[English] 日本語
Yorodumi
- PDB-3n26: Cpn0482 : the arginine binding protein from the periplasm of chla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3n26
TitleCpn0482 : the arginine binding protein from the periplasm of chlamydia Pneumoniae
ComponentsAmino acid ABC transporter, periplasmic amino acid-binding protein
KeywordsTRANSPORT PROTEIN / Vaccine development / Alpha and Beta protein (a/b) / Structural Genomics / BacAbs - EU FP6 programme / Marseilles Structural Genomics Program @ AFMB / MSGP
Function / homology
Function and homology information


amino acid transport / cell surface / extracellular region
Similarity search - Function
Probable ABC transporter arginine-binding protein ArtJ, PBP2 domain / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / Probable ABC transporter arginine-binding protein ArtJ / Probable ABC transporter arginine-binding protein ArtJ
Similarity search - Component
Biological speciesChlamydophila pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPetit, P. / Garcia, C. / Vuillard, L. / Soriani, M. / Grandi, G. / Marseilles Structural Genomics Program AFMB (MSGP) / Marseilles Structural Genomics Program @ AFMB (MSGP)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Exploiting antigenic diversity for vaccine design: the Chlamydia ArtJ paradigm.
Authors: Soriani, M. / Petit, P. / Grifantini, R. / Petracca, R. / Gancitano, G. / Frigimelica, E. / Nardelli, F. / Garcia, C. / Spinelli, S. / Scarabelli, G. / Fiorucci, S. / Affentranger, R. / ...Authors: Soriani, M. / Petit, P. / Grifantini, R. / Petracca, R. / Gancitano, G. / Frigimelica, E. / Nardelli, F. / Garcia, C. / Spinelli, S. / Scarabelli, G. / Fiorucci, S. / Affentranger, R. / Ferrer-Navarro, M. / Zacharias, M. / Colombo, G. / Vuillard, L. / Daura, X. / Grandi, G.
History
DepositionMay 17, 2010Deposition site: RCSB / Processing site: PDBJ
SupersessionJun 16, 2010ID: 3G41
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8502
Polymers27,6751
Non-polymers1751
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.600, 51.600, 206.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

-
Components

#1: Protein Amino acid ABC transporter, periplasmic amino acid-binding protein / Arginine periplasmic binding protein


Mass: 27674.795 Da / Num. of mol.: 1 / Fragment: Soluble domain (UNP residues 23-259)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydophila pneumoniae (bacteria) / Gene: artJ, CP_0272 / Plasmid: pET21b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JS59, UniProt: Q9Z869*PLUS
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2008
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→34.4 Å / Num. all: 17234 / Num. obs: 16816 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.3 / Rsym value: 0.2 / % possible all: 92.4

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DEL

3del


Resolution: 2.1→20 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 856 -RANDOM
Rwork0.19 ---
obs0.193 16272 100 %-
all-17128 --
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 12 203 2028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.025
X-RAY DIFFRACTIONr_angle_refined_deg1.91
X-RAY DIFFRACTIONr_chiral_restr0.15
X-RAY DIFFRACTIONr_gen_planes_refined0.01

+
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