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- PDB-3dri: Crystal structure of Lactococcal OppA co-crystallized with an oct... -

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Basic information

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


peptide transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / 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: peptide AASASA


Theoretical massNumber of molelcules
Total (without water)65,6212
Polymers65,6212
Non-polymers00
Water13,944774
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-4 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.669, 123.224, 59.604
Angle α, β, γ (deg.)90.00, 101.90, 90.00
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 peptide AASASA


Mass: 476.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesis
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 2.17 Å3/Da / Density % sol: 43.39 % / Mosaicity: 0.57 °
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: ID14-2 / 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
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 2.3 / Number: 192649 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / D res high: 1.8 Å / D res low: 61.663 Å / Num. obs: 51727 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.6942.3799.210.0520.0523.5
4.025.6910010.050.053.7
3.294.0210010.0540.0543.8
2.853.2910010.0610.0613.8
2.552.8510010.0980.0983.7
2.322.5510010.1470.1473.7
2.152.3210010.2130.2133.7
2.012.1510010.1330.1333.8
1.92.0110010.4850.4853.7
1.81.910010.2590.2593.7
ReflectionResolution: 1.8→61.663 Å / Num. obs: 51727 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 2.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.93.70.2592.82801675510.259100
1.9-2.013.70.4850.52646071220.485100
2.01-2.153.80.1335.32502566620.133100
2.15-2.323.70.2131.12345062660.213100
2.32-2.553.70.1471.22124757480.147100
2.55-2.853.70.0982.51944352100.098100
2.85-3.293.80.0618.91733146080.061100
3.29-4.023.80.05410.31462538930.054100
4.02-5.693.70.05111118430060.05100
5.69-42.373.50.0528586816610.05299.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.36 Å
Translation2.5 Å42.36 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DRF

3drf


Resolution: 1.8→42.37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.805 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2626 5.1 %RANDOM
Rwork0.161 ---
obs0.164 51692 99.93 %-
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: 14.571 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2---0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 0 0 774 5159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224493
X-RAY DIFFRACTIONr_bond_other_d0.0010.023016
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9526087
X-RAY DIFFRACTIONr_angle_other_deg0.85437410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53125.736197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57215764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.639159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02861
X-RAY DIFFRACTIONr_mcbond_it0.6411.52811
X-RAY DIFFRACTIONr_mcbond_other0.1561.51148
X-RAY DIFFRACTIONr_mcangle_it1.19124517
X-RAY DIFFRACTIONr_scbond_it1.92231682
X-RAY DIFFRACTIONr_scangle_it3.0894.51570
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 189 -
Rwork0.189 3590 -
all-3779 -
obs--99.97 %
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)
10.6413-0.13690.09750.3594-0.1410.43060.03450.1471-0.11980.0707-0.02380.0494-0.0548-0.0165-0.0107-0.01440.01710.00020.0061-0.03360.01142.85813.9337-4.8253
20.8305-0.16490.09650.4333-0.09470.5066-0.0196-0.1280.1180.06010.06480.00240.0292-0.0266-0.04520.01580.00270.00270.0046-0.00780.0124-0.276332.363519.7053
30.4321-0.2062-0.00310.56330.05750.0068-0.00890.06610.04030.00540.03770.01250.0337-0.0076-0.02880.03970.00120.00590.00270.01690.00568.370921.67174.8486
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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