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- PDB-7e03: Room temperature structure of glucose isomerase delivered in beef... -

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Basic information

Entry
Database: PDB / ID: 7000
TitleRoom temperature structure of glucose isomerase delivered in beef tallow by serial millisecond crystallography
ComponentsXylose isomerase
KeywordsISOMERASE / serial crystallography / beef tallow / room temperature / glucose isomerase
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: 1.6 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: To Be Published
Title: Room temperature structure of glucose isomerase delivered in beef tallow by serial millisecond crystallography
Authors: Nam, K.H.
History
DepositionJan 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
Water5,441302
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 area31170 Å2
ΔGint-189 kcal/mol
Surface area46860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.330, 99.910, 103.300
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-508-

HOH

21A-662-

HOH

31A-766-

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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.25 %
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: 293.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.6→72.46 Å / Num. obs: 64497 / % possible obs: 100 % / Redundancy: 250.9 % / CC1/2: 0.9656 / Net I/σ(I): 4.79
Reflection shellResolution: 1.6→1.66 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 6368 / CC1/2: 0.5348
Serial crystallography sample deliveryMethod: injection

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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: 5Y4I

5y4i


Resolution: 1.6→71.82 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1862 1990 3.09 %
Rwork0.1681 62450 -
obs0.1686 64440 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.76 Å2 / Biso mean: 22.9293 Å2 / Biso min: 8.69 Å2
Refinement stepCycle: final / Resolution: 1.6→71.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 2 302 3337
Biso mean--11.73 33.89 -
Num. residues----385
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
1.6-1.640.27921390.289943864525
1.64-1.680.32831410.272144514592
1.68-1.730.25651390.257743724511
1.73-1.790.25541380.23344534591
1.79-1.850.26341430.223744084551
1.85-1.930.23791400.190644284568
1.93-2.020.21861440.18744394583
2.02-2.120.22131400.180944544594
2.12-2.260.20961420.171944474589
2.26-2.430.17931440.154344484592
2.43-2.670.15651420.162844804622
2.67-3.060.19471430.158844994642
3.06-3.860.17321440.137345114655
3.86-71.820.12151510.139946744825

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