[English] 日本語
Yorodumi
- PDB-4zze: Raffinose and panose binding protein from Bifidobacterium animali... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zze
TitleRaffinose and panose binding protein from Bifidobacterium animalis subsp. lactis Bl-04, bound with panose
ComponentsSugar binding protein of ABC transporter system
KeywordsTRANSPORT PROTEIN / Panose / ABC transporter / complex
Function / homology
Function and homology information


transmembrane transport / metal ion binding
Similarity search - Function
Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sugar binding protein of ABC transporter system / :
Similarity search - Component
Biological speciesBifidobacterium animalis subsp. lactis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsFredslund, F. / Ejby, M. / Andersen, J.M. / Slotboom, D.J. / Hachem, M.A.
CitationJournal: J. Biol. Chem. / Year: 2016
Title: An ATP Binding Cassette Transporter Mediates the Uptake of alpha-(1,6)-Linked Dietary Oligosaccharides in Bifidobacterium and Correlates with Competitive Growth on These Substrates.
Authors: Ejby, M. / Fredslund, F. / Andersen, J.M. / Vujicic Zagar, A. / Henriksen, J.R. / Andersen, T.L. / Svensson, B. / Slotboom, D.J. / Abou Hachem, M.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
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 / database_PDB_caveat / 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_validate_chiral / 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.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 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: Sugar binding protein of ABC transporter system
B: Sugar binding protein of ABC transporter system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,79817
Polymers88,4292
Non-polymers1,36915
Water17,781987
1
A: Sugar binding protein of ABC transporter system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9119
Polymers44,2141
Non-polymers6978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sugar binding protein of ABC transporter system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8878
Polymers44,2141
Non-polymers6737
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.880, 91.330, 142.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Sugar binding protein of ABC transporter system


Mass: 44214.480 Da / Num. of mol.: 2 / Fragment: UNP residues 46-437
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium animalis subsp. lactis (bacteria)
Strain: Bl-04 / DGCC2908 / RB 4825 / SD5219 / Gene: Balac_1599 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DE3 / References: UniProt: C6A9Y6, UniProt: A0A1A9TAB8*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 987 / 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: 2.01 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25% PEG 4000, 0.8M magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97734 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97734 Å / Relative weight: 1
ReflectionResolution: 1.76→23.2 Å / Num. obs: 71009 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 16.58 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.098 / Χ2: 0.921 / Net I/σ(I): 10.64 / Num. measured all: 241213
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.76-1.813.20.670.6612.0516737521151730.79499.3
1.81-1.860.7650.5452.4716863511550820.65299.4
1.86-1.910.8290.4453.1617416497149440.52799.5
1.91-1.970.8610.3623.7416748481547930.42999.5
1.97-2.030.9110.2874.5816105469846720.3499.4
2.03-2.10.9380.2285.5315145450344520.27198.9
2.1-2.180.9530.1836.4313849438643350.2298.8
2.18-2.270.9670.1577.7214229423142070.18899.4
2.27-2.370.9780.1319.0214222404540310.15599.7
2.37-2.490.9830.1110.5813507388338610.1399.4
2.49-2.620.9870.111.2512723369336670.11899.3
2.62-2.780.990.07913.3211376350934480.09498.3
2.78-2.970.9930.06615.8911205330332880.07899.5
2.97-3.210.9960.05419.5410976308730720.06399.5
3.21-3.520.9970.04123.479929284828400.04999.7
3.52-3.940.9980.03626.488673261525760.04398.5
3.94-4.540.9980.0328.267382230022670.03598.6
4.54-5.570.9990.02828.576782197919570.03398.9
5.57-7.870.9980.03124.944822156215230.03797.5
7.870.9990.02628.1325249348210.03187.9

-
Processing

Software
NameVersionClassification
xia2data reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZZA

4zza


Resolution: 1.76→23.113 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 3538 4.99 %Random selection
Rwork0.1578 67402 --
obs0.1602 70940 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.29 Å2 / Biso mean: 21.2313 Å2 / Biso min: 4.52 Å2
Refinement stepCycle: final / Resolution: 1.76→23.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5941 0 81 987 7009
Biso mean--14.82 28.94 -
Num. residues----753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056255
X-RAY DIFFRACTIONf_angle_d0.9598506
X-RAY DIFFRACTIONf_chiral_restr0.041941
X-RAY DIFFRACTIONf_plane_restr0.0051110
X-RAY DIFFRACTIONf_dihedral_angle_d13.9062338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.76-1.78410.26341310.25112656278799
1.7841-1.80960.28151330.241326692802100
1.8096-1.83660.27811510.2332667281899
1.8366-1.86530.28961420.220726642806100
1.8653-1.89580.26781360.213526922828100
1.8958-1.92850.25121500.20182647279799
1.9285-1.96360.25911490.19392664281399
1.9636-2.00130.24841330.180426792812100
2.0013-2.04210.22971240.17672702282699
2.0421-2.08650.22761520.17082671282399
2.0865-2.1350.22421350.16232638277399
2.135-2.18840.23211460.16272689283599
2.1884-2.24750.20581250.158926822807100
2.2475-2.31360.22381510.14822704285599
2.3136-2.38820.18141390.145926932832100
2.3882-2.47340.17971410.141726912832100
2.4734-2.57230.23591420.1482685282799
2.5723-2.68920.19471460.1482701284799
2.6892-2.83080.22951450.1532655280098
2.8308-3.00780.16991390.154427492888100
3.0078-3.23940.22821470.14682731287899
3.2394-3.56440.17561380.136927472885100
3.5644-4.07770.1491440.12062709285398
4.0777-5.12820.14251510.12422788293999
5.1282-23.1150.21471480.17862829297797

+
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