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- PDB-4r2b: Crystal structure of sugar transporter Oant_3817 from Ochrobactru... -

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Basic information

Entry
Database: PDB / ID: 4r2b
TitleCrystal structure of sugar transporter Oant_3817 from Ochrobactrum anthropi, target EFI-510528, with bound glucose
ComponentsExtracellular solute-binding protein family 1
KeywordsTRANSPORT PROTEIN / SUGAR TRANSPORTER / SBP-TYPE / ENZYME FUNCTION INITIATIVE (EFI) / STRUCTURAL GENOMICS
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 / alpha-D-glucopyranose / Extracellular solute-binding protein family 1
Function and homology information
Biological speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / 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 Glucose Transporter Oant_3817 from Ochrobactrum Anthropi, Target EFI-510528
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.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Structure summary
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular solute-binding protein family 1
B: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5314
Polymers86,1712
Non-polymers3602
Water9,332518
1
A: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2662
Polymers43,0851
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2662
Polymers43,0851
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.457, 61.374, 96.260
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.998487, -0.010578, -0.05396), (0.011131, 0.999888, 0.009962), (0.053849, -0.010547, 0.998493)11.18781, 1.28313, -48.41073

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Components

#1: Protein Extracellular solute-binding protein family 1


Mass: 43085.453 Da / Num. of mol.: 2 / Fragment: UNP residues 28-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: ATCC 49188 / DSM 6882 / NCTC 12168 / Gene: Oant_3817 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6X5L9
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4
Details: PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 5% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100 RATIO). RESERVOIR: 1.0 M LITHIUM CHLORIDE, 0.1 M SODIUM CITRATE:HCL, 20% PEG6000, pH 4.0, VAPOR DIFFUSION, SITTING DROP

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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: Jul 31, 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: 1.87→50 Å / Num. obs: 57914 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 6 % / Biso Wilson estimate: 19.139 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 13
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.98 / % possible all: 98.2

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→36.76 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.173 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 1708 3 %RANDOM
Rwork0.17504 ---
obs0.17667 55794 99.33 %-
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: 24.937 Å2
Baniso -1Baniso -2Baniso -3
1-12.95 Å20 Å2-10.61 Å2
2---14.73 Å2-0 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.87→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 0 24 518 6578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196200
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9428400
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5795788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6225.652276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.906151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5051518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021370
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_it7.3084.2353158
X-RAY DIFFRACTIONr_mcbond_other7.9086.0813157
X-RAY DIFFRACTIONr_mcangle_it7.1336.2353944
X-RAY DIFFRACTIONr_mcangle_other7.6559.0223945
X-RAY DIFFRACTIONr_scbond_it15.8025.3943042
X-RAY DIFFRACTIONr_scbond_other18.8157.343042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.7510.2414457
X-RAY DIFFRACTIONr_long_range_B_refined14.53518.9167618
X-RAY DIFFRACTIONr_long_range_B_other14.66318.7957405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 120 -
Rwork0.314 3870 -
obs--93.2 %

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