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- PDB-3drh: Crystal structure of Lactococcal OppA co-crystallized with Leu-en... -

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Basic information

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


peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / 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: 1.7 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 AAAAAA


Theoretical massNumber of molelcules
Total (without water)65,5892
Polymers65,5892
Non-polymers00
Water13,439746
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-5 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.707, 123.007, 59.308
Angle α, β, γ (deg.)90.00, 102.10, 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 AAAAAA


Mass: 444.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / 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: 2.16 Å3/Da / Density % sol: 43.05 % / Mosaicity: 0.52 °
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: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC Q210 / Detector: CCD / Date: Jul 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionRedundancy: 1.6 % / Av σ(I) over netI: 10.8 / Number: 171359 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / D res high: 1.7 Å / D res low: 41.03 Å / Num. obs: 105411 / % possible obs: 87.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.3852.4175.710.0290.0291.8
3.85.388110.0280.0281.8
3.13.883.710.0290.0291.7
2.693.185.210.0380.0381.7
2.42.6986.710.0540.0541.6
2.192.487.810.0740.0741.6
2.032.1988.610.1050.1051.6
1.92.0389.310.1570.1571.6
1.791.989.810.2470.2471.6
1.71.798910.3650.3651.6
ReflectionResolution: 1.7→41.03 Å / Num. obs: 60984 / % possible obs: 87.1 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.791.60.365224425157070.36589
1.79-1.91.60.2473.123710150800.24789.8
1.9-2.031.60.1574.822135139500.15789.3
2.03-2.191.60.1057.120911130340.10588.6
2.19-2.41.60.0749.919146117700.07487.8
2.4-2.691.60.05413.117438105770.05486.7
2.69-3.11.70.03816.81533491420.03885.2
3.1-3.81.70.02919.21297075740.02983.7
3.8-5.381.80.02819.61002256830.02881
5.38-52.411.80.02918.1526828940.02975.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.93 Å
Translation2.5 Å35.93 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: 1.7→41 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.013 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3103 5.1 %RANDOM
Rwork0.165 ---
obs0.167 60836 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.592 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å2-0.06 Å2
2---0.35 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 0 746 5129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224548
X-RAY DIFFRACTIONr_bond_other_d0.0010.023049
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9526170
X-RAY DIFFRACTIONr_angle_other_deg0.88237499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5075577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41325.8200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95115776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.253159
X-RAY DIFFRACTIONr_chiral_restr0.080.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02873
X-RAY DIFFRACTIONr_mcbond_it0.7261.52847
X-RAY DIFFRACTIONr_mcbond_other0.1951.51160
X-RAY DIFFRACTIONr_mcangle_it1.28524582
X-RAY DIFFRACTIONr_scbond_it2.08731701
X-RAY DIFFRACTIONr_scangle_it3.2384.51588
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 232 -
Rwork0.219 4296 -
all-4528 -
obs--99.85 %
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)
10.6261-0.15650.13770.5008-0.1290.48860.03060.1205-0.09610.0497-0.0150.0639-0.0433-0.0172-0.0156-0.00210.01280.00370.0174-0.02370.03012.85813.9337-4.8253
20.9343-0.28030.12030.6726-0.16810.5542-0.0357-0.14650.09030.09370.07330.00540.0051-0.0256-0.03760.02810.00030.00390.0266-0.00350.0187-0.276332.363519.7053
30.4069-0.1327-0.01450.57370.0480.004-0.00270.04170.0378-0.01440.0312-0.01020.0366-0.007-0.02850.05190.0020.00560.02280.00920.02468.370921.67174.8486
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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