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- PDB-1qka: OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KRK -

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Basic information

Entry
Database: PDB / ID: 1qka
TitleOLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KRK
Components
  • LYS-ARG-LYS
  • PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN
KeywordsPROTEIN TRANSPORT / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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.H.
#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
DepositionJul 14, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_conn_angle ...pdbx_entity_src_syn / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.5Nov 20, 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: PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN
B: LYS-ARG-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,28313
Polymers59,3132
Non-polymers2,97011
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.926, 75.446, 70.061
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 / OPPA


Mass: 58878.984 Da / Num. of mol.: 1
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 LYS-ARG-LYS


Mass: 433.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: O2U
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.45 Å3/Da / Density % sol: 45 % / Description: FLASH COOLED TO 120K
Crystal growpH: 5.5 / Details: CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 %(w/v)PEG40001drop
250 mMsodium acetate1drop
31 mMuranyl acetate1drop
430 mg/mlpeptide1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: R-AXIS IIC / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: 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: 52404 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.2 / % possible all: 72.4

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OLB

1olb
PDB Unreleased entry


Resolution: 1.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: SEVERAL WATER MOLECULES IN THE MODEL HAVE LOW TEMPERATURE FACTORS BUT FORM NO HYDROGEN BONDS. THESE MAY IN FACT BE URANYL IONS AT LOW OCCUPANCY.
RfactorNum. reflection% reflection
Rfree0.22194 2614 5 %
Rwork0.17586 --
obs-55059 95.2 %
Displacement parametersBiso mean: 20.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 11 456 4662
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_d0.0270.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2252
X-RAY DIFFRACTIONp_mcangle_it2.7723
X-RAY DIFFRACTIONp_scbond_it2.992
X-RAY DIFFRACTIONp_scangle_it4.1483
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.2430.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1210.3
X-RAY DIFFRACTIONp_planar_tor3.67
X-RAY DIFFRACTIONp_staggered_tor1415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS

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