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- PDB-3ryb: Lactococcal OppA complexed with SLSQSLSQS -

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Basic information

Entry
Database: PDB / ID: 3ryb
TitleLactococcal OppA complexed with SLSQSLSQS
Components
  • Oligopeptide-binding protein oppA
  • Oligopeptide
KeywordsPEPTIDE BINDING PROTEIN / Substrate-binding protein / Peptide binding / Membrane anchored
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
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. / 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
Water15,475859
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-6 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.379, 58.921, 61.404
Angle α, β, γ (deg.)100.660, 101.310, 103.450
Int Tables number1
Space group name H-MP1

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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: llmg_0701, oppA / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 42.71 %
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: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→30.73 Å / Num. all: 83660 / Num. obs: 83652 / % possible obs: 93.4 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.034 / Rsym value: 0.048 / Net I/σ(I): 15.78
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.610.2812.92892014543192.8
1.61-1.740.1694.752723913696193.5
1.74-1.910.0918.312521512688194.1
1.91-2.130.04615.232281711476194.3
2.13-2.460.03122.542022410185194.8
2.46-3.010.02229.54169148532194.1
3.01-4.240.01641.34129956567193.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.77 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.73 Å
Translation2.5 Å30.73 Å

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Processing

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

3drf


Resolution: 1.5→30.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1952 / WRfactor Rwork: 0.1571 / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8855 / SU B: 2.595 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0779 / SU Rfree: 0.0819 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 4128 5 %RANDOM
Rwork0.1626 ---
obs0.1645 82542 93.77 %-
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 max: 68.68 Å2 / Biso mean: 18.5045 Å2 / Biso min: 6.96 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4444 0 0 859 5303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224611
X-RAY DIFFRACTIONr_bond_other_d0.0010.023089
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9536260
X-RAY DIFFRACTIONr_angle_other_deg0.86437602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4535588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5725.8200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53715788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.163159
X-RAY DIFFRACTIONr_chiral_restr0.080.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02893
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 299 -
Rwork0.236 5688 -
all-5987 -
obs--92.48 %
Refinement TLS params.Method: refined / Origin x: -11.7093 Å / Origin y: -10.2658 Å / Origin z: 19.9996 Å
111213212223313233
T0.0098 Å2-0.0056 Å20.003 Å2-0.0128 Å20.0024 Å2--0.0176 Å2
L0.5922 °2-0.0932 °20.0292 °2-0.3132 °2-0.1107 °2--0.3955 °2
S0.0534 Å °-0.0475 Å °-0.0016 Å °0.0018 Å °-0.0363 Å °0.0269 Å °0.037 Å °0.0041 Å °-0.0171 Å °

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