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- PDB-8wl9: X-ray structure of Enterobacter cloacae allose-binding protein in... -

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Basic information

Entry
Database: PDB / ID: 8wl9
TitleX-ray structure of Enterobacter cloacae allose-binding protein in complex with D-ribose
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 / beta-D-ribopyranose / Allose ABC transporter
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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)32,9722
Polymers32,8221
Non-polymers1501
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.850, 110.680, 37.260
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: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10 mM D-ribose, 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: Dec 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→37.29 Å / Num. obs: 20335 / % possible obs: 95.9 % / Redundancy: 6.3 % / CC1/2: 0.995 / Net I/σ(I): 8.7
Reflection shellResolution: 1.93→1.98 Å / Num. unique obs: 1440 / CC1/2: 0.83

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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: 1.93→37.29 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.236 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28978 1026 5 %RANDOM
Rwork0.2386 ---
obs0.24109 19639 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.617 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.93→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 10 59 2210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132180
X-RAY DIFFRACTIONr_bond_other_d00.0162175
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.6392947
X-RAY DIFFRACTIONr_angle_other_deg1.1851.5945013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3795287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02825.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87315388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.32156
X-RAY DIFFRACTIONr_chiral_restr0.0440.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022487
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02445
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_it2.0782.4971151
X-RAY DIFFRACTIONr_mcbond_other2.072.4961150
X-RAY DIFFRACTIONr_mcangle_it2.7433.7421437
X-RAY DIFFRACTIONr_mcangle_other2.7423.7431438
X-RAY DIFFRACTIONr_scbond_it3.1272.8341029
X-RAY DIFFRACTIONr_scbond_other3.1272.8341029
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5694.0781511
X-RAY DIFFRACTIONr_long_range_B_refined5.29330.5232396
X-RAY DIFFRACTIONr_long_range_B_other5.29630.5162390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 72 -
Rwork0.267 1369 -
obs--91.38 %

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