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- PDB-3drj: Crystal structure of Lactococcal OppA co-crystallized with pTH-re... -

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Basic information

Entry
Database: PDB / ID: 3drj
TitleCrystal structure of Lactococcal OppA co-crystallized with pTH-related peptide in an open conformation
Components
  • Oligopeptide-binding protein oppA
  • pTH-related peptide
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: 1.5 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: pTH-related peptide


Theoretical massNumber of molelcules
Total (without water)65,6432
Polymers65,6432
Non-polymers00
Water16,232901
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-3 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.140, 123.356, 59.704
Angle α, β, γ (deg.)90.000, 103.910, 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 pTH-related peptide


Mass: 498.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
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: 1.5→37.165 Å / Num. obs: 86038 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.434 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 17.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.590.1915.1334451371194.5
1.59-1.70.1177.7323431310696.3
1.7-1.840.07611.1303211228996.6
1.84-2.010.05216.5261031075291.7
2.01-2.250.03622.2250151021596.4
2.25-2.590.0326.921976900996.4
2.59-3.170.02531.318496759295.8
3.17-4.480.02235.814732604798.1
4.480.022377739325094.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.15 Å
Translation2.5 Å37.15 Å

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Processing

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

3drf


Resolution: 1.5→37.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.491 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.208 4288 5 %RANDOM
Rwork0.162 ---
obs0.165 85971 95.77 %-
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: 10.793 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å2-0.03 Å2
2---0.11 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 0 901 5293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224545
X-RAY DIFFRACTIONr_bond_other_d0.0010.023046
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9516166
X-RAY DIFFRACTIONr_angle_other_deg0.92337489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96325.75200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63915775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.095159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
X-RAY DIFFRACTIONr_mcbond_it0.881.52841
X-RAY DIFFRACTIONr_mcbond_other0.2571.51158
X-RAY DIFFRACTIONr_mcangle_it1.54224575
X-RAY DIFFRACTIONr_scbond_it2.34431704
X-RAY DIFFRACTIONr_scangle_it3.5394.51591
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 308 -
Rwork0.188 5723 -
all-6031 -
obs--90.72 %
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)
10.51480.07740.26780.6625-0.1620.57870.04810.0974-0.05310.15870.03840.0419-0.0171-0.0556-0.08650.01320.01240.00460.01110.00070.02512.8583.934-4.825
20.31930.0716-0.23580.5829-0.28660.72180.0249-0.08310.02020.06610.02830.0779-0.03350.0562-0.05310.011-0.00140.01150.0231-0.0020.0305-0.27632.36319.705
30.2847-0.08840.1141.21950.31810.15050.0265-0.00210.031-0.03780.0551-0.02530.0557-0.0091-0.08170.04590.00770.00410.01850.0130.01438.37121.6724.849
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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