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- PDB-8jq5: Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase... -

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Basic information

Entry
Database: PDB / ID: 8jq5
TitleCrystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with D-allulose
ComponentsL-rhamnose isomerase
KeywordsISOMERASE / TIM barrel
Function / homology: / D-psicose / alpha-D-psicofuranose
Function and homology information
Biological speciesLacticaseibacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsYoshida, H. / Yoshihara, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2024
Title: X-ray structure and characterization of a probiotic Lactobacillus rhamnosus Probio-M9 L-rhamnose isomerase.
Authors: Yoshida, H. / Yamamoto, N. / Kurahara, L.H. / Izumori, K. / Yoshihara, A.
History
DepositionJun 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-rhamnose isomerase
B: L-rhamnose isomerase
C: L-rhamnose isomerase
D: L-rhamnose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,86920
Polymers198,9884
Non-polymers1,88116
Water14,898827
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21730 Å2
ΔGint-72 kcal/mol
Surface area53040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.887, 139.445, 146.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
L-rhamnose isomerase


Mass: 49746.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lacticaseibacillus rhamnosus (bacteria)
Gene: rhaA / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar
ChemComp-PSJ / D-psicose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar
ChemComp-PSV / alpha-D-psicofuranose / alpha-D-psicose / D-psicose / psicose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DPsifaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-psicofuranoseCOMMON NAMEGMML 1.0
a-D-PsifIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
PsiSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG550MME, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→48.94 Å / Num. obs: 192191 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.033 / Rrim(I) all: 0.123 / Χ2: 1.01 / Net I/σ(I): 17.5 / Num. measured all: 2569188
Reflection shellResolution: 1.73→1.76 Å / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 1.414 / Num. measured all: 127215 / Num. unique obs: 9422 / CC1/2: 0.722 / Rpim(I) all: 0.396 / Rrim(I) all: 1.469 / Χ2: 0.99 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
REFMAC5.8refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→46.23 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.854 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18671 9442 4.9 %RANDOM
Rwork0.13936 ---
obs0.14174 182641 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å2-0 Å2
2---0.32 Å20 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.73→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13531 0 104 827 14462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01313989
X-RAY DIFFRACTIONr_bond_other_d00.01712661
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.6518955
X-RAY DIFFRACTIONr_angle_other_deg1.3071.59229437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2751665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13122.792788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.429152352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6861580
X-RAY DIFFRACTIONr_chiral_restr0.060.21777
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215595
X-RAY DIFFRACTIONr_gen_planes_other00.023037
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_it1.7372.1166678
X-RAY DIFFRACTIONr_mcbond_other1.7162.1166677
X-RAY DIFFRACTIONr_mcangle_it2.3013.1818337
X-RAY DIFFRACTIONr_mcangle_other2.3033.1828338
X-RAY DIFFRACTIONr_scbond_it2.1042.3967311
X-RAY DIFFRACTIONr_scbond_other2.1042.3967311
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7143.48810619
X-RAY DIFFRACTIONr_long_range_B_refined3.1625.02516023
X-RAY DIFFRACTIONr_long_range_B_other3.10924.91615870
X-RAY DIFFRACTIONr_rigid_bond_restr4.796326650
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.87

Ens-IDDom-IDNumberRms dev position (Å)
1133816.31
2233454.7
3333456.31
4433536.13
5533534.81
6633456.68
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 685 -
Rwork0.197 13387 -
obs--99.98 %

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