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- PDB-9so1: Glucose/ xylose isomerase under ambient pressure with xylose -

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Basic information

Entry
Database: PDB / ID: 9so1
TitleGlucose/ xylose isomerase under ambient pressure 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 / alpha-D-xylopyranose / 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 ambient pressure 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)43,7866
Polymers43,2831
Non-polymers5025
Water5,963331
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)175,14224
Polymers173,1334
Non-polymers2,00920
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 area34370 Å2
ΔGint-145 kcal/mol
Surface area45090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.562, 99.367, 102.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-689-

HOH

21A-771-

HOH

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Components

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Protein , 1 types, 1 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

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: 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 , 3 types, 334 molecules

#4: 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
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
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: Dec 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.83→49.68 Å / Num. obs: 41298 / % possible obs: 98.5 % / Redundancy: 2.4 % / Biso Wilson estimate: 29.44 Å2 / CC1/2: 0.996 / Net I/σ(I): 5.1
Reflection shellResolution: 1.83→1.87 Å / Num. unique obs: 2936 / CC1/2: 0.335

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PDB_EXTRACTdata extraction
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→39.1 Å / SU ML: 0.3146 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7584
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 1928 4.67 %
Rwork0.1775 39367 -
obs0.1796 41295 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.02 Å2
Refinement stepCycle: LAST / Resolution: 1.83→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 28 331 3401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013225
X-RAY DIFFRACTIONf_angle_d1.00334375
X-RAY DIFFRACTIONf_chiral_restr0.0564454
X-RAY DIFFRACTIONf_plane_restr0.0107594
X-RAY DIFFRACTIONf_dihedral_angle_d16.24731217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.44561330.39752745X-RAY DIFFRACTION97
1.88-1.930.39671520.35632757X-RAY DIFFRACTION97.98
1.93-1.990.3531390.32932750X-RAY DIFFRACTION97.97
1.99-2.050.35371240.28262778X-RAY DIFFRACTION98.34
2.05-2.130.2641260.24312832X-RAY DIFFRACTION98.24
2.13-2.210.27881360.21672731X-RAY DIFFRACTION98.15
2.21-2.310.27191560.20022806X-RAY DIFFRACTION98.63
2.31-2.430.24921770.18112755X-RAY DIFFRACTION98.75
2.43-2.590.24091580.18352797X-RAY DIFFRACTION99.03
2.59-2.790.22631090.16552816X-RAY DIFFRACTION98.39
2.79-3.070.2125780.16192893X-RAY DIFFRACTION98.84
3.07-3.510.18861530.14832847X-RAY DIFFRACTION99.11
3.51-4.420.19131440.12812866X-RAY DIFFRACTION99.21
4.42-39.10.15871430.14892994X-RAY DIFFRACTION98.87

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