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- PDB-4yo7: Crystal Structure of an ABC transporter solute binding protein (I... -

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Basic information

Entry
Database: PDB / ID: 4yo7
TitleCrystal Structure of an ABC transporter solute binding protein (IPR025997) from Bacillus halodurans C-125 (BH2323, TARGET EFI-511484) with bound myo-inositol
ComponentsSugar ABC transporter (Sugar-binding protein)
KeywordsSOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / Sugar ABC transporter (Sugar-binding protein)
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. ...Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal Structure of an ABC transporter solute binding protein (IPR025997) from Bacillus halodurans C-125 (BH2323, TARGET EFI-511484) with bound myo-inositol
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, ...Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9577
Polymers35,6451
Non-polymers3126
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.155, 79.845, 118.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-403-

MG

21A-551-

HOH

31A-572-

HOH

41A-588-

HOH

51A-593-

HOH

61A-595-

HOH

71A-607-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sugar ABC transporter (Sugar-binding protein)


Mass: 35644.988 Da / Num. of mol.: 1 / Fragment: residues 21-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: BH2323 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KAG4

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Non-polymers , 5 types, 301 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL / Inositol


Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Comment: neurotransmitter, hormone*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.26 Å3/Da / Density % sol: 45.53 % / Description: Flat Tetragonal plate with some thickness
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM myo-inositol); Reservoir (0.2 M Magnisium chloride, 0.1M Sodium cacodylate, pH 6.50, 50%(w/v) PEG 200); Cryoprotection 100% Reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 24, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 35728 / % possible obs: 98.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 13.01 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.021 / Rrim(I) all: 0.068 / Χ2: 0.893 / Net I/av σ(I): 30.779 / Net I/σ(I): 10.6 / Num. measured all: 369580
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.739.70.74517520.8510.2480.7870.88997.9
1.73-1.769.60.63117680.8790.2110.6670.8797.7
1.76-1.799.80.55617380.8980.1840.5870.89297.9
1.79-1.839.70.49217250.920.1630.5190.90297.7
1.83-1.879.80.37417630.950.1230.3950.88498
1.87-1.919.80.2917640.9710.0950.3050.85798.2
1.91-1.969.90.2317480.9790.0750.2420.85698.6
1.96-2.029.90.18617810.9850.0610.1960.84298.7
2.02-2.07100.14617620.990.0470.1540.82498.7
2.07-2.1410.10.12817840.9920.0420.1340.82198.8
2.14-2.2210.30.10317500.9940.0330.1080.78798.5
2.22-2.3110.40.09517800.9950.030.10.79899.1
2.31-2.4110.60.08418130.9960.0270.0880.82499.3
2.41-2.5410.80.08217760.9960.0250.0860.98699.1
2.54-2.711.10.08518030.9960.0260.0891.27299.4
2.7-2.9111.20.07718130.9950.0230.0811.47899.5
2.91-3.211.30.06518250.9970.020.0681.31899.6
3.2-3.6611.20.0418210.9980.0120.0420.71699.8
3.66-4.6111.10.0318570.9990.0090.0310.50699.7
4.61-10010.40.02919050.9970.0090.030.46697.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→24.539 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1693 1760 5.01 %
Rwork0.1387 33362 -
obs0.1402 35122 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.64 Å2 / Biso mean: 19.7567 Å2 / Biso min: 5.49 Å2
Refinement stepCycle: final / Resolution: 1.7→24.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 17 295 2476
Biso mean--12.34 32.78 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122237
X-RAY DIFFRACTIONf_angle_d1.2183000
X-RAY DIFFRACTIONf_chiral_restr0.052353
X-RAY DIFFRACTIONf_plane_restr0.006405
X-RAY DIFFRACTIONf_dihedral_angle_d13.844832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74030.21151190.18592193231284
1.7403-1.79150.18851300.16842413254391
1.7915-1.84930.20871330.16752467260095
1.8493-1.91540.17861220.15372562268498
1.9154-1.99210.18641460.13932563270998
1.9921-2.08270.14841360.12482603273999
2.0827-2.19240.16411630.11782572273599
2.1924-2.32970.15761460.11732582272899
2.3297-2.50940.17121530.12182596274999
2.5094-2.76160.14441300.12632655278599
2.7616-3.16050.17261180.132426722790100
3.1605-3.97920.17441330.133626892822100
3.9792-24.54170.16191310.15822795292699
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)
10.40250.17210.02181.19870.64170.76210.0143-0.0041-0.06140.10480.0564-0.23090.0920.1046-0.05490.08680.0227-0.00910.10760.00170.137754.1654-1.384832.7779
20.43850.08960.14370.97530.31620.56350.0425-0.02010.00470.0512-0.03930.07-0.0507-0.02720.00740.063-0.01620.0150.06750.0080.075243.41457.241336.0887
30.6305-0.0437-0.08021.16590.06991.04230.0741-0.07660.02090.2513-0.0147-0.0759-0.11670.0934-0.05370.1149-0.02460.0020.1103-0.01350.095650.601726.948947.6081
40.32540.02460.14641.08160.52250.71660.0428-0.2588-0.12570.7303-0.0222-0.08360.23570.0538-0.04930.2711-0.0352-0.0740.11820.01150.002751.2428.606651.5656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 96 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 161 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 247 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 323 )A0

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