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- PDB-3fto: Crystal structure of OppA in a open conformation -

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Basic information

Entry
Database: PDB / ID: 3fto
TitleCrystal structure of OppA in a open conformation
ComponentsOligopeptide-binding protein oppA
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 subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.38 Å
AuthorsBerntsson, R.P.-A. / Oktaviani, N.A. / Fusetti, F. / Thunnissen, A.-M.W.H. / Poolman, B. / Slotboom, D.-J.
CitationJournal: Protein Sci. / Year: 2009
Title: Selenomethionine incorporation in proteins expressed in Lactococcus lactis.
Authors: Berntsson, R.P. / Alia Oktaviani, N. / Fusetti, F. / Thunnissen, A.M. / Poolman, B. / Slotboom, D.J.
History
DepositionJan 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oligopeptide-binding protein oppA


Theoretical massNumber of molelcules
Total (without water)65,8011
Polymers65,8011
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.577, 122.287, 59.408
Angle α, β, γ (deg.)90.000, 102.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Oligopeptide-binding protein oppA


Mass: 65801.320 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 subsp. cremoris (lactic acid bacteria)
Strain: MG1363 / Gene: llmg_0701, oppA / Plasmid: pAMP21
Production host: Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Strain (production host): MG1363 / References: UniProt: A2RJ53
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.14 Å3/Da / Density % sol: 42.43 % / Mosaicity: 0.814 °
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: BM16 / Wavelength: 0.979 Å
DetectorType: ADSC Q210r / Detector: CCD / Date: Apr 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 6.2 % / Av σ(I) over netI: 44.89 / Number: 136650 / Rmerge(I) obs: 0.083 / Χ2: 4.59 / D res high: 2.38 Å / D res low: 50 Å / Num. obs: 22117 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.135098.510.08511.0066.1
4.075.1310010.0665.8396.2
3.554.0710010.0715.6056.2
3.233.5510010.0774.5036.2
33.2310010.0834.0186.3
2.82310010.0983.5236.2
2.682.8210010.1163.3556.2
2.562.6810010.1373.0616.3
2.472.5610010.1462.7026.1
2.382.4710010.1582.2776
ReflectionResolution: 2.38→50 Å / Num. obs: 22117 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.083 / Χ2: 4.591 / Net I/σ(I): 44.886
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.38-2.4760.15822382.277100
2.47-2.566.10.14621732.702100
2.56-2.686.30.13722153.061100
2.68-2.826.20.11622093.355100
2.82-36.20.09821933.523100
3-3.236.30.08322164.018100
3.23-3.556.20.07722284.503100
3.55-4.076.20.07121915.605100
4.07-5.136.20.06622295.839100
5.13-506.10.085222511.00698.5

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.38 Å / D res low: 19.8 Å / FOM : 0.349 / FOM acentric: 0.359 / FOM centric: 0 / Reflection: 22071 / Reflection acentric: 21450 / Reflection centric: 621
Phasing MAD setR cullis acentric: 1.68 / R cullis centric: 1 / Highest resolution: 2.38 Å / Lowest resolution: 19.8 Å / Loc acentric: 0.2 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 21450 / Reflection centric: 621
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
10.34-19.81.180.30.221823
7-10.341.360.30.257941
5.29-71.560.30.1110256
4.25-5.291.210.20.2180769
3.55-4.251.250.20.1267685
3.05-3.551.530.20.1375299
2.67-3.052.350.10.14977117
2.38-2.673.20.106339131
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1SE30-0.637-0.914-0.20
2SE30-0.439-1.118-0.5970
3SE30-0.674-0.826-0.6170
4SE30-0.364-1.132-0.5530
5SE30-0.831-1.117-0.6390
6SE30-0.342-0.865-0.7190
7SE30-0.279-0.889-0.8010
8SE30-0.827-1.055-0.4490
9SE30-0.627-0.85-0.8470
10SE30-0.662-1.101-0.8090
11SE30-0.637-0.925-0.2620
12SE30-0.659-0.985-0.7540
13SE30-0.714-0.992-0.5650
14SE30-0.677-0.939-0.2160
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10.34-19.80.4840.535024121823
7-10.340.4940.529062057941
5.29-70.4410.46301158110256
4.25-5.290.480.49901876180769
3.55-4.250.3430.35302761267685
3.05-3.550.4170.42803851375299
2.67-3.050.3050.312050944977117
2.38-2.670.2720.277064706339131
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 22071
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.26-10057.60.818513
6.57-8.2656.30.864510
5.79-6.5754.60.846503
5.28-5.79520.854501
4.89-5.2853.80.886522
4.57-4.89500.884575
4.31-4.5749.50.879604
4.09-4.3153.20.872668
3.9-4.0956.60.875653
3.73-3.955.30.86721
3.58-3.7362.50.85726
3.45-3.5851.40.868785
3.33-3.4554.10.855776
3.23-3.3357.40.86816
3.13-3.2354.20.862858
3.04-3.13550.84854
2.96-3.0456.90.841910
2.89-2.96560.815915
2.82-2.89620.824922
2.75-2.8262.20.7851003
2.69-2.7563.60.795954
2.64-2.6961.50.8131012
2.58-2.6463.60.791033
2.53-2.58660.7931061
2.48-2.5363.70.7531063
2.44-2.4868.20.7421099
2.38-2.4468.40.691514

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.38→21.23 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.861 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.9 / FOM work R set: 0.806 / SU B: 8.967 / SU ML: 0.213 / SU R Cruickshank DPI: 0.713 / SU Rfree: 0.315 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.713 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1128 5.1 %RANDOM
Rwork0.211 ---
obs0.214 22093 99.44 %-
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: 68.39 Å2 / Biso mean: 35.666 Å2 / Biso min: 9.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20.63 Å2
2---1.16 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.38→21.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4354 0 0 235 4589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0224456
X-RAY DIFFRACTIONr_bond_other_d00.023857
X-RAY DIFFRACTIONr_angle_refined_deg0.6421.9526037
X-RAY DIFFRACTIONr_angle_other_deg0.50339081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.995558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28225.736197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55915761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.979159
X-RAY DIFFRACTIONr_chiral_restr0.040.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214985
X-RAY DIFFRACTIONr_gen_planes_other00.02854
X-RAY DIFFRACTIONr_mcbond_it0.1611.52777
X-RAY DIFFRACTIONr_mcbond_other0.0161.51137
X-RAY DIFFRACTIONr_mcangle_it0.30824467
X-RAY DIFFRACTIONr_scbond_it0.43131679
X-RAY DIFFRACTIONr_scangle_it0.6964.51570
LS refinement shellResolution: 2.38→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 67 -
Rwork0.24 1463 -
all-1530 -
obs--94.8 %

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