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- PDB-8wdg: Subatomic crystal structure of glucose isomerase from Streptomyce... -

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Basic information

Entry
Database: PDB / ID: 8wdg
TitleSubatomic crystal structure of glucose isomerase from Streptomyces rubiginosus
ComponentsXylose isomerase
KeywordsISOMERASE / glucose isomerase / subatomic resolution
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: 0.99 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2020M3H1A1075314 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Xylitol binding to the M1 site of glucose isomerase induces a conformational change in the substrate binding channel.
Authors: Xu, Y. / Nam, K.H.
History
DepositionSep 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)43,2065
Polymers42,9811
Non-polymers2254
Water9,044502
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)172,82420
Polymers171,9244
Non-polymers90016
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 area32710 Å2
ΔGint-224 kcal/mol
Surface area45730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.675, 98.626, 102.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-888-

HOH

21A-917-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 42980.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-XYL / Xylitol / D-Xylitol


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


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, pH 8.0, PEG400, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.8265 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8265 Å / Relative weight: 1
ReflectionResolution: 0.99→40.77 Å / Num. obs: 255970 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.999 / Net I/σ(I): 12.2
Reflection shellResolution: 0.99→1.01 Å / Num. unique obs: 12132 / CC1/2: 0.561 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.99→40.77 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.353 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17071 12883 5 %RANDOM
Rwork0.15812 ---
obs0.15874 243532 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.999 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.42 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 0.99→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 13 502 3548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0133232
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152972
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.6474389
X-RAY DIFFRACTIONr_angle_other_deg1.6771.5886826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.95720.81210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18715510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8051536
X-RAY DIFFRACTIONr_chiral_restr0.120.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023800
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02816
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9430.8941597
X-RAY DIFFRACTIONr_mcbond_other0.9070.8921596
X-RAY DIFFRACTIONr_mcangle_it1.2771.3492012
X-RAY DIFFRACTIONr_mcangle_other1.2851.352013
X-RAY DIFFRACTIONr_scbond_it2.3061.1531635
X-RAY DIFFRACTIONr_scbond_other2.3061.1541636
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3971.652378
X-RAY DIFFRACTIONr_long_range_B_refined4.74512.7753904
X-RAY DIFFRACTIONr_long_range_B_other4.38311.8343768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.99→1.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 952 -
Rwork0.307 17153 -
obs--95.57 %

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