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- PDB-1jeu: OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KEK -

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Basic information

Entry
Database: PDB / ID: 1jeu
TitleOLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KEK
Components
  • OLIGO-PEPTIDE BINDING PROTEIN
  • PEPTIDE LYS GLU LYS
KeywordsCOMPLEX (PEPTIDE TRANSPORT/PEPTIDE) / COMPLEX (PEPTIDE TRANSPORT-PEPTIDE) / PEPTIDE TRANSPORT / COMPLEX (PEPTIDE TRANSPORT-PEPTIDE) complex
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / protein transport / outer membrane-bounded 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
URANYL (VI) ION / Periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsTame, J. / Wilkinson, A.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: The role of water in sequence-independent ligand binding by an oligopeptide transporter protein.
Authors: Tame, J.R. / Sleigh, S.H. / Wilkinson, A.J. / Ladbury, J.E.
#1: Journal: Structure / Year: 1995
Title: The Crystal Structures of the Oligopeptide-Binding Protein Oppa Complexed with Tripeptide and Tetrapeptide Ligands
Authors: Tame, J.R. / Dodson, E.J. / Murshudov, G. / Higgins, C.F. / Wilkinson, A.J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure Determination of Oppa at 2.3 Angstroms Resolution Using Multiple Wavelength Anomalous Methods
Authors: Glover, I.D. / Denny, R. / Nguti, N.D. / Mcsweeney, S. / Thompson, A. / Dodson, E. / Wilkinson, A.J. / Tame, J.R.H.
#3: Journal: Science / Year: 1994
Title: The Structural Basis of Sequence-Independent Peptide Binding by Oppa Protein
Authors: Tame, J.R. / Murshudov, G.N. / Dodson, E.J. / Neil, T.K. / Dodson, G.G. / Higgins, C.F. / Wilkinson, A.J.
History
DepositionJul 3, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OLIGO-PEPTIDE BINDING PROTEIN
B: PEPTIDE LYS GLU LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,44510
Polymers59,2842
Non-polymers2,1608
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-21 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.410, 76.410, 71.250
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 OLIGO-PEPTIDE BINDING PROTEIN / OPPA


Mass: 58878.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / References: UniProt: P06202
#2: Protein/peptide PEPTIDE LYS GLU LYS


Mass: 405.489 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Chemical
ChemComp-IUM / URANYL (VI) ION / Uranyl


Mass: 270.028 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2U
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.56 Å3/Da / Density % sol: 45 % / Description: FLASH COOLED TO 120K
Crystal growpH: 5.5 / Details: CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5
Crystal grow
*PLUS
Method: unknown / Details: Tame, J.R., (1994) Science, 264, 1578.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM11NaOAc
215 %PEG400011
31 mMuranyl acetate11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.25→10 Å / Num. obs: 167630 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9
Reflection shell
*PLUS
% possible obs: 93.2 %

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Processing

Software
NameClassification
DENZOdata reduction
CCP4model building
PROLSQrefinement
CCP4phasing
RefinementStarting model: PDB ENTRY 2OLB

2olb


Resolution: 1.25→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.252 8409 5 %
Rwork0.224 --
obs-164131 97.8 %
Displacement parametersBiso mean: 16.9 Å2
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4193 0 18 407 4618
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.025
X-RAY DIFFRACTIONp_angle_d0.020.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2384
X-RAY DIFFRACTIONp_mcangle_it1.9876
X-RAY DIFFRACTIONp_scbond_it3.5758
X-RAY DIFFRACTIONp_scangle_it5.18110
X-RAY DIFFRACTIONp_plane_restr0
X-RAY DIFFRACTIONp_chiral_restr0.0950.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2440.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1610.3
X-RAY DIFFRACTIONp_planar_tor2.37
X-RAY DIFFRACTIONp_staggered_tor15.720
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.42 / Rfactor obs: 0.41

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