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- PDB-2hfb: Crystal structure of selenomethionine-labelled RafE from Streptoc... -

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Basic information

Entry
Database: PDB / ID: 2hfb
TitleCrystal structure of selenomethionine-labelled RafE from Streptococcus pneumoniae
ComponentsSugar ABC transporter, sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / Periplasmic binding protein
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
Bacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sugar ABC transporter, sugar-binding protein / Sugar ABC transporter, sugar-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsPaterson, N.G. / Riboldi-Tunnicliffe, A. / Mitchell, T.J. / Isaacs, N.W.
CitationJournal: To be Published
Title: Crystal structure of selenomethionine-labelled RafE from Streptococcus pneumoniae
Authors: Paterson, N.G. / Riboldi-Tunnicliffe, A. / Mitchell, T.J. / Isaacs, N.W.
History
DepositionJun 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar ABC transporter, sugar-binding protein
B: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7543
Polymers92,7182
Non-polymers351
Water362
1
A: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3952
Polymers46,3591
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sugar ABC transporter, sugar-binding protein


Theoretical massNumber of molelcules
Total (without water)46,3591
Polymers46,3591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.538, 144.538, 224.082
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Sugar ABC transporter, sugar-binding protein


Mass: 46359.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: rafE / Plasmid: pQE-10 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97NW2, UniProt: A0A0H2URJ7*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 1.8M Ammonium sulfate, 0.1M Na citrate pH 5.1, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 11.54 % / Av σ(I) over netI: 15.2 / Number: 673644 / Rmerge(I) obs: 0.083 / Χ2: 0.97 / D res high: 2.9 Å / D res low: 29.51 Å / Num. obs: 57961 / % possible obs: 100
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
6.2329.5199.90.0350.7911.33651
4.956.231000.0730.9111.47784
4.334.951000.0821.1311.411130
3.934.331000.0940.8711.48767
3.653.931000.1120.6711.73141
3.443.651000.130.7111.7676
3.273.441000.1820.7511.7746
3.123.271000.2651.2611.41591
33.121000.3481.3711.44550
2.931000.4171.2611.56317
ReflectionResolution: 2.9→29.51 Å / Num. obs: 57961 / % possible obs: 100 % / Redundancy: 11.54 % / Rmerge(I) obs: 0.083 / Χ2: 0.97 / Net I/σ(I): 15.2 / Scaling rejects: 5053
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.9-311.560.4175.46714957831.26100
3-3.1211.440.3486.56671457821.37100
3.12-3.2711.410.26586677057981.26100
3.27-3.4411.770.18286861658250.75100
3.44-3.6511.760.1310.26797557760.71100
3.65-3.9311.730.11212.16805657910.67100
3.93-4.3311.480.09415.36731257980.87100
4.33-4.9511.410.08221.46740958091.13100
4.95-6.2311.470.07322.86727057990.91100
6.23-29.5111.330.03542.96637358000.7999.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.5Ldata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementResolution: 2.9→29.51 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1568 5.1 %RANDOM
Rwork0.248 ---
all0.25 ---
obs-31023 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.269 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å21.6 Å20 Å2
2--3.2 Å20 Å2
3----4.8 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 1 2 6045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225721
X-RAY DIFFRACTIONr_bond_other_d00.023704
X-RAY DIFFRACTIONr_angle_refined_deg2.2391.9397777
X-RAY DIFFRACTIONr_angle_other_deg4.4238969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.885738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.55425.763262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.48515846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.571513
X-RAY DIFFRACTIONr_chiral_restr0.2130.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026602
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021135
X-RAY DIFFRACTIONr_nbd_refined0.2790.21702
X-RAY DIFFRACTIONr_nbd_other0.2960.24219
X-RAY DIFFRACTIONr_nbtor_refined0.2150.22878
X-RAY DIFFRACTIONr_nbtor_other0.130.22835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2192
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0740.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3870.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4290.21
X-RAY DIFFRACTIONr_mcbond_it4.2431.53651
X-RAY DIFFRACTIONr_mcbond_other18.9321.51509
X-RAY DIFFRACTIONr_mcangle_it7.06525798
X-RAY DIFFRACTIONr_scbond_it4.78932070
X-RAY DIFFRACTIONr_scangle_it7.4954.51979
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 120 -
Rwork0.294 2110 -
obs-2230 100 %

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