[English] 日本語
Yorodumi
- PDB-3fj7: Crystal structure of L-phospholactate Bound PEB3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fj7
TitleCrystal structure of L-phospholactate Bound PEB3
ComponentsMajor antigenic peptide PEB3
KeywordsPROTEIN BINDING / PEB3 / PEP
Function / homology
Function and homology information


sulfate transmembrane transport / molecular carrier activity / periplasmic space
Similarity search - Function
Thiosulphate/Sulfate-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
L-PHOSPHOLACTATE / Major antigenic peptide PEB3
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMin, T. / Matte, A. / Cygler, M.
CitationJournal: Biochemistry / Year: 2009
Title: Specificity of Campylobacter jejuni adhesin PEB3 for phosphates and structural differences among its ligand complexes.
Authors: Min, T. / Vedadi, M. / Watson, D.C. / Wasney, G.A. / Munger, C. / Cygler, M. / Matte, A. / Young, N.M.
History
DepositionDec 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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: Major antigenic peptide PEB3
B: Major antigenic peptide PEB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5924
Polymers51,2522
Non-polymers3402
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-16 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.231, 79.239, 99.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Major antigenic peptide PEB3


Mass: 25626.092 Da / Num. of mol.: 2 / Fragment: UNP residues 21-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: 11168 / Gene: cj0289c / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): AD202 / References: UniProt: Q0PBL7
#2: Chemical ChemComp-PEQ / L-PHOSPHOLACTATE


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% [w/v] polyethylene glycol 3350, 0.2 M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 19, 2008 / Details: Vertical and Horizontal focusing Mirrors
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→43.9 Å / Num. obs: 54648 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.083 / Net I/σ(I): 11.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 7.7 / Num. unique all: 7879 / Rsym value: 0.287 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.4.0067refinement
d*TREKdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HWX,PEB3 citrate bound form

2hwx


Resolution: 1.7→43.9 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.221 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24246 2725 5 %RANDOM
Rwork0.21879 ---
obs0.21997 51857 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.756 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--0.3 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 20 400 4042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0223718
X-RAY DIFFRACTIONr_angle_refined_deg0.8211.9455022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5345460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92825.122164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75815658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.051514
X-RAY DIFFRACTIONr_chiral_restr0.0620.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212782
X-RAY DIFFRACTIONr_mcbond_it0.2141.52288
X-RAY DIFFRACTIONr_mcangle_it0.41123676
X-RAY DIFFRACTIONr_scbond_it0.55631430
X-RAY DIFFRACTIONr_scangle_it0.9744.51346
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 188 -
Rwork0.311 3806 -
obs--99.87 %

+
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