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- PDB-9so2: Glucose/xylose isomerase under 18MPa with xylose -

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Basic information

Entry
Database: PDB / ID: 9so2
TitleGlucose/xylose isomerase under 18MPa with xylose
ComponentsXylose isomerase
KeywordsISOMERASE / high pressure / high-pressure / xylose
Function / homology
Function and homology information


D-xylose metabolic process / xylose isomerase / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / D-xylose / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces pseudogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsKlonecka, A. / Slawek, J. / Kurpiewska, K. / Taube, M. / Janicki, M. / Kozak, M.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2020/39/O/ST4/O3465 Poland
Ministry of Science and Higher Education (Poland)1/SOL/2021/2 Poland
CitationJournal: To Be Published
Title: Glucose/xylose isomerase under 18MPa with xylose
Authors: Klonecka, A. / Slawek, J. / Kurpiewska, K. / Taube, M. / Janicki, M. / Kozak, M.
History
DepositionSep 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6847
Polymers43,2831
Non-polymers4016
Water11,169620
1
A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,73628
Polymers173,1334
Non-polymers1,60324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2_555-x,-y,z1
point symmetry operation3_555-x,y,-z1
point symmetry operation4_555x,-y,-z1
Buried area35570 Å2
ΔGint-140 kcal/mol
Surface area45260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.853, 99.679, 102.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

21A-925-

HOH

31A-952-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces pseudogriseolus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Sugar ChemComp-XLS / D-xylose / D-XYLOSE (LINEAR FORM)


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 625 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 4K, 0.15 mM ammonium sulphate, and 20 mM Tris at pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.83→71.52 Å / Num. obs: 53354 / % possible obs: 90.8 % / Redundancy: 2.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.08232 / Rrim(I) all: 0.1114 / Net I/σ(I): 5.07
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 0.823 / Num. unique obs: 4204 / CC1/2: 0.592 / CC star: 0.862

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
REFMACphasing
PDB_EXTRACTdata extraction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→71.52 Å / SU ML: 0.2049 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.212 2183 5.11 %
Rwork0.1673 40539 -
obs0.1696 42722 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.47 Å2
Refinement stepCycle: LAST / Resolution: 1.83→71.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 20 622 3683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01283310
X-RAY DIFFRACTIONf_angle_d1.05694498
X-RAY DIFFRACTIONf_chiral_restr0.0624456
X-RAY DIFFRACTIONf_plane_restr0.0113621
X-RAY DIFFRACTIONf_dihedral_angle_d16.14031243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.870.35971020.37012505X-RAY DIFFRACTION99.5
1.87-1.910.30141620.33842487X-RAY DIFFRACTION100
1.91-1.960.31091580.32082487X-RAY DIFFRACTION99.96
1.96-2.010.32031330.28222492X-RAY DIFFRACTION99.92
2.01-2.070.30721470.26492510X-RAY DIFFRACTION99.89
2.07-2.140.27931290.22522542X-RAY DIFFRACTION99.93
2.14-2.220.20691160.2012483X-RAY DIFFRACTION99.77
2.22-2.310.23531370.18632528X-RAY DIFFRACTION99.96
2.31-2.410.23661080.16842534X-RAY DIFFRACTION99.92
2.41-2.540.22051480.1652524X-RAY DIFFRACTION100
2.54-2.70.19311580.16562509X-RAY DIFFRACTION100
2.7-2.90.19911290.1512548X-RAY DIFFRACTION99.96
2.9-3.20.19321070.152579X-RAY DIFFRACTION100
3.2-3.660.19351400.13442558X-RAY DIFFRACTION99.85
3.66-4.610.1531980.122620X-RAY DIFFRACTION99.96
4.61-71.520.19992110.15092633X-RAY DIFFRACTION99.75

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