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- PDB-7cj7: Crystal structure of homo dimeric D-allulose 3-epimerase from Met... -

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Basic information

Entry
Database: PDB / ID: 7cj7
TitleCrystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp. in complex with L-tagatose
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
Chem-FZU / L-tagatose / : / L-sorbose / L-ribulose 3-epimerase
Similarity search - Component
Biological speciesMethylomonas sp. DH-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 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 21, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)65,2898
Polymers64,6152
Non-polymers6756
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.056, 81.777, 140.033
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: GLY / End label comp-ID: GLY / Refine code: 1 / Auth seq-ID: 2 - 287 / Label seq-ID: 2 - 287

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99054, 0.136433, -0.014687), (0.120669, 0.815091, -0.566626), (-0.065335, -0.563038, -0.823844)11.73769, 13.4083, 46.32766

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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: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: A0A172U6X0

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-SOL / L-sorbose


Type: L-saccharide / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Sugar ChemComp-LTG / L-tagatose


Type: L-saccharide / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 235 molecules

#3: 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.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-FZU / (2R,3R,4R,5S)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol


Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG3350, Tris, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 58671 / % possible obs: 98.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.052 / Rrim(I) all: 0.126 / Χ2: 1.185 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.736.10.63528750.8510.2690.6910.51798.4
1.73-1.766.10.55528760.9010.2360.6040.51298.1
1.76-1.7960.49328660.90.2130.5380.56398
1.79-1.835.90.43628800.9080.1910.4770.55498.6
1.83-1.875.60.37428860.9170.170.4120.61498.2
1.87-1.915.70.33529060.9430.1520.3690.64698.3
1.91-1.965.80.29129050.9540.1310.320.70399.1
1.96-2.026.20.25128800.9690.1080.2730.78798.1
2.02-2.076.30.22629290.9720.0970.2460.87899.9
2.07-2.146.10.19729170.9760.0860.2150.9898.6
2.14-2.225.90.16529150.9790.0750.1821.1398.9
2.22-2.315.70.15329420.9820.070.1681.22798.9
2.31-2.415.50.12929560.9880.060.1421.25499.7
2.41-2.545.20.11529310.9870.0560.1291.4299.1
2.54-2.74.80.09829040.990.0490.1111.50397.2
2.7-2.915.10.09129000.9920.0440.1021.77497.7
2.91-3.25.60.07429750.9950.0340.0822.05599.3
3.2-3.665.50.06130140.9960.0280.0672.46999.2
3.66-4.614.80.0530380.9970.0250.0562.58898.8
4.61-505.10.04531760.9970.0220.0512.17798.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZFS

5zfs


Resolution: 1.695→39.25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.527 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2961 5.1 %RANDOM
Rwork0.1479 ---
obs0.1501 55647 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.67 Å2 / Biso mean: 14.755 Å2 / Biso min: 6.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.695→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4406 0 39 231 4676
Biso mean--24.92 21.89 -
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134541
X-RAY DIFFRACTIONr_bond_other_d00.0174143
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.6346163
X-RAY DIFFRACTIONr_angle_other_deg1.3531.589568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47522.181243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64515714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8031530
X-RAY DIFFRACTIONr_chiral_restr0.0540.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025187
X-RAY DIFFRACTIONr_gen_planes_other00.02995
X-RAY DIFFRACTIONr_rigid_bond_restr4.23438684
Refine LS restraints NCSNumber: 2203 / Type: TIGHT THERMAL / Rms dev position: 3.2 Å / Weight position: 0.5
LS refinement shellResolution: 1.695→1.738 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 212 -
Rwork0.181 3826 -
all-4038 -
obs--93.04 %

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