[English] 日本語
Yorodumi
- PDB-3zs6: The Structural characterization of Burkholderia pseudomallei OppA. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zs6
TitleThe Structural characterization of Burkholderia pseudomallei OppA.
Components
  • OLIGOPEPTIDE DVA
  • PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN
KeywordsPEPTIDE BINDING PROTEIN / ABC TRANSPORT SYSTEM
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
UNIDENTIFIED (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLassaux, P. / Gourlay, L.J. / Bolognesi, M.
CitationJournal: Structure / Year: 2013
Title: A Structure-Based Strategy for Epitope Discovery in Burkholderia Pseudomallei Oppa Antigen.
Authors: Lassaux, P. / Peri, C. / Ferrer-Navarro, M. / Gourlay, L.J. / Gori, A. / Conchillo-Sole, O. / Rinchai, D. / Lertmemongkolchai, G. / Longhi, R. / Daura, X. / Colombo, G. / Bolognesi, M.
History
DepositionJun 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references / Structure summary
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN
B: OLIGOPEPTIDE DVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4487
Polymers57,0442
Non-polymers4045
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-12.4 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.860, 81.930, 74.180
Angle α, β, γ (deg.)90.00, 104.34, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN


Mass: 56740.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: K96423 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: Q63ID0
#2: Protein/peptide OLIGOPEPTIDE DVA


Mass: 303.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) UNIDENTIFIED (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.31 Å3/Da / Density % sol: 46.79 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 7.5, 20% PEG 8000.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→40.97 Å / Num. obs: 31801 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 20.29 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QKA

1qka


Resolution: 2.1→38.464 Å / SU ML: 0.56 / σ(F): 1.35 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 1604 5 %
Rwork0.1575 --
obs0.1602 31796 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.402 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.1885 Å20 Å23.095 Å2
2--1.9065 Å20 Å2
3----2.095 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 25 221 4266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064211
X-RAY DIFFRACTIONf_angle_d0.9095735
X-RAY DIFFRACTIONf_dihedral_angle_d12.7531570
X-RAY DIFFRACTIONf_chiral_restr0.063627
X-RAY DIFFRACTIONf_plane_restr0.004740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.25341390.15932734X-RAY DIFFRACTION100
2.1678-2.24530.23311550.15522736X-RAY DIFFRACTION100
2.2453-2.33520.21071500.14842726X-RAY DIFFRACTION100
2.3352-2.44140.2011310.15142733X-RAY DIFFRACTION100
2.4414-2.57010.24091340.15862761X-RAY DIFFRACTION100
2.5701-2.73110.23361360.16482725X-RAY DIFFRACTION100
2.7311-2.94190.2371380.162756X-RAY DIFFRACTION100
2.9419-3.23780.20551580.15812727X-RAY DIFFRACTION100
3.2378-3.7060.19711480.15782750X-RAY DIFFRACTION100
3.706-4.66790.1691520.14852760X-RAY DIFFRACTION100
4.6679-38.470.21631630.16832784X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5732-0.29350.02110.9459-0.26051.17790.0760.17850.0242-0.20730.01590.00410.0515-0.0979-0.05710.111-0.0122-0.0010.08610.01480.066813.9567-9.97174.7849
21.0899-0.3881-0.21390.5373-0.01280.9103-0.0297-0.15410.14160.09370.1146-0.0724-0.1573-0.0369-0.04120.08930.0449-0.01250.0867-0.02950.093412.4727-2.161329.6793
35.8118-3.23966.2475.3056-2.07477.5178-0.4528-0.1102-0.3267-0.3464-0.4628-1.17290.44521.36490.95670.11610.00480.03150.18730.03370.207212.2394-7.546420.2648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 48:274)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 275:553)
3X-RAY DIFFRACTION3CHAIN B

+
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