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- PDB-7dfk: Crystal structure of xylitol-bound glucose isomerase by serial mi... -

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Basic information

Entry
Database: PDB / ID: 7dfk
TitleCrystal structure of xylitol-bound glucose isomerase by serial millisecond crystallography
ComponentsXylose isomerase
KeywordsISOMERASE / glucose isomerase / xylose isomerase / serial crystallography / serial millisecond crystallography / room temperature / xylitol
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
Xylitol / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of xylitol-bound glucose isomerase by serial millisecond crystallography
Authors: Nam, K.H.
History
DepositionNov 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)43,4603
Polymers43,2831
Non-polymers1762
Water5,657314
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)173,83912
Polymers173,1334
Non-polymers7068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area32960 Å2
ΔGint-137 kcal/mol
Surface area46460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.138, 99.936, 103.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-598-

HOH

21A-765-

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 rubiginosus (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: Sugar ChemComp-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 293.5 K / Method: batch mode / pH: 7 / Details: Tris-HCl, Ammonium sulfate, Magnesium sulfate

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.4→72.4 Å / Num. obs: 95564 / % possible obs: 100 % / Redundancy: 277.9 % / CC1/2: 0.952 / Net I/σ(I): 4.15
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 9462 / CC1/2: 0.5968
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: nylon mesh / Support base: goniometer

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CK0

7ck0


Resolution: 1.4→71.78 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 1287 1.35 %
Rwork0.235 93934 -
obs0.2352 95221 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.24 Å2 / Biso mean: 21.0188 Å2 / Biso min: 3.82 Å2
Refinement stepCycle: final / Resolution: 1.4→71.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 23 314 3370
Biso mean--14 29.95 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.460.41321390.3788102811042099
1.46-1.520.3671410.3276103291047099
1.52-1.60.3041410.29211033510476100
1.6-1.70.33621400.2705102861042699
1.7-1.830.24071470.23651041410561100
1.83-2.020.24211440.22631044310587100
2.02-2.310.25031450.21591046910614100
2.31-2.910.22121460.22621053110677100
2.91-71.780.22171440.21371084610990100

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