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- PDB-4qse: Crystal structure of ATU4361 sugar transporter from Agrobacterium... -

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Basic information

Entry
Database: PDB / ID: 4qse
TitleCrystal structure of ATU4361 sugar transporter from Agrobacterium Fabrum c58, target efi-510558, with bound glycerol
ComponentsABC-TYPE SUGAR TRANSPORTER
KeywordsTRANSPORT PROTEIN / SUGAR TRANSPORTER / ABC-TYPE / MALTOSE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS / ISOME
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / periplasmic space / 3-Layer(aba) Sandwich / Alpha Beta / ABC transporter, substrate binding protein (Sugar)
Function and homology information
Biological speciesAGROBACTERIUM FABRUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.37 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, K.L. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, K.L. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of maltoside transporter ATU4361 from Agrobacterium Fabrum, target EFI-510558
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionJul 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC-TYPE SUGAR TRANSPORTER
B: ABC-TYPE SUGAR TRANSPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3766
Polymers90,0072
Non-polymers3684
Water19,7081094
1
A: ABC-TYPE SUGAR TRANSPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1883
Polymers45,0041
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC-TYPE SUGAR TRANSPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1883
Polymers45,0041
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.088, 67.538, 75.960
Angle α, β, γ (deg.)90.00, 90.11, 90.74
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99999, -0.00086, -0.004389), (0.000858, -1, 0.000409), (-0.004389, 0.000405, 0.99999)24.54057, -13.12705, -37.90919

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Components

#1: Protein ABC-TYPE SUGAR TRANSPORTER


Mass: 45003.676 Da / Num. of mol.: 2 / Fragment: unp residues 27-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM FABRUM (bacteria) / Strain: C58 / Gene: ATU4361 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CGI0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 1094 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.6
Details: 2.07 CRYSTALLIZATION CONDITIONS, PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 10% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100 RATIO); RESERVOIR: 0.085 M SODIUM ACETATE, PH 4.6, 0.017 M AMMONIUM ...Details: 2.07 CRYSTALLIZATION CONDITIONS, PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 10% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100 RATIO); RESERVOIR: 0.085 M SODIUM ACETATE, PH 4.6, 0.017 M AMMONIUM ACETATE, 25% PEG4000, 15% (VOL/VOL/ GLYCEROL, VAPOR DIFFUSION, SITTING DROP
Temp details: 293

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2014 / Details: MIRRORS
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 277288 / % possible obs: 92 % / Observed criterion σ(I): -5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 21.1
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 3 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 5.8 / Rsym value: 0.179 / % possible all: 88.9

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.8.0071refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.37→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.31 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14811 4244 3 %RANDOM
Rwork0.11792 ---
obs0.1188 138020 94.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.02 Å2-0.28 Å2
2---0.16 Å2-0.5 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.37→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 0 24 1094 7054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.026260
X-RAY DIFFRACTIONr_bond_other_d0.0010.025987
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9628532
X-RAY DIFFRACTIONr_angle_other_deg0.79313879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6585804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4325.299268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.418151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9281522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021366
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7131.8333105
X-RAY DIFFRACTIONr_mcbond_other1.6631.8323104
X-RAY DIFFRACTIONr_mcangle_it1.8453.1063892
X-RAY DIFFRACTIONr_mcangle_other1.8493.1073893
X-RAY DIFFRACTIONr_scbond_it2.992.1883155
X-RAY DIFFRACTIONr_scbond_other2.992.1883155
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.233.534623
X-RAY DIFFRACTIONr_long_range_B_refined3.7258.0268527
X-RAY DIFFRACTIONr_long_range_B_other3.7248.0278528
X-RAY DIFFRACTIONr_rigid_bond_restr2.801312247
X-RAY DIFFRACTIONr_sphericity_free22.4875178
X-RAY DIFFRACTIONr_sphericity_bonded7.9513011
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.144 302 -
Rwork0.095 10153 -
obs--92.78 %

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