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- PDB-5yn3: Crystal structure of xylose isomerase from Piromyces sp. E2 -

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Basic information

Entry
Database: PDB / ID: 5yn3
TitleCrystal structure of xylose isomerase from Piromyces sp. E2
ComponentsXylose isomerase
KeywordsISOMERASE / Xylose isomerase
Function / homology
Function and homology information


xylose catabolic process to ethanol / xylose isomerase / xylose isomerase activity / metal ion binding / cytoplasm
Similarity search - Function
Xylose isomerase, bacterial-type / Xylose isomerase / Xylose isomerase family profile. / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Xylose isomerase
Similarity search - Component
Biological speciesPiromyces sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSon, H.-F. / Kim, K.-J.
CitationJournal: J. Microbiol. Biotechnol. / Year: 2018
Title: Crystal Structure and Biochemical Characterization of Xylose Isomerase fromPiromycessp. E2.
Authors: Son, H. / Lee, S.M. / Kim, K.J.
History
DepositionOct 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Sep 9, 2020Group: Derived calculations / Structure summary / Category: struct / struct_conn
Item: _struct.title / _struct_conn.pdbx_dist_value ..._struct.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,35717
Polymers203,4574
Non-polymers90013
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Tetramer in gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31920 Å2
ΔGint-162 kcal/mol
Surface area55100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.472, 126.417, 171.181
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Xylose isomerase /


Mass: 50864.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piromyces sp. (strain E2) (fungus) / Strain: E2 / Gene: xylA / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-T1R / References: UniProt: Q9P8C9, xylose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 43.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Calcium acetate hydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 2, 2016
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→101.7 Å / Num. obs: 48118 / % possible obs: 91.8 % / Redundancy: 4.2 % / Net I/σ(I): 15.1
Reflection shellResolution: 2.7→2.75 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data collection
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A0E

1a0e


Resolution: 2.7→37.378 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.881 / SU B: 16.166 / SU ML: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 2167 4.9 %RANDOM
Rwork0.1942 ---
obs0.1982 41844 91.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.62 Å2 / Biso mean: 17.811 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å20 Å2
2--0.47 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.7→37.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13852 0 38 190 14080
Biso mean--38.01 9 -
Num. residues----1740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914189
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212838
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9419093
X-RAY DIFFRACTIONr_angle_other_deg0.841329910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69351736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63825.141708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87152520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4081552
X-RAY DIFFRACTIONr_chiral_restr0.0820.21969
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215916
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022920
LS refinement shellResolution: 2.701→2.771 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 143 -
Rwork0.264 2888 -
all-3031 -
obs--85.89 %

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