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- PDB-8jq3: Crystal structure of L-rhamnose isomerase from Lactobacillus rhamnosus -

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Basic information

Entry
Database: PDB / ID: 8jq3
TitleCrystal structure of L-rhamnose isomerase from Lactobacillus rhamnosus
ComponentsL-rhamnose isomerase
KeywordsISOMERASE / TIM barrel
Function / homology:
Function and homology information
Biological speciesLacticaseibacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)199,42712
Polymers198,9884
Non-polymers4408
Water13,349741
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21990 Å2
ΔGint-121 kcal/mol
Surface area53970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.700, 139.940, 147.310
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 550MME, 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: 1.9→50 Å / Num. obs: 146232 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.089 / Net I/σ(I): 22.94
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.9-1.950.689107400.8920.7151
1.95-20.619104330.930.6421
2-2.060.481101030.9550.4991
2.06-2.120.3798990.9730.3841
2.12-2.190.30395880.9820.3151
2.19-2.270.26192520.9850.2721
2.27-2.360.22689430.990.2351
2.36-2.450.18586180.9920.1931
2.45-2.560.15582910.9950.1611
2.56-2.690.13279030.9960.1371
2.69-2.830.10275670.9980.1061
2.83-30.08571590.9980.0881
3-3.210.06867410.9990.0711
3.21-3.470.05862990.9990.061
3.47-3.80.04657780.9990.0481
3.8-4.250.03952820.9990.0411
4.25-4.910.03546750.9990.0371
4.91-6.010.03639990.9990.0371
6.01-8.50.035314010.0361
8.5-500.028182210.0291

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
REFMAC5.8refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.51 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.215 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 7237 5 %RANDOM
Rwork0.15975 ---
obs0.16264 138900 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0 Å2
2---0.35 Å20 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.9→44.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13367 0 8 741 14116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01313750
X-RAY DIFFRACTIONr_bond_other_d0.0020.01712488
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.64118626
X-RAY DIFFRACTIONr_angle_other_deg1.2461.58529010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97551643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75522.64784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.304152331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5921582
X-RAY DIFFRACTIONr_chiral_restr0.0540.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215393
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023026
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_it1.8112.6046584
X-RAY DIFFRACTIONr_mcbond_other1.812.6036582
X-RAY DIFFRACTIONr_mcangle_it2.4433.9098217
X-RAY DIFFRACTIONr_mcangle_other2.4433.9098217
X-RAY DIFFRACTIONr_scbond_it1.9892.8037166
X-RAY DIFFRACTIONr_scbond_other1.9892.8037167
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5784.12210408
X-RAY DIFFRACTIONr_long_range_B_refined3.73530.53515841
X-RAY DIFFRACTIONr_long_range_B_other3.69930.40415684
X-RAY DIFFRACTIONr_rigid_bond_restr6.584326238
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)
1133227.58
2233167.52
3333175.3
4433304.92
5533196.58
6633277.46
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 522 -
Rwork0.202 10205 -
obs--99.96 %

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