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- PDB-9g5w: Xylose Isomerase collected at 40C using serial fixed-target cryst... -

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Basic information

Entry
Database: PDB / ID: 9g5w
TitleXylose Isomerase collected at 40C using serial fixed-target crystallography
ComponentsXylose isomerase
KeywordsISOMERASE / Sugar / Serial crystallography / Temperature
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 rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchulz, E.C. / Prester, A. / Stetten, D.V. / Gore, G. / Hatton, C.E. / Bartels, K. / Leimkohl, J.P. / Schikora, H. / Ginn, H.M. / Tellkamp, F. / Mehrabi, P.
Funding support Germany, European Union, 7items
OrganizationGrant numberCountry
German Research Foundation (DFG)451079909 Germany
German Research Foundation (DFG)458246365 Germany
European Research Council (ERC)101071843European Union
German Research Foundation (DFG)194651731 Germany
German Federal Ministry for Education and Research05K16GU1 Germany
German Federal Ministry for Education and Research05K19GU1 Germany
German Federal Ministry for Education and Research05K22GU6 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography.
Authors: Schulz, E.C. / Prester, A. / von Stetten, D. / Gore, G. / Hatton, C.E. / Bartels, K. / Leimkohl, J.P. / Schikora, H. / Ginn, H.M. / Tellkamp, F. / Mehrabi, P.
History
DepositionJul 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 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
Water5,603311
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
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area31030 Å2
ΔGint-188 kcal/mol
Surface area46680 Å2
Unit cell
Length a, b, c (Å)94.200, 103.050, 99.250
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-507-

HOH

21A-517-

HOH

31A-519-

HOH

41A-645-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Escherichia coli (E. coli) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
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: 55.79 %
Crystal growTemperature: 295 K / Method: batch mode
Details: (35% (w/v) PEG 3350, 200 mM LiSO4 and 10 mM Hepes/NaOH, pH 7.5)

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Data collection

DiffractionMean temperature: 313 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→71.49 Å / Num. obs: 53317 / % possible obs: 98.89 % / Redundancy: 198.8 % / Biso Wilson estimate: 20.14 Å2 / CC1/2: 0.9227 / Net I/σ(I): 3.59
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 5271 / CC1/2: 0.3803
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→71.49 Å / SU ML: 0.246 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.6163
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2072 2606 4.89 %
Rwork0.1727 50710 -
obs0.1743 53316 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→71.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 2 311 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393424
X-RAY DIFFRACTIONf_angle_d0.64644668
X-RAY DIFFRACTIONf_chiral_restr0.0423467
X-RAY DIFFRACTIONf_plane_restr0.0071657
X-RAY DIFFRACTIONf_dihedral_angle_d12.73731315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.47681480.39092639X-RAY DIFFRACTION99.79
1.73-1.760.35021540.34272600X-RAY DIFFRACTION99.67
1.76-1.80.31921440.27292629X-RAY DIFFRACTION99.78
1.8-1.840.28751160.252684X-RAY DIFFRACTION99.79
1.84-1.880.26611280.22812627X-RAY DIFFRACTION99.82
1.88-1.930.27671260.23332635X-RAY DIFFRACTION99.75
1.93-1.980.2721210.2422674X-RAY DIFFRACTION99.86
1.98-2.040.25861310.21232661X-RAY DIFFRACTION99.96
2.04-2.110.2071620.17522604X-RAY DIFFRACTION99.89
2.11-2.180.19371800.16932607X-RAY DIFFRACTION99.96
2.18-2.270.20781570.16042644X-RAY DIFFRACTION99.96
2.27-2.370.18621390.16332659X-RAY DIFFRACTION99.93
2.37-2.50.2151430.15862650X-RAY DIFFRACTION99.96
2.5-2.650.19821590.17282648X-RAY DIFFRACTION100
2.65-2.860.19581440.16712699X-RAY DIFFRACTION99.93
2.86-3.150.18351240.15832684X-RAY DIFFRACTION100
3.15-3.60.17651200.14192726X-RAY DIFFRACTION100
3.6-4.530.1333870.12582775X-RAY DIFFRACTION100
4.54-71.490.17731230.15392865X-RAY DIFFRACTION99.93

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