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- PDB-3drg: Lactococcal OppA complexed with bradykinin in the closed conformation -

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Basic information

Entry
Database: PDB / ID: 3drg
TitleLactococcal OppA complexed with bradykinin in the closed conformation
Components
  • Bradykinin
  • Oligopeptide-binding protein oppA
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: 2.5 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: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Bradykinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1563
Polymers66,1212
Non-polymers351
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-22 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.175, 58.636, 61.277
Angle α, β, γ (deg.)100.970, 101.120, 103.020
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
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 Bradykinin


Mass: 976.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesis
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 43.38 % / Mosaicity: 0.97 °
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: 0.933 Å
DetectorType: ADSC Q4 / Detector: CCD / Date: Feb 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionRedundancy: 1.9 % / Av σ(I) over netI: 2 / Number: 35303 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / D res high: 2.5 Å / D res low: 58.321 Å / Num. obs: 18131 / % possible obs: 96.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.9158.3296.910.0460.0461.9
5.597.9197.110.0360.0361.9
4.565.5996.410.0380.0381.9
3.954.5696.710.0550.0552
3.543.9596.310.050.051.9
3.233.549610.0690.0692
2.993.2396.310.0940.0942
2.82.999610.1410.1412
2.642.89610.1970.1972
2.52.6495.710.2590.2591.9
ReflectionResolution: 2.5→58.321 Å / Num. all: 35303 / Num. obs: 18131 / % possible obs: 96.2 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.641.90.2592.7517226600.25995.7
2.64-2.820.1973.7488824980.19796
2.8-2.9920.1415.2457623380.14196
2.99-3.2320.0947.5434022210.09496.3
3.23-3.5420.06910.1388919890.06996
3.54-3.951.90.0513.4351618060.0596.3
3.95-4.5620.0551.2315516160.05596.7
4.56-5.591.90.03818265413670.03896.4
5.59-7.911.90.03618.8202410530.03697.1
7.91-58.321.90.0466.610895830.04696.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å58.3 Å
Translation2.5 Å58.3 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: 2.5→58.32 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.844 / SU B: 13.901 / SU ML: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 927 5.1 %RANDOM
Rwork0.218 ---
obs0.22 18131 96.22 %-
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: 38.656 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0.05 Å20.03 Å2
2--0.01 Å20.07 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4441 0 1 137 4579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224546
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.9546158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0645569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71725.6200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3515770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9851510
X-RAY DIFFRACTIONr_chiral_restr0.0590.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213464
X-RAY DIFFRACTIONr_mcbond_it0.1571.52837
X-RAY DIFFRACTIONr_mcangle_it0.28924561
X-RAY DIFFRACTIONr_scbond_it0.27531709
X-RAY DIFFRACTIONr_scangle_it0.4824.51597
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 64 -
Rwork0.278 1289 -
all-1353 -
obs--95.48 %

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