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- PDB-7bvl: Crystal structure of glucose isomerase delivered in wheat starch -

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Basic information

Entry
Database: PDB / ID: 7bvl
TitleCrystal structure of glucose isomerase delivered in wheat starch
ComponentsXylose isomerase
KeywordsISOMERASE / glucose isomerase
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / 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: 2 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2020
Title: Polysaccharide-Based Injection Matrix for Serial Crystallography.
Authors: Nam, K.H.
History
DepositionApr 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: 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
Water4,360242
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 area31080 Å2
ΔGint-185 kcal/mol
Surface area45410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.490, 99.920, 100.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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 / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→72.4 Å / Num. obs: 33248 / % possible obs: 100 % / Redundancy: 148.5 % / CC1/2: 0.9755 / CC star: 0.9937 / R split: 1.722E-6 / Net I/σ(I): 4.01
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 3247 / CC1/2: 0.5966 / CC star: 0.8644 / R split: 6.564E-6
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: commercial syringe / Flow rate: 0.2 µL/min / Injector diameter: 168 µm / Injector temperature: 298.15 K

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZYD

5zyd


Resolution: 2→70.749 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.17
RfactorNum. reflection% reflection
Rfree0.213 1987 6.13 %
Rwork0.1705 --
obs0.1731 32409 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.71 Å2 / Biso mean: 30.0184 Å2 / Biso min: 14.87 Å2
Refinement stepCycle: final / Resolution: 2→70.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 2 243 3278
Biso mean--38.88 36.39 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.05010.31281340.26872160
2.0501-2.10550.37271280.27222156
2.1055-2.16740.35221440.26252151
2.1674-2.23740.26781450.22222147
2.2374-2.31740.27171400.20762125
2.3174-2.41020.26371460.19532154
2.4102-2.51990.22631420.20342145
2.5199-2.65270.26211280.19342189
2.6527-2.81890.24561490.21662138
2.8189-3.03660.22911460.17682182
3.0366-3.34220.21421430.16342168
3.3422-3.82570.1771390.13882190
3.8257-4.81990.15571510.12262210
4.8199-70.7490.16991520.13822307

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