Crystal structure of carbohydrate transporter solute binding protein Arad_9553 from Agrobacterium Radiobacter, Target EFI-511541, in complex with D-arabinose
Components
Sugar ABC transporter
Keywords
TRANSPORT PROTEIN / SUGAR TRANSPORTER / ABC-TYPE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS
Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal grow
Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-ARABINOSE); RESERVOIR: 0.1 M TRIS-HCL, PH 8.5, 2.5 M AMMONIUM SULFATE; CRYOPROTECTION: RESERVOIR SOLUTION; VAPOR DIFFUSION, SITTING DROP, temperature 294K
Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Resolution: 1.35→50 Å / Num. obs: 55996 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.3
Reflection shell
Resolution: 1.35→1.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.4 / % possible all: 99.2
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Processing
Software
Name
Version
Classification
SHELX
modelbuilding
ARP/wARP
modelbuilding
REFMAC
5.8.0073
refinement
HKL-3000
datareduction
HKL-3000
datascaling
SHELX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.739 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20547
1633
3 %
RANDOM
Rwork
0.15597
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obs
0.15747
53008
98.63 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK