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- PDB-1b3l: OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KGK -

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Basic information

Entry
Database: PDB / ID: 1b3l
TitleOLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KGK
Components
  • PROTEIN (LYS-GLY-LYS)
  • PROTEIN (OLIGO-PEPTIDE BINDING PROTEIN)
KeywordsPEPTIDE BINDING PROTEIN / COMPLEX (PEPTIDE TRANSPORT-PEPTIDE) / PEPTIDE TRANSPORT
Function / homology
Function and homology information


peptide transmembrane transporter activity / peptide transport / 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 / OTHER / Resolution: 2 Å
AuthorsTame, J.R.H. / Wilkinson, A.J.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystallographic and calorimetric analysis of peptide binding to OppA protein.
Authors: Sleigh, S.H. / Seavers, P.R. / Wilkinson, A.J. / Ladbury, J.E. / Tame, J.R.
#1: 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.H. / Sleigh, S.H. / Wilkinson, A.J. / Ladbury, J.E.
#2: Journal: Structure / Year: 1995
Title: The Crystal Structures of the Oligopeptide-Binding Protein OppA Complexed with Tripeptide and Tetrapeptide Ligands
Authors: Tame, J.R.H. / Dodson, E.J. / Murshudov, G. / Higgins, C.F. / Wilkinson, A.J.
#3: 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.
#4: Journal: Science / Year: 1994
Title: The Structural Basis of Sequence-Independent Peptide Binding by OppA Protein
Authors: Tame, J.R.H. / Murshudov, G.N. / Dodson, E.J. / Neil, T.K. / Dodson, G.G. / Higgins, C.F. / Wilkinson, A.J.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (OLIGO-PEPTIDE BINDING PROTEIN)
B: PROTEIN (LYS-GLY-LYS)
C: PROTEIN (OLIGO-PEPTIDE BINDING PROTEIN)
D: PROTEIN (LYS-GLY-LYS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6955
Polymers118,4254
Non-polymers2701
Water6,107339
1
A: PROTEIN (OLIGO-PEPTIDE BINDING PROTEIN)
B: PROTEIN (LYS-GLY-LYS)


Theoretical massNumber of molelcules
Total (without water)59,2122
Polymers59,2122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-0 kcal/mol
Surface area20260 Å2
MethodPISA
2
C: PROTEIN (OLIGO-PEPTIDE BINDING PROTEIN)
D: PROTEIN (LYS-GLY-LYS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4823
Polymers59,2122
Non-polymers2701
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-4 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.910, 74.800, 103.770
Angle α, β, γ (deg.)90.00, 91.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.995, 0.071, 0.072), (-0.079, -0.989, -0.128), (0.062, -0.133, 0.989)
Vector: 58.79204, 21.41094, -53.27153)

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Components

#1: Protein PROTEIN (OLIGO-PEPTIDE BINDING PROTEIN) / OPPA


Mass: 58878.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: OPPA / Production host: Escherichia coli (E. coli) / References: UniProt: P06202
#2: Protein/peptide PROTEIN (LYS-GLY-LYS)


Mass: 333.427 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2U
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.29 Å3/Da / Density % sol: 40 % / Description: FLASH COOLED TO 120K
Crystal growpH: 5.5 / Details: CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
25-10 %(w/v)PEG40001reservoir
350 mMsodium acetate1reservoir
41 mMuranyl acetate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 40411 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.12 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3.4 / % possible all: 80.3
Reflection
*PLUS
Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CCP4model building
REFMACrefinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1OLB

1olb
PDB Unreleased entry


Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.241 2154 3 %
Rwork0.178 --
obs-72216 94.8 %
Displacement parametersBiso mean: 29.1 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8390 0 1 339 8730
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8862
X-RAY DIFFRACTIONp_mcangle_it2.6493
X-RAY DIFFRACTIONp_scbond_it2.3482
X-RAY DIFFRACTIONp_scangle_it3.5263
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.2550.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1540.3
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor17.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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