[English] 日本語
Yorodumi
- PDB-6aal: Crystal Structure of putative amino acid binding periplasmic ABC ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aal
TitleCrystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Arginine
ComponentsPutative amino acid-binding periplasmic ABC transporter protein
KeywordsTRANSPORT PROTEIN / Periplasmic / Solute binding / Candidatus Liberibacter asiaticus / ABC transporter
Function / homology
Function and homology information


periplasmic space / membrane
Similarity search - Function
Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ARGININE / Putative amino acid-binding periplasmic ABC transporter protein
Similarity search - Component
Biological speciesLiberibacter asiaticus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKumar, P. / Kesari, P. / Ghosh, D.K. / Kumar, P. / Sharma, A.K.
CitationJournal: Febs J. / Year: 2019
Title: Crystal structures of a putative periplasmic cystine-binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding.
Authors: Kumar, P. / Kesari, P. / Kokane, S. / Ghosh, D.K. / Kumar, P. / Sharma, A.K.
History
DepositionJul 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative amino acid-binding periplasmic ABC transporter protein
B: Putative amino acid-binding periplasmic ABC transporter protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,76923
Polymers55,2312
Non-polymers1,53721
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-30 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.342, 86.000, 123.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Putative amino acid-binding periplasmic ABC transporter protein


Mass: 27615.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Liberibacter asiaticus (strain psy62) (bacteria)
Strain: psy62 / Gene: CLIBASIA_05070 / Plasmid: pET28C / Production host: Escherichia coli (E. coli) / References: UniProt: C6XGT2

-
Non-polymers , 5 types, 101 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.75 % / Description: Cubic
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2M Ammonium sulphate, 0.1M Sodium acetate trihydrate pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→70.64 Å / Num. obs: 15666 / % possible obs: 98.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.15 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 741 / Rsym value: 0.8 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000v703gdata reduction
HKL-2000v703gdata scaling
MoRDa22(2018-05-05)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLN

2yln


Resolution: 2.6→70.64 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.869 / SU B: 17.454 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29013 826 5.3 %RANDOM
Rwork0.20018 ---
obs0.20509 14811 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.13 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 2.6→70.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 96 80 3936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193920
X-RAY DIFFRACTIONr_bond_other_d0.0010.023722
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9695260
X-RAY DIFFRACTIONr_angle_other_deg0.84338599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4675468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66223.262187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07515699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3141533
X-RAY DIFFRACTIONr_chiral_restr0.0890.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02824
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_it2.6963.9531883
X-RAY DIFFRACTIONr_mcbond_other2.6953.9511878
X-RAY DIFFRACTIONr_mcangle_it4.1795.9212344
X-RAY DIFFRACTIONr_mcangle_other4.1785.9212345
X-RAY DIFFRACTIONr_scbond_it2.8964.3152037
X-RAY DIFFRACTIONr_scbond_other2.8964.3152038
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.486.3242917
X-RAY DIFFRACTIONr_long_range_B_refined6.56646.3034275
X-RAY DIFFRACTIONr_long_range_B_other6.56746.3044275
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 65 -
Rwork0.296 1038 -
obs--97.35 %

+
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