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- PDB-8yud: Crystal structure of Xylose isomerase from Streptomyces avermitilis -

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Basic information

Entry
Database: PDB / ID: 8yud
TitleCrystal structure of Xylose isomerase from Streptomyces avermitilis
ComponentsXylose isomerase
KeywordsISOMERASE / Xylose isomerase / glucose isomerase / Streptomyces avermitilis
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion 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 avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: Data Brief / Year: 2025
Title: Data of the crystal structure of xylose isomerase from Streptomyces avermitilis.
Authors: Nam, K.H.
History
DepositionMar 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase
B: Xylose isomerase
C: Xylose isomerase
D: Xylose isomerase
E: Xylose isomerase
F: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,60818
Polymers257,3166
Non-polymers29212
Water00
1
A: Xylose isomerase
B: Xylose isomerase
hetero molecules

A: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,73912
Polymers171,5444
Non-polymers1948
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area31260 Å2
ΔGint-190 kcal/mol
Surface area45830 Å2
MethodPISA
2
C: Xylose isomerase
D: Xylose isomerase
E: Xylose isomerase
F: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,73912
Polymers171,5444
Non-polymers1948
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31310 Å2
ΔGint-190 kcal/mol
Surface area46030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.135, 129.135, 233.058
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Xylose isomerase


Mass: 42886.043 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: xylA, SAV14893_068640, SAV31267_017200 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4D4M698, xylose isomerase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: Tris, Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 54119 / % possible obs: 97.8 % / Redundancy: 6.4 % / CC1/2: 0.977 / Net I/σ(I): 11.24
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 2664 / CC1/2: 0.627

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→34.21 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 1994 3.69 %
Rwork0.1867 --
obs0.1888 53972 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18078 0 12 0 18090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918504
X-RAY DIFFRACTIONf_angle_d1.13625086
X-RAY DIFFRACTIONf_dihedral_angle_d6.3112550
X-RAY DIFFRACTIONf_chiral_restr0.0522646
X-RAY DIFFRACTIONf_plane_restr0.0213384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.880.38461410.263519X-RAY DIFFRACTION95
2.88-2.960.34291420.23913633X-RAY DIFFRACTION97
2.96-3.050.31631400.23493662X-RAY DIFFRACTION97
3.05-3.150.25081400.22533636X-RAY DIFFRACTION97
3.15-3.260.32641360.21413653X-RAY DIFFRACTION97
3.26-3.390.27371410.2053664X-RAY DIFFRACTION97
3.39-3.540.27571400.18093651X-RAY DIFFRACTION97
3.54-3.730.2081410.17823650X-RAY DIFFRACTION97
3.73-3.960.24261410.17143674X-RAY DIFFRACTION97
3.96-4.270.20111450.16813753X-RAY DIFFRACTION98
4.27-4.70.23011410.16543759X-RAY DIFFRACTION98
4.7-5.370.22221410.17713807X-RAY DIFFRACTION99
5.37-6.760.2041480.19373883X-RAY DIFFRACTION100
6.76-34.210.19391570.15764034X-RAY DIFFRACTION100

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