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- PDB-7dfj: Crystal structure of glucose isomerase by serial millisecond crys... -

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Basic information

Entry
Database: PDB / ID: 7dfj
TitleCrystal structure of glucose isomerase by serial millisecond crystallography
ComponentsXylose isomerase
KeywordsISOMERASE / glucose isomerase / xylose isomerase / serial crystallography / serial millisecond crystallography / room 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: 1.5 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 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

Downloads & links

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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
Water5,044280
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_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area30970 Å2
ΔGint-192 kcal/mol
Surface area46550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.940, 99.600, 102.920
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-591-

HOH

21A-686-

HOH

31A-741-

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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
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: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.5→71.9 Å / Num. obs: 77277 / % possible obs: 100 % / Redundancy: 736.2 % / CC1/2: 0.9484 / Net I/σ(I): 3.46
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 1.13 / Num. unique obs: 7646 / CC1/2: 0.7026
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: 1.5→71.57 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 1997 2.59 %
Rwork0.2233 75086 -
obs0.2239 77083 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.2 Å2 / Biso mean: 34.3507 Å2 / Biso min: 18.58 Å2
Refinement stepCycle: final / Resolution: 1.5→71.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 2 280 3304
Biso mean--24.77 41.4 -
Num. residues----384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.540.37041420.337953035445
1.54-1.580.36581410.322553085449
1.58-1.630.37231410.313253055446
1.63-1.680.33011460.29353355481
1.68-1.740.30171340.274953055439
1.74-1.810.30631370.278753425479
1.81-1.890.28951430.255753245467
1.89-1.990.29111430.243853625505
1.99-2.110.26441450.235553145459
2.11-2.280.26831450.232653375482
2.28-2.510.27591410.227353895530
2.51-2.870.25411460.236653915537
2.87-3.610.23331440.205654335577
3.62-71.570.19721490.191956385787

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