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- PDB-6e3d: Atomic structure of Mycobacterium tuberculosis DppA -

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Basic information

Entry
Database: PDB / ID: 6e3d
TitleAtomic structure of Mycobacterium tuberculosis DppA
Components
  • Periplasmic dipeptide-binding lipoprotein DPPA
  • tetra-peptide picked up from the expression host
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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.271 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 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic dipeptide-binding lipoprotein DPPA
B: tetra-peptide picked up from the expression host


Theoretical massNumber of molelcules
Total (without water)55,7742
Polymers55,7742
Non-polymers00
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-2 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.739, 69.092, 62.363
Angle α, β, γ (deg.)90.000, 106.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic dipeptide-binding lipoprotein DPPA


Mass: 55381.469 Da / Num. of mol.: 1
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 tetra-peptide picked up from the expression host


Mass: 392.405 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.84 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 102717 / % possible obs: 91.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.5 Å2 / Rpim(I) all: 0.0028 / Rsym value: 0.0066 / Net I/σ(I): 37.8
Reflection shellResolution: 1.27→1.32 Å / Redundancy: 3.2 % / Rpim(I) all: 0.029 / Rsym value: 0.0507 / % possible all: 51.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B7H

1b7h


Resolution: 1.271→38.007 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.93
RfactorNum. reflection% reflectionSelection details
Rfree0.1653 1957 1.95 %RANDOM
Rwork0.1322 ---
obs0.1328 100455 89.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.61 Å2 / Biso mean: 22.2998 Å2 / Biso min: 9.58 Å2
Refinement stepCycle: final / Resolution: 1.271→38.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3943 0 0 566 4509
Biso mean---30.41 -
Num. residues----514
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 (%)
1.2706-1.30240.2609660.17043386345243
1.3024-1.33760.2268920.17084663475559
1.3376-1.3770.20291240.16886090621477
1.377-1.42140.24991430.14947302744593
1.4214-1.47220.19221520.13047531768396
1.4722-1.53120.19661530.12337562771596
1.5312-1.60090.16371490.11427574772396
1.6009-1.68530.16851520.11417716786898
1.6853-1.79090.1431530.11557684783798
1.7909-1.92910.15331530.11927709786297
1.9291-2.12320.16121540.11797797795199
2.1232-2.43040.1491530.12427714786798
2.4304-3.06190.17111560.14297876803299
3.0619-38.02430.15621570.1397894805198

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