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

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Basic information

Entry
Database: PDB / ID: 8wlb
TitleX-ray structure of Enterobacter cloacae allose-binding protein in complex with D-psicose
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 / alpha-D-psicopyranose / Allose ABC transporter
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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)33,0022
Polymers32,8221
Non-polymers1801
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.110, 113.140, 38.950
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-WEB / alpha-D-psicopyranose / (2~{S},3~{R},4~{R},5~{R})-2-(hydroxymethyl)oxane-2,3,4,5-tetrol


Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 20 mM D-psicose, 100 mM sodium citrate tribasic dihydrate, 22% (w/v) polyethylene glycol 1,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→43.29 Å / Num. obs: 32299 / % possible obs: 98.1 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 27.6
Reflection shellResolution: 1.71→1.75 Å / Num. unique obs: 2172 / CC1/2: 0.911

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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: 1.71→43.29 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.07 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24208 1591 4.9 %RANDOM
Rwork0.16747 ---
obs0.17125 30708 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.992 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.71→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 12 146 2299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132182
X-RAY DIFFRACTIONr_bond_other_d00.0162176
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.6412951
X-RAY DIFFRACTIONr_angle_other_deg1.2931.5945015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3945287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1525.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29515388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.993156
X-RAY DIFFRACTIONr_chiral_restr0.060.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022487
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02445
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_it4.7682.9791151
X-RAY DIFFRACTIONr_mcangle_it5.224.4811437
X-RAY DIFFRACTIONr_mcangle_other5.22431.7161438
X-RAY DIFFRACTIONr_scbond_it8.5213.5451031
X-RAY DIFFRACTIONr_scbond_other8.5173.5441032
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2285.0331515
X-RAY DIFFRACTIONr_rigid_bond_restr7.45432170
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 120 -
Rwork0.276 2046 -
obs--90.63 %

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