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- PDB-3drk: Crystal structure of Lactococcal OppA co-crystallized with Neurop... -

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Basic information

Entry
Database: PDB / ID: 3drk
TitleCrystal structure of Lactococcal OppA co-crystallized with Neuropeptide S in an open conformation
Components
  • Neuropeptide S
  • Oligopeptide-binding protein oppA
KeywordsPEPTIDE BINDING PROTEIN / oligo-peptide binding / voluminous binding cavity / venus fly-trap
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / protein transport / periplasmic space
Similarity search - Function
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Oligopeptide-binding protein oppA
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBerntsson, R.P.-A. / Doeven, M.K. / Duurkens, R.H. / Sengupta, D. / Marrink, S.-J. / Thunnissen, A.-M. / Poolman, B. / Slotboom, D.-J.
CitationJournal: Embo J. / Year: 2009
Title: The structural basis for peptide selection by the transport receptor OppA
Authors: Berntsson, R.P.-A. / Doeven, M.K. / Fusetti, F. / Duurkens, R.H. / Sengupta, D. / Marrink, S.-J. / Thunnissen, A.-M. / Poolman, B. / Slotboom, D.-J.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oligopeptide-binding protein oppA
B: Neuropeptide S


Theoretical massNumber of molelcules
Total (without water)65,6392
Polymers65,6392
Non-polymers00
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-4 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.622, 123.126, 59.281
Angle α, β, γ (deg.)90.000, 102.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Oligopeptide-binding protein oppA


Mass: 65144.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Construct lacking N-terminal signal sequence and cysteine used for lipid modification
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: subsp. cremoris MG1363 / Gene: oppA, llmg_0701 / Plasmid: pAMP21 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): MG1363 / References: UniProt: A2RJ53
#2: Protein/peptide Neuropeptide S


Mass: 494.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.15 Å3/Da / Density % sol: 42.85 % / Mosaicity: 0.49 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M NaCl, 0.1M Na-Hepes, 20% PEG 6000, pH 7.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC Q210 / Detector: CCD / Date: Sep 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.7→42.18 Å / Num. obs: 54564 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.03 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.810.405216013750576.5
1.81-1.930.3043.219609838091.8
1.93-2.090.1625.917715763689.2
2.09-2.280.1078.717657752395.7
2.28-2.550.07611.615333657192.8
2.55-2.940.05216.213142568490.2
2.94-3.60.03422.112102514496.2
3.6-5.070.03126.99290393295.3
5.070.02927.95032218993.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.77 Å
Translation2.5 Å32.77 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DRF

3drf


Resolution: 1.8→32.77 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.728 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 2518 5.1 %RANDOM
Rwork0.19425 ---
obs0.19693 47251 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.233 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.13 Å2
2---0.84 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4387 0 0 497 4884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224513
X-RAY DIFFRACTIONr_bond_other_d0.0010.023031
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9516116
X-RAY DIFFRACTIONr_angle_other_deg0.85237447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4885568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89425.729199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94815769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.748159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02869
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.581.52817
X-RAY DIFFRACTIONr_mcbond_other0.1441.51151
X-RAY DIFFRACTIONr_mcangle_it1.03124532
X-RAY DIFFRACTIONr_scbond_it1.66531696
X-RAY DIFFRACTIONr_scangle_it2.5854.51584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 170 -
Rwork0.255 3420 -
obs--95.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5232-0.18880.15090.5072-0.17660.60560.04450.1158-0.10780.0401-0.02610.0478-0.0379-0.0072-0.0183-0.01930.00920.00280.0055-0.02320.00672.85813.9337-4.8253
20.8155-0.0010.06560.5345-0.00030.6173-0.0285-0.13310.09760.08250.05270.0040.0215-0.0287-0.02420.01390.0049-0.00060.0096-0.0041-0.0013-0.276332.363519.7053
30.3303-0.22290.00320.84180.06080.0058-0.00220.03130.0309-0.0140.0328-0.00210.0278-0.0128-0.03050.0232-0.0010.00220.01080.01450.01218.370921.67174.8486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA14 - 29914 - 299
2X-RAY DIFFRACTION2AA300 - 470300 - 470
3X-RAY DIFFRACTION3AA471 - 572471 - 572

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