[English] 日本語
Yorodumi
- PDB-5aza: Crystal structure of MBP-sAglB fusion protein with a 20-residue s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aza
TitleCrystal structure of MBP-sAglB fusion protein with a 20-residue spacer in the connector helix
ComponentsMaltose-binding periplasmic protein,Oligosaccharyl transferase stt3 subunit related protein
KeywordsSUGAR BINDING PROTEIN / TRANSFERASE / Fusion protein
Function / homology
Function and homology information


dolichyl-phosphooligosaccharide-protein glycotransferase / oligosaccharyl transferase activity / : / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport ...dolichyl-phosphooligosaccharide-protein glycotransferase / oligosaccharyl transferase activity / : / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / metal ion binding / membrane / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3020 / Immunoglobulin-like - #3030 / Oligosaccharyltransferase, peripheral 2 domain / Oligosaccharyltransferase insert domain / : / Oligosaccharyltransferase Peripheral 2 domain / Oligosaccharyltransferase Insert domain / Oligosaccharyl transferase, Peripheral 1 domain / : / Oligosaccharyl transferase, STT3 subunit ...Immunoglobulin-like - #3020 / Immunoglobulin-like - #3030 / Oligosaccharyltransferase, peripheral 2 domain / Oligosaccharyltransferase insert domain / : / Oligosaccharyltransferase Peripheral 2 domain / Oligosaccharyltransferase Insert domain / Oligosaccharyl transferase, Peripheral 1 domain / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-maltose / dolichyl-phosphooligosaccharide-protein glycotransferase / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Pyrococcus furiosus COM1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsMatsuoka, R. / Kohda, D.
CitationJournal: Protein Sci. / Year: 2016
Title: Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.
Authors: Matsuoka, R. / Shimada, A. / Komuro, Y. / Sugita, Y. / Kohda, D.
History
DepositionSep 27, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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: Maltose-binding periplasmic protein,Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5023
Polymers97,1201
Non-polymers3822
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.468, 100.467, 140.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Maltose-binding periplasmic protein,Oligosaccharyl transferase stt3 subunit related protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 97119.969 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-394,UNP RESIDUES 491-967 / Mutation: A312V
Source method: isolated from a genetically manipulated source
Details: The fusion protein of 1-369 Maltose binding protein, 370-389 Linker 390-866 AglB (C-terminal domain, UNP residue 491-967), and 867-872 HisTag
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Pyrococcus furiosus COM1 (archaea)
Strain: K12 / Gene: malE, b4034, JW3994, PFC_07420 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: I6V0B8
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG 10000, 0.1M Ammounium phosphate, 0.1M Bis-Tris pH5.5, 1.0M Lithium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 57642 / % possible obs: 100 % / Redundancy: 12 % / Net I/σ(I): 18.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF, 2ZAI

1anf

2zai


Resolution: 2.08→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.149 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24821 2914 5.1 %RANDOM
Rwork0.19576 ---
obs0.19845 54578 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6551 0 24 126 6701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.026761
X-RAY DIFFRACTIONr_bond_other_d0.0010.026441
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.9699185
X-RAY DIFFRACTIONr_angle_other_deg0.898314871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2235841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23324.983299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.043151139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5471526
X-RAY DIFFRACTIONr_chiral_restr0.1250.21019
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021478
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_it3.2973.6953361
X-RAY DIFFRACTIONr_mcbond_other3.2973.6943360
X-RAY DIFFRACTIONr_mcangle_it4.4145.5194203
X-RAY DIFFRACTIONr_mcangle_other4.4145.524204
X-RAY DIFFRACTIONr_scbond_it4.2094.1123400
X-RAY DIFFRACTIONr_scbond_other4.2084.1123400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2935.9734983
X-RAY DIFFRACTIONr_long_range_B_refined8.06729.8387619
X-RAY DIFFRACTIONr_long_range_B_other8.06929.837596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.077→2.131 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 213 -
Rwork0.25 3870 -
obs--97.96 %

+
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