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- PDB-3rya: Lactococcal OppA complexed with SLSQLSSQS -

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Basic information

Entry
Database: PDB / ID: 3rya
TitleLactococcal OppA complexed with SLSQLSSQS
Components
  • Oligopeptide-binding protein oppA
  • Oligopeptide
KeywordsPEPTIDE BINDING PROTEIN / Substrate-binding protein / Peptide binding / Membrane anchored
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: 2.9 Å
AuthorsBerntsson, R.P.-A. / Thunnissen, A.-M.W.H. / Poolman, B. / Slotboom, D.-J.
CitationJournal: J.Bacteriol. / Year: 2011
Title: Importance of a Hydrophobic Pocket for Peptide Binding in Lactococcal OppA.
Authors: Berntsson, R.P. / Thunnissen, A.M. / Poolman, B. / Slotboom, D.J.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 13, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,0812
Polymers66,0812
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-7 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.628, 99.555, 123.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: MG1363 / Gene: oppA, llmg_0701 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): MG1363 / References: UniProt: A2RJ53
#2: Protein/peptide Oligopeptide /


Mass: 935.977 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 1.94 Å3/Da / Density % sol: 36.69 %
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: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→38.41 Å / Num. all: 11913 / Num. obs: 11804 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.211 / Rsym value: 0.237 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.9-2.960.8052.069403201195.3
2.96-3.160.5313.29804198999.8
3.16-3.410.3634.639107185899.6
3.41-3.740.2366.968398172399.3
3.74-4.180.1839.067562155498.3
4.18-4.820.13611.556683137398.8
4.82-5.880.14310.675674119598.4
5.88-8.250.11612.75437793397.6
8.250.04526.16241056495.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.11 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.79 Å46.19 Å
Translation2.79 Å46.19 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DRF, chain A

3drf


Resolution: 2.9→38.4 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.843 / WRfactor Rfree: 0.2302 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.06 / FOM work R set: 0.8628 / SU B: 39.125 / SU ML: 0.348 / SU R Cruickshank DPI: 0.4413 / SU Rfree: 0.4805 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 590 5 %RANDOM
Rwork0.2244 ---
obs0.2261 11801 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 86.93 Å2 / Biso mean: 29.6917 Å2 / Biso min: 8.18 Å2
Baniso -1Baniso -2Baniso -3
1--3.47 Å2-0 Å2-0 Å2
2---1.49 Å2-0 Å2
3---4.96 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4414 0 0 0 4414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224604
X-RAY DIFFRACTIONr_bond_other_d0.0010.023088
X-RAY DIFFRACTIONr_angle_refined_deg0.9481.9526251
X-RAY DIFFRACTIONr_angle_other_deg0.76637601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5925.842202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47615788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.973159
X-RAY DIFFRACTIONr_chiral_restr0.060.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02884
LS refinement shellResolution: 2.9→2.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 42 -
Rwork0.293 803 -
all-845 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 9.6937 Å / Origin y: 0.086 Å / Origin z: 18.6584 Å
111213212223313233
T0.0567 Å2-0.0092 Å2-0.0102 Å2-0.0664 Å2-0.0078 Å2--0.0291 Å2
L0.0963 °2-0.1228 °20.0558 °2-0.3926 °2-0.1042 °2--0.2441 °2
S0.0229 Å °-0.02 Å °-0.0297 Å °-0.0288 Å °-0.0071 Å °-0.0134 Å °-0.0232 Å °-0.0031 Å °-0.0158 Å °

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