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- PDB-7jls: RV3666c bound to tripeptide -

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Basic information

Entry
Database: PDB / ID: 7jls
TitleRV3666c bound to tripeptide
Components
  • Peptide SER-VAL-ALA
  • Probable periplasmic dipeptide-binding lipoprotein DppA
KeywordsPEPTIDE BINDING PROTEIN / RV3666c 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 / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / periplasmic space / Probable periplasmic dipeptide-binding lipoprotein DppA
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.52 Å
AuthorsLee, R.E. / Griffith, E.C. / Miller, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI090810-08 United States
CitationJournal: Tuberculosis (Edinb) / Year: 2021
Title: Biophysical analysis of the Mycobacteria tuberculosis peptide binding protein DppA reveals a stringent peptide binding pocket.
Authors: Fernando, D.M. / Gee, C.T. / Griffith, E.C. / Meyer, C.J. / Wilt, L.A. / Tangallapally, R. / Wallace, M.J. / Miller, D.J. / Lee, R.E.
History
DepositionJul 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable periplasmic dipeptide-binding lipoprotein DppA
B: Peptide SER-VAL-ALA


Theoretical massNumber of molelcules
Total (without water)60,8912
Polymers60,8912
Non-polymers00
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-3 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.050, 69.960, 65.390
Angle α, β, γ (deg.)90.000, 109.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable periplasmic dipeptide-binding lipoprotein DppA


Mass: 60615.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: dppA, Rv3666c / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6X811
#2: Protein/peptide Peptide SER-VAL-ALA


Mass: 275.302 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 1.91 Å3/Da / Density % sol: 35.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M ammonium sulfate pH7.0, 18-23% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→61.64 Å / Num. obs: 70699 / % possible obs: 99.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.039 / Rrim(I) all: 0.08 / Χ2: 1.51 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.52-1.553.40.79635340.6340.490.9380.842100
1.55-1.573.70.72735110.7390.4330.8480.832100
1.57-1.63.90.66935250.7860.3870.7760.882100
1.6-1.644.10.59335800.8320.3340.6830.942100
1.64-1.674.10.50435530.8620.280.5780.964100
1.67-1.714.20.39935240.910.220.4571.013100
1.71-1.754.20.3435340.940.1880.3891.061100
1.75-1.84.20.26535620.9580.1460.3041.211100
1.8-1.864.20.21135460.9710.1170.2421.271100
1.86-1.924.20.19335130.9720.1070.2211.46100
1.92-1.984.20.15535720.9790.0860.1771.768100
1.98-2.064.20.12735720.9840.070.1451.946100
2.06-2.164.20.10735440.9880.0590.1222.005100
2.16-2.274.20.09535650.9880.0530.1092.176100
2.27-2.414.10.08535480.990.0480.0972.10799.9
2.41-2.64.10.07835760.9910.0440.092.16599.9
2.6-2.864.10.07135550.9920.040.0822.27399.8
2.86-3.274.10.05935620.9940.0330.0681.92899.9
3.27-4.133.70.04932950.9950.0280.0571.63191.2
4.13-503.90.04735280.9950.0270.0541.42796.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data scaling
HKL2Mapphasing
PDB_EXTRACT3.25data extraction
SHELXCDphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.52→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.512 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0872 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 3433 5.1 %RANDOM
Rwork0.1851 ---
obs0.1869 64231 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.64 Å2 / Biso mean: 22.506 Å2 / Biso min: 11.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-0.04 Å2
2--0.01 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 0 403 4228
Biso mean---33.93 -
Num. residues----500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133957
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173526
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.6415418
X-RAY DIFFRACTIONr_angle_other_deg1.5481.5728147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1045502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77821.705217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17615552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.171530
X-RAY DIFFRACTIONr_chiral_restr0.090.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02879
LS refinement shellResolution: 1.514→1.553 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 185 -
Rwork0.274 3869 -
all-4054 -
obs--77.07 %

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