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- PDB-2z23: Crystal structure of Y.pestis oligo peptide binding protein OppA ... -

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Basic information

Entry
Database: PDB / ID: 2z23
TitleCrystal structure of Y.pestis oligo peptide binding protein OppA with tri-lysine ligand
Components
  • Periplasmic oligopeptide-binding protein
  • peptide (LYS)(LYS)(LYS)
KeywordsPEPTIDE BINDING PROTEIN / ABC TRANSPORTER / PERIPLASMIC BINDING PROTEIN / OLIGOPEPTIDE
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / 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 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / 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
Periplasmic oligopeptide-binding protein / Periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTanabe, M. / Bertland, T. / Mirza, O. / Byrne, B. / Brown, K.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structures of OppA and PstS from Yersinia pestis indicate variability of interactions with transmembrane domains.
Authors: Tanabe, M. / Mirza, O. / Bertrand, T. / Atkins, H.S. / Titball, R.W. / Iwata, S. / Brown, K.A. / Byrne, B.
History
DepositionMay 17, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic oligopeptide-binding protein
B: peptide (LYS)(LYS)(LYS)


Theoretical massNumber of molelcules
Total (without water)59,2652
Polymers59,2652
Non-polymers00
Water7,008389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.827, 90.637, 93.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Periplasmic oligopeptide-binding protein / Oligo-peptide periplasmic binding protein OppA


Mass: 58859.156 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q74TY5, UniProt: A0A0H2W5P5*PLUS
#2: Protein/peptide peptide (LYS)(LYS)(LYS)


Mass: 405.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 32% (W/V) PEG 1500, 3% AMINO CAPROIC ACID, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 71053 / % possible obs: 87.4 %
Reflection shellResolution: 1.8→1.85 Å / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.239 -RAMDOM
Rwork0.21 --
obs0.21 71053 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 0 389 4570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0078
X-RAY DIFFRACTIONc_angle_deg1.8

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