[English] 日本語
Yorodumi
- PDB-4r74: Structure of the periplasmic binding protein AfuA from Actinobaci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r74
TitleStructure of the periplasmic binding protein AfuA from Actinobacillus pleuropneumoniae (exogenous fructose-6-phosphate bound)
ComponentsABC-type Fe3+ transport system, periplasmic component
KeywordsTRANSPORT PROTEIN / ABC transporter / sugar transporter / glucose-6-phosphate / fructose-6-phosphate / sedoheptulose-7-phosphate
Function / homology
Function and homology information


thiamine binding / thiamine transport / thiamine pyrophosphate binding / outer membrane-bounded periplasmic space
Similarity search - Function
Bacterial extracellular solute-binding protein / Ferric binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-fructofuranose / ABC-type Fe3+ transport system, periplasmic component
Similarity search - Component
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSit, B. / Calmettes, C. / Moraes, T.F.
CitationJournal: Plos Pathog. / Year: 2015
Title: Active Transport of Phosphorylated Carbohydrates Promotes Intestinal Colonization and Transmission of a Bacterial Pathogen.
Authors: Sit, B. / Crowley, S.M. / Bhullar, K. / Lai, C.C. / Tang, C. / Hooda, Y. / Calmettes, C. / Khambati, H. / Ma, C. / Brumell, J.H. / Schryvers, A.B. / Vallance, B.A. / Moraes, T.F.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC-type Fe3+ transport system, periplasmic component
B: ABC-type Fe3+ transport system, periplasmic component
C: ABC-type Fe3+ transport system, periplasmic component
D: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,70632
Polymers141,5684
Non-polymers3,13828
Water17,276959
1
A: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0206
Polymers35,3921
Non-polymers6295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3199
Polymers35,3921
Non-polymers9278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2979
Polymers35,3921
Non-polymers9058
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0698
Polymers35,3921
Non-polymers6777
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.202, 96.988, 145.075
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
ABC-type Fe3+ transport system, periplasmic component / AfuA


Mass: 35391.980 Da / Num. of mol.: 4 / Fragment: UNP residues 28-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria)
Gene: afuA, APL_1446 / Production host: Escherichia coli (E. coli) / References: UniProt: A3N294
#2: Sugar
ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 983 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium chloride, 0.1 M Tris, pH 6.5, 25% PEG3350, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.93→48.494 Å / Num. all: 89478 / Num. obs: 89478 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 18.89 Å2 / Rsym value: 0.131 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.93-2.037.50.8170.90.817199.9
2.03-2.167.60.5131.50.5131100
2.16-2.317.60.3432.20.3431100
2.31-2.497.60.2530.251100
2.49-2.737.60.1844.10.1841100
2.73-3.057.60.1216.30.1211100
3.05-3.527.60.07310.20.0731100
3.52-4.317.40.04715.30.0471100
4.31-6.17.40.03917.40.0391100
6.1-48.4947.50.03320.40.033199.9

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→48.494 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 4485 5.01 %
Rwork0.1514 --
obs0.154 89444 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.9459 Å2
Refinement stepCycle: LAST / Resolution: 1.93→48.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9919 0 199 959 11077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810447
X-RAY DIFFRACTIONf_angle_d1.12514121
X-RAY DIFFRACTIONf_dihedral_angle_d16.1843928
X-RAY DIFFRACTIONf_chiral_restr0.0451534
X-RAY DIFFRACTIONf_plane_restr0.0051793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.95150.25571720.21582801X-RAY DIFFRACTION100
1.9515-1.97450.25531430.21812864X-RAY DIFFRACTION100
1.9745-1.99860.27651420.20532805X-RAY DIFFRACTION100
1.9986-2.02390.25661720.19742786X-RAY DIFFRACTION100
2.0239-2.05050.24981590.19122833X-RAY DIFFRACTION100
2.0505-2.07860.23551540.18382816X-RAY DIFFRACTION100
2.0786-2.10830.2461480.17772783X-RAY DIFFRACTION100
2.1083-2.13980.24741470.17152817X-RAY DIFFRACTION100
2.1398-2.17320.25641410.17152874X-RAY DIFFRACTION100
2.1732-2.20880.22611370.17252811X-RAY DIFFRACTION100
2.2088-2.24690.22451200.16372837X-RAY DIFFRACTION100
2.2469-2.28780.22661400.1642873X-RAY DIFFRACTION100
2.2878-2.33180.23151550.16062771X-RAY DIFFRACTION100
2.3318-2.37940.2261600.16212830X-RAY DIFFRACTION100
2.3794-2.43110.21661350.1592836X-RAY DIFFRACTION100
2.4311-2.48760.19851480.15752820X-RAY DIFFRACTION100
2.4876-2.54990.22431360.15712879X-RAY DIFFRACTION100
2.5499-2.61880.21231350.15112791X-RAY DIFFRACTION100
2.6188-2.69580.22821510.15082861X-RAY DIFFRACTION100
2.6958-2.78290.19431310.15022828X-RAY DIFFRACTION100
2.7829-2.88230.22591550.15182870X-RAY DIFFRACTION100
2.8823-2.99770.2241300.15032797X-RAY DIFFRACTION100
2.9977-3.13410.20011570.15022842X-RAY DIFFRACTION100
3.1341-3.29930.19311600.14422839X-RAY DIFFRACTION100
3.2993-3.5060.17531590.13772802X-RAY DIFFRACTION100
3.506-3.77660.17731610.1262829X-RAY DIFFRACTION100
3.7766-4.15640.16571520.11712848X-RAY DIFFRACTION100
4.1564-4.75740.14281530.12382880X-RAY DIFFRACTION100
4.7574-5.99210.17251820.13832808X-RAY DIFFRACTION100
5.9921-48.50930.17041500.14542928X-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://pdbjlvh1.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