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- PDB-5iai: Crystal structure of ABC transporter Solute Binding Protein Arad_... -

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Basic information

Entry
Database: PDB / ID: 5iai
TitleCrystal structure of ABC transporter Solute Binding Protein Arad_9887 from Agrobacterium radiobacter K84, target EFI-510945 in complex with Ribitol
ComponentsSugar ABC transporter
KeywordsSOLUTE-BINDING PROTEIN / ABC TRANSPORTER SOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-ribitol / Sugar ABC transporter
Similarity search - Component
Biological speciesAgrobacterium radiobacter (Agrobacterium genomosp. 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsVetting, M.W. / Bonanno, J.B. / Al Obaidi, N.F. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal structure of ABC transporter Solute Binding Protein Arad_9887 from Agrobacterium radiobacter K84, target EFI-510945 in complex with Ribitol
Authors: Vetting, M.W. / Bonanno, J.B. / Al Obaidi, N.F. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionFeb 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7643
Polymers46,5191
Non-polymers2442
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)166.272, 56.342, 52.095
Angle α, β, γ (deg.)90.000, 93.890, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1101-

HOH

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Components

#1: Protein Sugar ABC transporter


Mass: 46519.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium radiobacter (Agrobacterium genomosp. 4)
Strain: K84 / ATCC BAA-868 / Gene: Arad_9887 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9JM84
#2: Chemical ChemComp-RB0 / D-ribitol


Mass: 152.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H12O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 52.99 % / Mosaicity: 0.24 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM Ribitol); Reservoir (MCSG1 H7)(2.0 M Ammonium Sulfate, 0.1 M Bis-Tris pH 5.5); Cryoprotection (80% 2.5 LiSO4, 20% 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: Mar 18, 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: 1.6→82.94 Å / Num. obs: 63514 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 19.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.036 / Rrim(I) all: 0.098 / Net I/σ(I): 15.1 / Num. measured all: 470882 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.637.40.9262327831450.8310.3630.9952.2100
8.76-82.946.10.07222933790.990.0320.07935.690.9

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Processing

Software
NameVersionClassification
Aimless0.2.8data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→26.674 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.59
RfactorNum. reflection% reflection
Rfree0.1907 3220 5.08 %
Rwork0.1632 --
obs0.1647 63428 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.19 Å2 / Biso mean: 31.3381 Å2 / Biso min: 10.85 Å2
Refinement stepCycle: final / Resolution: 1.6→26.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 16 508 3563
Biso mean--27.37 39.46 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083141
X-RAY DIFFRACTIONf_angle_d0.9574276
X-RAY DIFFRACTIONf_chiral_restr0.054467
X-RAY DIFFRACTIONf_plane_restr0.007560
X-RAY DIFFRACTIONf_dihedral_angle_d11.8081866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62390.26791430.267626012744100
1.6239-1.64920.30781260.251726072733100
1.6492-1.67630.27641270.241226242751100
1.6763-1.70520.26341490.225525912740100
1.7052-1.73620.28871410.207226132754100
1.7362-1.76960.21941370.195626122749100
1.7696-1.80570.21721430.181526042747100
1.8057-1.84490.21891520.181225812733100
1.8449-1.88780.22131320.179325952727100
1.8878-1.9350.26371470.23152622276999
1.935-1.98730.1821400.165426112751100
1.9873-2.04580.19261490.154526012750100
2.0458-2.11180.18811270.158226132740100
2.1118-2.18730.17591170.15526752792100
2.1873-2.27480.22611380.18092573271198
2.2748-2.37830.18471260.148726282754100
2.3783-2.50360.16461490.148325992748100
2.5036-2.66030.16221480.156326222770100
2.6603-2.86550.2161280.168526482776100
2.8655-3.15340.20581640.169726032767100
3.1534-3.60880.20181610.153426282789100
3.6088-4.5430.13471260.132326812807100
4.543-26.67820.15971500.14722676282699
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)
10.62130.26410.19750.4909-0.350.5619-0.1549-0.22680.52890.04930.0428-0.0281-0.4548-0.09130.01470.28360.0643-0.03560.2003-0.09340.272764.113820.338360.559
20.9469-0.11190.29890.7655-0.07251.2290.0179-0.4325-0.16210.10160.06760.01040.0597-0.0736-0.05980.17540.03030.01280.21470.04260.159958.49134.649361.2229
33.09130.56530.47841.33860.57621.4041-0.1210.3053-0.1714-0.20390.17040.1702-0.0458-0.0487-0.0340.2333-0.0482-0.02280.18320.02570.224648.42221.161738.0715
41.8473-0.1750.17590.41580.45020.9553-0.01630.0437-0.2185-0.12690.10610.18450.0342-0.0838-0.08130.2267-0.0277-0.00930.14010.03910.220850.95072.072842.93
51.7225-0.34130.36050.88260.01081.336-0.115-0.547-0.07110.16910.14250.1927-0.0787-0.3265-0.01890.16970.06020.02960.30420.05380.161853.93587.185562.9007
61.0575-0.04370.27820.76930.13921.25470.10040.4207-0.2737-0.24360.0193-0.1780.22360.3269-0.10570.25160.02750.02140.2686-0.06540.251267.718-3.788438.7855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 88 )A33 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 175 )A89 - 175
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 213 )A176 - 213
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 300 )A214 - 300
5X-RAY DIFFRACTION5chain 'A' and (resid 301 through 394 )A301 - 394
6X-RAY DIFFRACTION6chain 'A' and (resid 395 through 431 )A395 - 431

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