydrolase family 47 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Glycosyltransferase / Alpha/alpha barrel / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Mainly Alpha
Similarity search - Domain/homology
Chem-IFL / Mannosyl-oligosaccharide 1,2-alpha-mannosidase
Similarity search - Component
Biological speciesCAULOBACTER SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsThompson, A.J. / Dabin, J. / Iglesias-Fernandez, J. / Iglesias-Fernandez, A. / Dinev, Z. / Williams, S.J. / Siriwardena, A. / Moreland, C. / Hu, T.C. / Smith, D.K. ...Thompson, A.J. / Dabin, J. / Iglesias-Fernandez, J. / Iglesias-Fernandez, A. / Dinev, Z. / Williams, S.J. / Siriwardena, A. / Moreland, C. / Hu, T.C. / Smith, D.K. / Gilbert, H.J. / Rovira, C. / Davies, G.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: The Reaction Coordinate of a Bacterial Gh47 Alpha-Mannosidase: A Combined Quantum Mechanical and Structural Approach.
Authors: Thompson, A.J. / Dabin, J. / Iglesias-Fernandez, J. / Ardevol, A. / Dinev, Z. / Williams, S.J. / Bande, O. / Siriwardena, A. / Moreland, C. / Hu, T.C. / Smith, D.K. / Gilbert, H.J. / Rovira, C. / Davies, G.J.
History
DepositionJun 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,74411
Polymers50,5471
Non-polymers2,19810
Water13,043724
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.919, 143.919, 50.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2118-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE / ALPHA-1 / 2-MANNOSIDASE


Mass: 50546.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER SP. (bacteria) / Strain: K31 / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER
References: UniProt: B0SWV2, mannosyl-oligosaccharide 1,2-alpha-mannosidase

-
Non-polymers , 5 types, 734 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-IFL / (3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE / ISOFAGOMINE LACTAM


Mass: 161.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO4
#5: Chemical
ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsN-TERMINAL TRUNCATION TO REMOVE SIGNAL PEPTIDE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.2 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M AMMONIUM ACTETATE, 0.1 M BIS-TRIS PH 6.5, 22% WT/VOL PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.1→46.55 Å / Num. obs: 140945 / % possible obs: 89.6 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 32.2
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.7 / % possible all: 49.5

-
Processing

Software
NameVersionClassification
REFMAC5.7.0025refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AYQ

4ayq


Resolution: 1.1→46.6 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.449 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.10208 7105 5 %RANDOM
Rwork0.08264 ---
obs0.08362 133840 89.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.843 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.1→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 84 724 4237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023747
X-RAY DIFFRACTIONr_bond_other_d0.0010.023508
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9515093
X-RAY DIFFRACTIONr_angle_other_deg0.81638052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09922.703185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15715597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6681535
X-RAY DIFFRACTIONr_chiral_restr0.280.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02945
X-RAY DIFFRACTIONr_nbd_refined0.2750.21697
X-RAY DIFFRACTIONr_nbd_other0.1720.23345
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21816
X-RAY DIFFRACTIONr_nbtor_other0.0850.21863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0190.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3380.2162
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.58837251
X-RAY DIFFRACTIONr_sphericity_free36.7355131
X-RAY DIFFRACTIONr_sphericity_bonded7.22957755
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.129 241 -
Rwork0.117 4702 -
obs--42.45 %

+
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