[English] 日本語
Yorodumi
- PDB-4r72: Structure of the periplasmic binding protein AfuA from Actinobaci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r72
TitleStructure of the periplasmic binding protein AfuA from Actinobacillus pleuropneumoniae (apo form)
ComponentsABC-type Fe3+ transport system, periplasmic component
KeywordsTRANSPORT PROTEIN / ABC transporter / sugar transporter / glucose-6-phosphate / fructose-6-phosphate / sedoheptulose-7-phosphate
Function / homologyBacterial extracellular solute-binding protein / Ferric binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / DI(HYDROXYETHYL)ETHER / ABC-type Fe3+ transport system, periplasmic component
Function and homology information
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,1169
Polymers35,3921
Non-polymers7248
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.950, 80.820, 126.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-690-

HOH

21A-694-

HOH

31A-718-

HOH

41A-727-

HOH

51A-849-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 35391.980 Da / Num. of mol.: 1 / 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

-
Non-polymers , 5 types, 433 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M magnesium chloride, 0.1 M MES/NaOH, pH 6.0, 27.5% PEG3350, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD
RadiationMonochromator: ACCEL/BRUKER double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→47.095 Å / Num. obs: 38225 / Biso Wilson estimate: 18.12 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.6-1.65178.8
1.65-1.71190.7
1.71-1.77198.4
1.77-1.85199.9
1.85-1.931100
1.93-2.02199.5
2.02-2.13199.9
2.13-2.261100
2.26-2.421100
2.41-2.611100
2.61-2.86199.8
2.86-3.2199.9
3.2-3.691100
3.69-4.52199.9
4.52-6.4199.9
6.4-47.1199.9

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.095 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 19.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 1912 5 %
Rwork0.1589 --
obs0.1609 38225 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.77 Å2 / Biso mean: 23.093 Å2 / Biso min: 9.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 46 425 2944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122666
X-RAY DIFFRACTIONf_angle_d1.6353618
X-RAY DIFFRACTIONf_chiral_restr0.091400
X-RAY DIFFRACTIONf_plane_restr0.007463
X-RAY DIFFRACTIONf_dihedral_angle_d14.1021019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.24821060.18252017212377
1.64-1.68440.24131210.19182301242287
1.6844-1.73390.23361330.17872511264495
1.7339-1.78990.25221390.178326472786100
1.7899-1.85390.22181380.170826312769100
1.8539-1.92810.21681410.17512663280499
1.9281-2.01590.20211380.162226262764100
2.0159-2.12220.21281400.156826522792100
2.1222-2.25510.1861400.158326792819100
2.2551-2.42920.23221400.164426502790100
2.4292-2.67370.18651410.16826822823100
2.6737-3.06050.21581420.165727002842100
3.0605-3.85560.18141440.146927292873100
3.8556-47.11510.16831490.144428252974100

+
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