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- PDB-2rkm: STRUCTURE OF OPPA COMPLEXED WITH LYS-LYS -

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Entry
Database: PDB / ID: 2rkm
TitleSTRUCTURE OF OPPA COMPLEXED WITH LYS-LYS
ComponentsOLIGO-PEPTIDE BINDING PROTEIN
KeywordsPEPTIDE BINDING PROTEIN / PEPTIDE TRANSPORT / COMPLEX (BINDING PROTEIN-DIPEPTIDE)
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 / LYSINE / Periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsSleigh, S.H. / Tame, J.R.H. / Wilkinson, A.J.
Citation
Journal: Biochemistry / Year: 1997
Title: Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine.
Authors: Sleigh, S.H. / Tame, J.R. / Dodson, E.J. / Wilkinson, A.J.
#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. / Sleigh, S.H. / Wilkinson, A.J. / Ladbury, J.E.
#2: 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.
#3: 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.
#4: 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.
History
DepositionMar 25, 1997Processing site: BNL
Revision 1.0Jul 29, 1997Provider: 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 DIFFER FROM THE LIST WHICH THE PDB HAS GENERATED ...SHEET THE HELIX AND SHEET RECORDS PRESENTED HERE DIFFER FROM 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

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Assembly

Deposited unit
A: OLIGO-PEPTIDE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,33411
Polymers58,8791
Non-polymers2,45510
Water9,350519
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.470, 77.150, 71.590
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 OLIGO-PEPTIDE BINDING PROTEIN / OPPA


Mass: 58878.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE OLIGOPEPTIDE BINDING PROTEIN OPPA IS SYNTHESISED AS A 542 AMINO ACID PRE-PROTEIN. THE 25 AMINO ACID SIGNAL PEPTIDE IS CLEAVED FROM THE N-TERMINUS TO GIVE A 517 RESIDUE MATURE PROTEIN IN ...Details: THE OLIGOPEPTIDE BINDING PROTEIN OPPA IS SYNTHESISED AS A 542 AMINO ACID PRE-PROTEIN. THE 25 AMINO ACID SIGNAL PEPTIDE IS CLEAVED FROM THE N-TERMINUS TO GIVE A 517 RESIDUE MATURE PROTEIN IN THE PERIPLASMIC SPACE. ALL 517 RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY MAP.
Source: (natural) Salmonella typhimurium (bacteria) / References: UniProt: P06202
#2: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#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.: 519 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE RESIDUES 2001 AND 2002 REPRESENT A DIPEPTIDE (LYS-LYS) BOUND TO PERIPLASMIC OLIGOPEPTIDE- ...THE RESIDUES 2001 AND 2002 REPRESENT A DIPEPTIDE (LYS-LYS) BOUND TO PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN SOLVENT STRUCTURE AROUND THE URANYL IONS IS TENTATIVE. URANIUM 8 IS PARTIALLY OCCUPIED AND THE DENSITY AROUND IT IS NOT CONCLUSIVE; HENCE THE SECOND OXYGEN IS MISSING.

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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: 2.58 Å3/Da / Density % sol: 52.2 %
Crystal growpH: 5.5
Details: 7% PEG 4K, 50MM SODIUM ACETATE PH5.5, 1MM URANYL ACETATE AND 30MG/ML OPPA
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
250 mMsodium acetate1drop
36 %PEG40001reservoir
41 mMuranyl acetate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 4, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 57099 / % possible obs: 92.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.6
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.4 / % possible all: 92.9
Reflection
*PLUS
Num. measured all: 379533
Reflection shell
*PLUS
% possible obs: 98.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CCP4data reduction
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 1.8→20 Å / Cross valid method: FREE R / σ(F): 0
Details: THE EIGHT URANIUM IONS HAVE ASSOCIATED OXYGEN ATOMS IN THE MODEL. THE GEOMETRY OF THESE URANYL IONS HAS NOT BEEN RESTRAINED OR MANUALLY MODIFIED. THE (O-U-O)2+ ION SHOULD BE LINEAR WITH AN O- ...Details: THE EIGHT URANIUM IONS HAVE ASSOCIATED OXYGEN ATOMS IN THE MODEL. THE GEOMETRY OF THESE URANYL IONS HAS NOT BEEN RESTRAINED OR MANUALLY MODIFIED. THE (O-U-O)2+ ION SHOULD BE LINEAR WITH AN O-U DISTANCE OF APPROXIMATELY 1.8 ANGSTROMS. SOLVENT STRUCTURE AROUND THE URANYL IONS IS TENTATIVE. URANIUM 8 IS PARTIALLY OCCUPIED AND THE DENSITY AROUND IT IS NOT CONCLUSIVE; HENCE THE SECOND OXYGEN IS MISSING. THE EIGHT URANIUM IONS HAVE ASSOCIATED OXYGEN ATOMS IN THE MODEL. THE GEOMETRY OF THESE URANYL IONS HAS NOT BEEN RESTRAINED OR MANUALLY MODIFIED. THE (O-U-O)2+ ION SHOULD BE LINEAR WITH AN O-U DISTANCE OF APPROXIMATELY 1.8 ANGSTROMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 -5 %COPIED FROM 1JET
Rwork0.167 ---
obs-57099 --
Displacement parametersBiso mean: 16.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 42 519 4750
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.02
X-RAY DIFFRACTIONp_angle_d0.0220.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0240.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5052
X-RAY DIFFRACTIONp_mcangle_it2.0463
X-RAY DIFFRACTIONp_scbond_it2.0172
X-RAY DIFFRACTIONp_scangle_it2.9843
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0830.15
X-RAY DIFFRACTIONp_singtor_nbd0.1720.3
X-RAY DIFFRACTIONp_multtor_nbd0.2420.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1690.3
X-RAY DIFFRACTIONp_planar_tor3.57
X-RAY DIFFRACTIONp_staggered_tor1615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.167 / Rfactor Rfree: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

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