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- PDB-8wl5: X-ray structure of Enterobacter cloacae allose-binding protein in... -

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Basic information

Entry
Database: PDB / ID: 8wl5
TitleX-ray structure of Enterobacter cloacae allose-binding protein in free form
ComponentsAllose ABC transporter
KeywordsSUGAR BINDING PROTEIN / Allose-binding protein
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / outer membrane-bounded periplasmic space / Allose ABC transporter
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsKamitori, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: X-ray structures of Enterobacter cloacae allose-binding protein in complexes with monosaccharides demonstrate its unique recognition mechanism for high affinity to allose.
Authors: Kamitori, S.
History
DepositionSep 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allose ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8842
Polymers32,8221
Non-polymers621
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.960, 82.430, 47.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Allose ABC transporter / D-allose-binding periplasmic protein


Mass: 32821.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: AI2656V1_0345, AI2799V1_0351, CGS27_05760 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G3F0C7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 200 mM ammonium fluoride, 20% (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→47.97 Å / Num. obs: 27510 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.6
Reflection shellResolution: 1.87→1.92 Å / Num. unique obs: 2013 / CC1/2: 0.773

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RPJ

1rpj


Resolution: 1.87→47.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.669 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24077 1319 4.8 %RANDOM
Rwork0.16609 ---
obs0.16976 26191 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.642 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0 Å2
2---0.11 Å20 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.87→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 4 117 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162188
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.6332960
X-RAY DIFFRACTIONr_angle_other_deg1.311.5885041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2895289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15825.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07915392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.787156
X-RAY DIFFRACTIONr_chiral_restr0.0570.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022507
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02449
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_it4.4992.3141159
X-RAY DIFFRACTIONr_mcangle_it4.8463.4731447
X-RAY DIFFRACTIONr_mcangle_other4.8837.3331448
X-RAY DIFFRACTIONr_scbond_it7.4382.8641033
X-RAY DIFFRACTIONr_scbond_other7.4352.8631034
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.714.0411514
X-RAY DIFFRACTIONr_rigid_bond_restr7.16832189
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
Rfree0.32 106 -
Rwork0.245 1903 -
obs--99.95 %

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