[English] 日本語
Yorodumi
- PDB-5gub: Crystal structure of solute-binding protein complexed with sulfat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gub
TitleCrystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin disaccharide
ComponentsExtracellular solute-binding protein family 1
KeywordsSUGAR BINDING PROTEIN / glycosaminoglycan / ABC transporter / solute-binding protein
Function / homology
Function and homology information


: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UNSATURATED CHONDROITIN DISACCHARIDE / Extracellular solute-binding protein family 1
Similarity search - Component
Biological speciesStreptobacillus moniliformis strain DSM 12112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsOiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
Funding support Japan, 3items
OrganizationGrant numberCountry
Grants-in-Aids for Scientific Research from the Japanese Society for the Promotion of Science Japan
Mizutani Foundation for Glycoscience Japan
Danone Institute of Japan Foundation Japan
CitationJournal: Sci Rep / Year: 2017
Title: A bacterial ABC transporter enables import of mammalian host glycosaminoglycans
Authors: Oiki, S. / Mikami, B. / Maruyama, Y. / Murata, K. / Hashimoto, W.
History
DepositionAug 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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 / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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: Extracellular solute-binding protein family 1
B: Extracellular solute-binding protein family 1
C: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,82816
Polymers165,7363
Non-polymers2,09213
Water20,7531152
1
A: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9225
Polymers55,2451
Non-polymers6774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint10 kcal/mol
Surface area20270 Å2
MethodPISA
2
B: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0467
Polymers55,2451
Non-polymers8016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint9 kcal/mol
Surface area20310 Å2
MethodPISA
3
C: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8604
Polymers55,2451
Non-polymers6153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint10 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.914, 112.213, 166.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Extracellular solute-binding protein family 1


Mass: 55245.367 Da / Num. of mol.: 3 / Fragment: UNP residues 19-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptobacillus moniliformis strain DSM 12112 (bacteria)
Strain: DSM 12112 / Gene: Smon_0123 / Production host: Escherichia coli (E. coli) / References: UniProt: D1AWE0
#2: Polysaccharide 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose / UNSATURATED CHONDROITIN DISACCHARIDE


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 379.317 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with ring modification on monosaccharide components
References: UNSATURATED CHONDROITIN DISACCHARIDE
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O][a21eEA-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-4-deoxy-GlcpA]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 1162 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1152 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium chloride, 0.1M MES (pH 6.0), 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 143362 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.8
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.31

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y3N

1y3n


Resolution: 1.78→41.569 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 6983 4.88 %
Rwork0.174 --
obs0.1756 143057 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→41.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11465 0 132 1152 12749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711924
X-RAY DIFFRACTIONf_angle_d1.06516156
X-RAY DIFFRACTIONf_dihedral_angle_d13.9344483
X-RAY DIFFRACTIONf_chiral_restr0.0451718
X-RAY DIFFRACTIONf_plane_restr0.0052067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7803-1.80050.2872240.20624328X-RAY DIFFRACTION97
1.8005-1.82170.23922190.19854497X-RAY DIFFRACTION99
1.8217-1.84390.25782490.19314463X-RAY DIFFRACTION100
1.8439-1.86730.26232100.18944489X-RAY DIFFRACTION100
1.8673-1.89180.23342260.18284511X-RAY DIFFRACTION100
1.8918-1.91780.21612290.17714476X-RAY DIFFRACTION100
1.9178-1.94520.25222390.18134498X-RAY DIFFRACTION100
1.9452-1.97420.21092430.17334468X-RAY DIFFRACTION100
1.9742-2.0050.20552330.17364538X-RAY DIFFRACTION100
2.005-2.03790.19132080.1744511X-RAY DIFFRACTION100
2.0379-2.07310.22422270.17074486X-RAY DIFFRACTION100
2.0731-2.11070.19172210.17224523X-RAY DIFFRACTION100
2.1107-2.15130.20872310.17284517X-RAY DIFFRACTION100
2.1513-2.19530.21842490.17964493X-RAY DIFFRACTION100
2.1953-2.2430.22592250.17474519X-RAY DIFFRACTION100
2.243-2.29520.22772310.1774542X-RAY DIFFRACTION100
2.2952-2.35250.22392270.17774538X-RAY DIFFRACTION100
2.3525-2.41610.19562370.1754508X-RAY DIFFRACTION100
2.4161-2.48720.23282390.18184535X-RAY DIFFRACTION100
2.4872-2.56750.2392310.1874536X-RAY DIFFRACTION100
2.5675-2.65930.23322340.18164524X-RAY DIFFRACTION100
2.6593-2.76570.2162240.18574570X-RAY DIFFRACTION100
2.7657-2.89160.21682310.18714525X-RAY DIFFRACTION100
2.8916-3.0440.21282420.18514586X-RAY DIFFRACTION100
3.044-3.23460.19682230.18454556X-RAY DIFFRACTION100
3.2346-3.48420.20922550.18374591X-RAY DIFFRACTION100
3.4842-3.83460.20582350.16734611X-RAY DIFFRACTION100
3.8346-4.3890.16272420.15134619X-RAY DIFFRACTION100
4.389-5.52760.16112510.14414653X-RAY DIFFRACTION100
5.5276-41.58030.17852480.15634863X-RAY DIFFRACTION100

+
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