[English] 日本語
Yorodumi
- PDB-6pu3: ABC transporter-associated periplasmic binding protein DppA from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pu3
TitleABC transporter-associated periplasmic binding protein DppA from Helicobacter pylori
Components
  • Heme-binding protein A
  • SER-THR-SER-ALA
KeywordsTRANSPORT PROTEIN / DppA / type II / periplasmic binding protein / Periplasmic peptide binding protein
Function / homologyPeptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / ATP-binding cassette (ABC) transporter complex / transmembrane transport / Heme-binding protein A
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRahman, M.M. / Machuca, M.A. / Khan, M.F. / Barlow, C.K. / Schittenhelm, R.B. / Roujeinikova, A.
CitationJournal: J.Bacteriol. / Year: 2019
Title: Molecular Basis of Unexpected Specificity of ABC Transporter-Associated Substrate-Binding Protein DppA from Helicobacter pylori.
Authors: Rahman, M.M. / Machuca, M.A. / Khan, M.F. / Barlow, C.K. / Schittenhelm, R.B. / Roujeinikova, A.
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heme-binding protein A
B: SER-THR-SER-ALA


Theoretical massNumber of molelcules
Total (without water)60,8752
Polymers60,8752
Non-polymers00
Water13,529751
1
A: Heme-binding protein A


Theoretical massNumber of molelcules
Total (without water)60,5111
Polymers60,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-2 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.100, 76.010, 127.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe author determined assembly is a monomer. The tetrapeptide, Chain B, has co-purified with the protein and is not a part of the biological assembly

-
Components

#1: Protein Heme-binding protein A


Mass: 60510.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: hbpA, HPPMSS1_c01141 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9Y393
#2: Protein/peptide SER-THR-SER-ALA


Mass: 364.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Probably co-purified with the protein / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 23% w/v polyethylene glycol (PEG) 3350, 0.25 M tri-ammonium citrate

-
Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→46.12 Å / Num. obs: 59276 / % possible obs: 99 % / Redundancy: 3.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.5
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.348 / Num. unique obs: 3464 / CC1/2: 0.86

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F1Q

5f1q


Resolution: 1.8→46.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.21 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.098
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1804 3001 5.1 %RANDOM
Rwork0.1458 ---
obs0.1476 56215 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.22 Å2 / Biso mean: 13.636 Å2 / Biso min: 3.71 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 0 751 4897
Biso mean---25.37 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024272
X-RAY DIFFRACTIONr_bond_other_d0.0010.024077
X-RAY DIFFRACTIONr_angle_refined_deg2.0161.965790
X-RAY DIFFRACTIONr_angle_other_deg1.06139414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40224.332187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50815743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6261515
X-RAY DIFFRACTIONr_chiral_restr0.1220.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02983
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 211 -
Rwork0.225 4118 -
all-4329 -
obs--100 %

+
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