[English] 日本語
Yorodumi
- PDB-6e4d: Atomic structure of Mycobacterium tuberculosis DppA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e4d
TitleAtomic structure of Mycobacterium tuberculosis DppA
Components
  • Periplasmic dipeptide-binding lipoprotein DPPA
  • VAL-VAL-VAL-ALA
KeywordsMETAL BINDING PROTEIN / heme-binding / periplasmic protein
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
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
Similarity search - Domain/homology
ABC transporter substrate-binding protein / Probable periplasmic dipeptide-binding lipoprotein DppA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.252 Å
AuthorsKo, Y. / Mitra, A. / Niederweis, M. / Cingolani, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA56036 United States
National Institutes of Health/Office of the DirectorS10OD017987 United States
CitationJournal: Nat Commun / Year: 2019
Title: Heme and hemoglobin utilization by Mycobacterium tuberculosis.
Authors: Mitra, A. / Ko, Y.H. / Cingolani, G. / Niederweis, M.
History
DepositionJul 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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: Periplasmic dipeptide-binding lipoprotein DPPA
F: VAL-VAL-VAL-ALA


Theoretical massNumber of molelcules
Total (without water)55,7842
Polymers55,7842
Non-polymers00
Water10,647591
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-5 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.620, 68.951, 62.108
Angle α, β, γ (deg.)90.000, 106.340, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Periplasmic dipeptide-binding lipoprotein DPPA


Mass: 55397.469 Da / Num. of mol.: 1 / Mutation: R179A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dppA, ERS007741_01322, ERS023446_02924 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A045KE34, UniProt: I6X811*PLUS
#2: Protein/peptide VAL-VAL-VAL-ALA


Mass: 386.485 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M Sodium malonate pH 6.0 and 22% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.25→15 Å / Num. obs: 114948 / % possible obs: 98.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 12.2 Å2 / Rpim(I) all: 0.05 / Rsym value: 0.089 / Net I/σ(I): 30.4
Reflection shellResolution: 1.25→1.29 Å / Mean I/σ(I) obs: 3.4 / Rpim(I) all: 0.359 / Rsym value: 0.723 / % possible all: 89.6

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E3D

6e3d


Resolution: 1.252→14.921 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.73
RfactorNum. reflection% reflection
Rfree0.1878 1999 1.74 %
Rwork0.1681 --
obs0.1684 114872 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.37 Å2 / Biso mean: 20.0352 Å2 / Biso min: 8.1 Å2
Refinement stepCycle: final / Resolution: 1.252→14.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 0 591 4533
Biso mean---27.29 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054052
X-RAY DIFFRACTIONf_angle_d0.7895543
X-RAY DIFFRACTIONf_chiral_restr0.106602
X-RAY DIFFRACTIONf_plane_restr0.006745
X-RAY DIFFRACTIONf_dihedral_angle_d16.1111444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2515-1.28280.27841160.27846541665780
1.2828-1.31750.33641430.26168075821899
1.3175-1.35620.26991440.242681748318100
1.3562-1.40.26591440.228981408284100
1.4-1.450.24841450.206381858330100
1.45-1.5080.25371460.180282098355100
1.508-1.57650.18561450.165281868331100
1.5765-1.65950.19461440.158581838327100
1.6595-1.76330.18811460.156181948340100
1.7633-1.89920.16631440.154881778321100
1.8992-2.08990.15611470.149182378384100
2.0899-2.39130.17551450.149282208365100
2.3913-3.00870.18521450.16438170831599
3.0087-14.92230.16241450.15948182832798

+
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