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- PDB-9xey: Room temperature structure of glucose isomerase by serial femtose... -

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Basic information

Entry
Database: PDB / ID: 9xey
TitleRoom temperature structure of glucose isomerase by serial femtosecond crystallography
ComponentsXylose isomerase
KeywordsISOMERASE / glucose isomerase / serial femtosecond crystallography
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / 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
Biological speciesStreptomyces pseudogriseolus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: To Be Published
Title: Room temperature structure of glucose isomerase by serial femtosecond crystallography
Authors: Nam, K.H.
History
DepositionOct 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3323
Polymers43,2831
Non-polymers492
Water5,278293
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)173,32812
Polymers173,1334
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2_655-x+1,-y,z1
point symmetry operation3_656-x+1,y,-z+11
point symmetry operation4_556x,-y,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)93.730, 99.530, 102.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

21A-700-

HOH

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Components

#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 273 K / Method: batch mode / Details: Tris, MgCl

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.3045 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Aug 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3045 Å / Relative weight: 1
ReflectionResolution: 1.65→71.94 Å / Num. obs: 58242 / % possible obs: 100 % / Redundancy: 436.9 % / CC1/2: 0.9069 / Net I/σ(I): 4.07
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 5759 / CC1/2: 0.5108
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→71.4 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 1429 2.47 %
Rwork0.1956 --
obs0.1964 57820 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→71.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 2 293 3317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053170
X-RAY DIFFRACTIONf_angle_d0.8224300
X-RAY DIFFRACTIONf_dihedral_angle_d31.149443
X-RAY DIFFRACTIONf_chiral_restr0.049441
X-RAY DIFFRACTIONf_plane_restr0.006588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.710.52631420.51085595X-RAY DIFFRACTION100
1.71-1.780.37211340.33415572X-RAY DIFFRACTION100
1.78-1.860.26431460.22515584X-RAY DIFFRACTION100
1.86-1.960.25051420.20585584X-RAY DIFFRACTION100
1.96-2.080.25271420.20685609X-RAY DIFFRACTION100
2.08-2.240.2491420.17375604X-RAY DIFFRACTION100
2.24-2.460.19371470.17425617X-RAY DIFFRACTION100
2.46-2.820.23851410.18655650X-RAY DIFFRACTION100
2.82-3.550.20391440.18315703X-RAY DIFFRACTION100
3.55-71.40.19911490.17645873X-RAY DIFFRACTION100

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