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- PDB-1b6h: OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NORVALYL-LYSINE -

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Basic information

Entry
Database: PDB / ID: 1b6h
TitleOLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NORVALYL-LYSINE
Components
  • LYS-NVA-LYS PEPTIDE
  • Periplasmic oligopeptide-binding protein
KeywordsPEPTIDE BINDING PROTEIN / PERIPLASMIC PEPTIDE BINDING 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
URANIUM ATOM / Periplasmic oligopeptide-binding protein OppA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDavies, T.G. / Tame, J.R.H.
Citation
Journal: Protein Sci. / Year: 1999
Title: Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes.
Authors: Davies, T.G. / Hubbard, R.E. / Tame, J.R.
#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.
History
DepositionNov 13, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 18, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic oligopeptide-binding protein
B: LYS-NVA-LYS PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,15910
Polymers59,2542
Non-polymers1,9048
Water9,890549
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.680, 75.770, 70.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Periplasmic oligopeptide-binding protein


Mass: 58878.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: oppA, STM1746 / Production host: Escherichia coli (E. coli) / References: UniProt: P06202
#2: Protein/peptide LYS-NVA-LYS PEPTIDE


Mass: 375.506 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-U1 / URANIUM ATOM


Mass: 238.029 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: U
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE SOLVENT STRUCTURE AROUND THE URANIUM IONS IS TENTATIVE

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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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
27 %PEG40001reservoir
31 mMuranyl acetate1reservoir
450 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 49701 / % possible obs: 90 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 3
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 89.7 % / Num. measured all: 290033
Reflection shell
*PLUS
% possible obs: 50.6 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 -5 %RANDOM
Rwork0.18 ---
all-47064 --
obs-47064 90 %-
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4219 0 8 549 4776
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2492
X-RAY DIFFRACTIONp_mcangle_it1.8133
X-RAY DIFFRACTIONp_scbond_it1.5772
X-RAY DIFFRACTIONp_scangle_it2.3753
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.2450.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1740.3
X-RAY DIFFRACTIONp_planar_tor3.57
X-RAY DIFFRACTIONp_staggered_tor13.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.182 / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05

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