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- PDB-1olc: OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH LYS-LYS-LYS-ALA -

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Basic information

Entry
Database: PDB / ID: 1olc
TitleOLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH LYS-LYS-LYS-ALA
Components
  • LYS-LYS-LYS-ALA
  • OLIGO-PEPTIDE BINDING PROTEIN
KeywordsCOMPLEX (BINDING PROTEIN/PEPTIDE) / PERIPLASMIC / COMPLEX (BINDING PROTEIN-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 / Resolution: 2.1 Å
AuthorsTame, J. / Wilkinson, A.J.
Citation
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.
#1: 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.
#2: Journal: Science / Year: 1994
Title: The Structural Basis of Sequence-Independent Peptide Binding by Oppa Protein
Authors: Tame, J.R.H. / Murshudov, G. / Neil, T. / Dodson, E. / Dodson, G.G. / Higgins, C.F. / Wilkinson, A.J.
History
DepositionSep 10, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700SHEET THE HELIX AND SHEET RECORDS PRESENTED HERE ARE SIMPLIFIED TO HELP NAVIGATE AROUND THE PROTEIN ...SHEET THE HELIX AND SHEET RECORDS PRESENTED HERE ARE SIMPLIFIED TO HELP NAVIGATE AROUND THE PROTEIN AND TO AVOID OBSCURING TOPOLOGICAL RELATIONSHIPS WITH RELATED PROTEINS. IT IS NOT INTENDED TO REPLACE THE LIST WHICH THE PDB HAS GENERATED USING DSSP WHICH APPEAR ON ACTUAL HELIX AND SHEET RECORDS FURTHER DOWN IN THE ENTRY. BECAUSE OF LINE LENGTH LIMITATIONS THE FORMAT OF THE SHEET INFORMATION PRESENTED IN THIS REMARK HAS BEEN MODIFIED. HELIX 1 1 VAL A 34 LEU A 43 1 HELIX 2 2 HIS A 91 ALA A 101 1 HELIX 3 3 TYR A 112 GLY A 116 1 HELIX 4 4 ILE A 121 ALA A 126 1 HELIX 5 5 LYS A 169 PHE A 175 1 HELIX 6 6 GLU A 229 SER A 238 1 HELIX 7 7 ILE A 250 GLU A 259 1 HELIX 8 8 VAL A 287 ALA A 296 1 HELIX 9 9 ARG A 299 LYS A 305 1 HELIX 10 10 GLN A 337 ALA A 351 1 HELIX 11 11 ASP A 369 LEU A 386 1 HELIX 12 12 TRP A 397 GLN A 406 1 HELIX 13 13 THR A 424 LEU A 427 1 HELIX 14 14 PRO A 444 LYS A 455 1 HELIX 15 15 ASP A 459 ASP A 476 1 SH 1 A 7 VAL A 264 PRO A 268 0 SH 2 A 7 VAL A 486 LEU A 490 -1 N ARG A 489 O ARG A 265 SH 3 A 7 ASP A 242 TYR A 245 -1 N THR A 244 O LEU A 490 SH 4 A 7 THR A 14 ASN A 18 1 N ASN A 18 O MET A 243 SH 5 A 7 GLN A 220 LEU A 224 1 N GLN A 220 O LEU A 15 SH 6 A 7 ARG A 201 ARG A 206 -1 N LEU A 204 O VAL A 221 SH 7 A 7 TYR A 191 VAL A 197 -1 N VAL A 197 O ARG A 201 SH 1 B 4 ALA A 61 LYS A 67 0 SH 2 B 4 VAL A 71 LEU A 76 -1 N HIS A 75 O GLU A 62 SH 3 B 4 THR A 143 THR A 147 -1 N VAL A 146 O TRP A 72 SH 4 B 4 VAL A 136 ASP A 140 -1 N ASP A 140 O THR A 143 SH 1 C 5 ASN A 389 GLN A 395 0 SH 2 C 5 THR A 360 ASN A 366 1 O TYR A 365 N GLN A 395 SH 3 C 5 VAL A 411 CYS A 417 1 O VAL A 411 N LEU A 364 SH 4 C 5 CYS A 271 ILE A 277 -1 N GLU A 276 O ALA A 412 SH 5 C 5 ILE A 479 TYR A 484 -1 N TYR A 483 O TYR A 273

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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: LYS-LYS-LYS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,51610
Polymers59,3562
Non-polymers2,1608
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-13 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.730, 77.080, 71.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 283

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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 LYS-LYS-LYS-ALA


Mass: 476.632 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CO-CRYSTALLIZED WITH URANIUM ACETATE
#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.: 337 / 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: 52.01 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 %PEG40001reservoir
250 mMsodium acetate1reservoir
31 mMuranyl acetate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 41810 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameClassification
DENZOdata reduction
PROLSQrefinement
RefinementResolution: 2.1→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.197 --
obs0.143 35923 99.9 %
Displacement parametersBiso mean: 20.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 18 337 4553
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.025
X-RAY DIFFRACTIONp_angle_d0.0350.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.0424
X-RAY DIFFRACTIONp_mcangle_it3.9996
X-RAY DIFFRACTIONp_scbond_it8.3468
X-RAY DIFFRACTIONp_scangle_it10.8710
X-RAY DIFFRACTIONp_plane_restr0.0170.03
X-RAY DIFFRACTIONp_chiral_restr0.1440.15
X-RAY DIFFRACTIONp_singtor_nbd0.1870.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2040.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.8183
X-RAY DIFFRACTIONp_staggered_tor18.89415
X-RAY DIFFRACTIONp_orthonormal_tor29.25620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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