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- PDB-9r46: Spitrobot-2 advances time-resolvedcryo-trapping crystallography t... -

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Basic information

Entry
Database: PDB / ID: 9r46
TitleSpitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: Xylose isomerase bound with glucose (25 ms soaking)
ComponentsXylose isomerase
KeywordsISOMERASE / Xylose isomerase / glucose / Spitrobot-2
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
beta-D-glucopyranose / : / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHatton, C.E. / Spiliopoulou, M. / Schulz, E.C. / Mehrabi, P.
Funding support Germany, European Union, 5items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)European Union
German Research Foundation (DFG)458246365 Germany
German Research Foundation (DFG)451079909 Germany
German Federal Ministry for Education and Research01KI2114 Germany
CitationJournal: Commun Chem / Year: 2025
Title: Spitrobot-2 advances time-resolved cryo-trapping crystallography to under 25 ms.
Authors: Spiliopoulou, M. / Hatton, C.E. / Kollewe, M. / Leimkohl, J.P. / Schikora, H. / Tellkamp, F. / Mehrabi, P. / Schulz, E.C.
History
DepositionMay 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 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)43,5434
Polymers43,2831
Non-polymers2593
Water4,720262
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)174,17116
Polymers173,1334
Non-polymers1,03812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area32780 Å2
ΔGint-176 kcal/mol
Surface area45660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.680, 93.760, 98.070
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-701-

HOH

21A-706-

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 BL21(DE3) (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.4
Details: 10 mM HEPES pH 7.5 0.2 M Lithium Sulphate 25% Peg3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→64.52 Å / Num. obs: 23420 / % possible obs: 100 % / Redundancy: 37.8 % / Biso Wilson estimate: 27.19 Å2 / CC1/2: 0.999 / Net I/σ(I): 24.6
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 1692 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.21.1_5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→64.52 Å / SU ML: 0.2726 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.9776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2426 1111 4.75 %
Rwork0.1869 22278 -
obs0.1895 23389 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→64.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 14 262 3317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073143
X-RAY DIFFRACTIONf_angle_d0.85044257
X-RAY DIFFRACTIONf_chiral_restr0.0464442
X-RAY DIFFRACTIONf_plane_restr0.0088577
X-RAY DIFFRACTIONf_dihedral_angle_d17.21421179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20.28431050.23722757X-RAY DIFFRACTION99.62
2.2-2.310.32571530.2322738X-RAY DIFFRACTION99.9
2.31-2.460.32021550.2372733X-RAY DIFFRACTION99.83
2.46-2.650.28751420.23812745X-RAY DIFFRACTION99.86
2.65-2.910.28711350.20712767X-RAY DIFFRACTION99.93
2.91-3.330.22341350.18512804X-RAY DIFFRACTION99.97
3.33-4.20.19981720.15062778X-RAY DIFFRACTION99.97
4.2-64.520.19821140.15812956X-RAY DIFFRACTION99.84

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