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- PDB-7cj5: Crystal structure of homo dimeric D-allulose 3-epimerase from Met... -

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Basic information

Entry
Database: PDB / ID: 7cj5
TitleCrystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp. in complex with D-fructose
ComponentsEpimerase
KeywordsISOMERASE / Epimerase / TIM barrel
Function / homology
Function and homology information


D-tagatose 3-epimerase / isomerase activity / metal ion binding
Similarity search - Function
: / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
beta-D-fructopyranose / D-fructose / : / L-ribulose 3-epimerase
Similarity search - Component
Biological speciesMethylomonas sp. DH-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYoshida, H. / Yoshihara, A. / Kamitori, S.
CitationJournal: Febs Open Bio / Year: 2021
Title: Crystal structure of a novel homodimeric l-ribulose 3-epimerase from Methylomonus sp.
Authors: Yoshida, H. / Yoshihara, A. / Kato, S. / Mochizuki, S. / Akimitsu, K. / Izumori, K. / Kamitori, S.
History
DepositionJul 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epimerase
B: Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3139
Polymers64,6152
Non-polymers6997
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-28 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.420, 70.540, 140.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 1 / Auth seq-ID: 2 - 286 / Label seq-ID: 2 - 286

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Epimerase


Mass: 32307.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylomonas sp. DH-1 (bacteria) / Gene: AYM39_05640 / Plasmid: PLASMID / Details (production host): pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: A0A172U6X0

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Sugars , 2 types, 3 molecules

#3: Sugar ChemComp-FUD / D-fructose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#5: Sugar ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 259 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.74 Å3/Da / Density % sol: 29.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: magnesium chloride, Tris, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.94 Å / Num. obs: 42687 / % possible obs: 99.9 % / Redundancy: 7.167 % / Biso Wilson estimate: 25.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.07 / Χ2: 0.935 / Net I/σ(I): 23.22 / Num. measured all: 305959 / Scaling rejects: 3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.64 / Num. measured obs: 3296 / Num. possible: 582 / Num. unique obs: 530 / CC1/2: 1 / Rrim(I) all: 0.017 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZFS

5zfs


Resolution: 1.8→19.94 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.867 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.159 2087 4.9 %RANDOM
Rwork0.126 ---
obs0.127 40536 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.81 Å2 / Biso mean: 19.37 Å2 / Biso min: 10.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2--0.66 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4462 0 40 255 4757
Biso mean--26.75 27.52 -
Num. residues----578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134624
X-RAY DIFFRACTIONr_bond_other_d00.0174195
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.6356280
X-RAY DIFFRACTIONr_angle_other_deg1.3211.5849695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.61622.169249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06315725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1911530
X-RAY DIFFRACTIONr_chiral_restr0.0540.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021016
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_rigid_bond_restr4.53238819
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 2213 / Type: TIGHT THERMAL / Rms dev position: 5.37 Å / Weight position: 0.5
LS refinement shellResolution: 1.8→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 174 -
Rwork0.151 2925 -
all-3099 -
obs--99.94 %

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