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- PDB-9so3: Glucose/ xylose isomerase under 125 MPa with xylose -

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Basic information

Entry
Database: PDB / ID: 9so3
TitleGlucose/ xylose isomerase under 125 MPa 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: 1.3 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 125 MPa 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)43,7088
Polymers43,2831
Non-polymers4257
Water12,052669
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)174,83332
Polymers173,1334
Non-polymers1,70028
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
MethodPISA
Unit cell
Length a, b, c (Å)93.009, 98.737, 102.903
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-977-

HOH

21A-986-

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, 675 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
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: 1.3→40.96 Å / Num. obs: 140423 / % possible obs: 98.74 % / Redundancy: 4.9 % / Biso Wilson estimate: 10.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09919 / Net I/σ(I): 7.9
Reflection shellResolution: 1.3→1.31 Å / Num. unique obs: 17574 / CC1/2: 0.425

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→40.96 Å / SU ML: 0.1229 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9838
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.162 5699 4.97 %
Rwork0.1333 108897 -
obs0.1347 114596 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.39 Å2
Refinement stepCycle: LAST / Resolution: 1.3→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 21 669 3729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693377
X-RAY DIFFRACTIONf_angle_d0.98184601
X-RAY DIFFRACTIONf_chiral_restr0.0784474
X-RAY DIFFRACTIONf_plane_restr0.0149634
X-RAY DIFFRACTIONf_dihedral_angle_d15.18911294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.3311960.27993612X-RAY DIFFRACTION98.73
1.31-1.330.24721930.26243628X-RAY DIFFRACTION98.58
1.33-1.350.281870.24943548X-RAY DIFFRACTION98.71
1.35-1.360.29941760.24613606X-RAY DIFFRACTION98.59
1.36-1.380.2951580.22783576X-RAY DIFFRACTION97.8
1.38-1.40.25951730.22453636X-RAY DIFFRACTION98.32
1.4-1.420.20461760.21593599X-RAY DIFFRACTION98.95
1.42-1.440.23891720.20453638X-RAY DIFFRACTION99.19
1.44-1.460.25241860.19133630X-RAY DIFFRACTION99.17
1.46-1.490.21852210.17443574X-RAY DIFFRACTION99.11
1.49-1.510.20461650.16063628X-RAY DIFFRACTION98.9
1.51-1.540.19321900.15053656X-RAY DIFFRACTION99.28
1.54-1.570.1641930.13783595X-RAY DIFFRACTION99.27
1.57-1.60.15882300.13063615X-RAY DIFFRACTION99.25
1.6-1.640.17362150.12493607X-RAY DIFFRACTION99.45
1.64-1.680.15032370.1223579X-RAY DIFFRACTION99.53
1.68-1.720.161830.12353645X-RAY DIFFRACTION99.45
1.72-1.760.1652150.12363638X-RAY DIFFRACTION99.64
1.76-1.820.17572220.1213609X-RAY DIFFRACTION99.4
1.82-1.870.13541960.123635X-RAY DIFFRACTION99.48
1.87-1.940.13791720.11843684X-RAY DIFFRACTION99.43
1.94-2.020.16511900.11973655X-RAY DIFFRACTION99.35
2.02-2.110.13711860.11933620X-RAY DIFFRACTION98.73
2.11-2.220.12981830.11143638X-RAY DIFFRACTION98.56
2.22-2.360.14721680.11463611X-RAY DIFFRACTION96.8
2.36-2.540.14921570.12373669X-RAY DIFFRACTION98.74
2.54-2.80.16351730.12113711X-RAY DIFFRACTION98.75
2.8-3.210.14642090.11953635X-RAY DIFFRACTION98.29
3.21-4.040.13311850.10563700X-RAY DIFFRACTION97.79
4.04-40.960.12111920.12013720X-RAY DIFFRACTION95.25

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