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- PDB-1ola: THE STRUCTURAL BASIS OF MULTISPECIFICITY IN THE OLIGOPEPTIDE-BIND... -

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Basic information

Entry
Database: PDB / ID: 1ola
TitleTHE STRUCTURAL BASIS OF MULTISPECIFICITY IN THE OLIGOPEPTIDE-BINDING PROTEIN OPPA
Components
  • OLIGO-PEPTIDE BINDING PROTEIN
  • PEPTIDE VAL-LYS-PRO-GLY
KeywordsBINDING PROTEIN
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 OppA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsTame, J. / Wilkinson, A.J.
Citation
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.
#1: Journal: To be Published
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.
History
DepositionApr 26, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 VAL-LYS-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8204
Polymers59,2792
Non-polymers5402
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-8 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.500, 74.500, 70.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO A 283

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Components

#1: Protein OLIGO-PEPTIDE BINDING PROTEIN


Mass: 58878.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P06202
#2: Protein/peptide PEPTIDE VAL-LYS-PRO-GLY


Mass: 400.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Chemical ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2U
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE ARE NO DISCONTINUITIES. THE PEPTIDE LIGAND IS A SEPARATE CHAIN.
Nonpolymer detailsTHE PROTEIN WAS CO-CRYSTALLIZED WITH URANYL (VI) ACETATE. TWO URANIUM ATOMS ARE INCLUDED IN THE ...THE PROTEIN WAS CO-CRYSTALLIZED WITH URANYL (VI) ACETATE. TWO URANIUM ATOMS ARE INCLUDED IN THE MODEL BUT THE ASSOCIATED OXYGEN ATOMS ARE NOT VISIBLE. THE SECOND URANIUM ATOM LIES ON A TWO-FOLD AXIS. THE PEPTIDE LIGAND WAS CO-PURIFIED WITH THE PROTEIN AND IS A RANDOM MIXTURE. THIS HAS BEEN MODELED AS VAL-LYS-PRO-GLY BUT THE SIDE-CHAIN DENSITY IS POOR.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal grow
*PLUS
pH: 5.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM11NaOAc
215 %PEG400011
31 mMuranyl acetate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 30656 / % possible obs: 89.7 % / Rmerge(I) obs: 0.067

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→8 Å / σ(F): 0
Details: CRYSTALS OF OPPA ARE ONLY OBTAINED IN THE PRESENCE OF URANYL IONS WHICH BIND TO THE PROTEIN AND ARE RESPONSIBLE FOR FORMING IMPORTANT CRYSTAL CONTACTS. TWO CRYSTAL FORMS OF URANYL OPPA HAVE ...Details: CRYSTALS OF OPPA ARE ONLY OBTAINED IN THE PRESENCE OF URANYL IONS WHICH BIND TO THE PROTEIN AND ARE RESPONSIBLE FOR FORMING IMPORTANT CRYSTAL CONTACTS. TWO CRYSTAL FORMS OF URANYL OPPA HAVE BEEN FOUND. OPPA CONTAINING CO-PURIFIED PEPTIDES CO-CRYSTALLIZED WITH URANYL ACETATE GIVES CRYSTALS IN SPACE-GROUP P 21 21 2 CONTAINING TWO URANIUM ATOMS. ONE URANIUM ATOM FORMS AN IMPORTANT CRYSTAL CONTACT. THE OTHER LIES VERY CLOSE TO THE TWO-FOLD AXIS AND HAS A HIGH TEMPERATURE FACTOR. NO ATTEMPT WAS MADE IN REFINEMENT TO CONSTRAIN THIS ATOM TO THE SYMMETRY AXIS. IT HAS BEEN ASSIGNED AN OCCUPANCY OF 0.5 TO ALLOW FOR SYMMETRY. OPPA LIGANDED WITH TRI-LYSINE CRYSTALLIZES WITH EIGHT URANYL IONS PER PROTEIN MOLECULE IN SPACE-GROUP P 21 21 21. THIS STRUCTURE IS PRESENTED IN PDB ENTRY 1OLB.
RfactorNum. reflection
obs0.167 29634
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4107 0 2 354 4463
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.015
X-RAY DIFFRACTIONp_angle_d0.0370.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it5.2754
X-RAY DIFFRACTIONp_mcangle_it6.5756
X-RAY DIFFRACTIONp_scbond_it11.078
X-RAY DIFFRACTIONp_scangle_it13.56110
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.2030.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.2720.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1960.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.7687
X-RAY DIFFRACTIONp_staggered_tor21.18220
X-RAY DIFFRACTIONp_orthonormal_tor30.0320
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Num. reflection all: 29634 / Rfactor all: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS

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