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- PDB-7cj4: Crystal structure of homo dimeric D-allulose 3-epimerase from Met... -

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Basic information

Entry
Database: PDB / ID: 7cj4
TitleCrystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp.
ComponentsEpimerase
KeywordsISOMERASE / Epimerase / TIM barrel
Function / homologyD-tagatose 3-epimerase / : / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / isomerase activity / metal ion binding / : / L-ribulose 3-epimerase
Function and homology information
Biological speciesMethylomonas sp. DH-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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)64,7244
Polymers64,6152
Non-polymers1102
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.730, 80.720, 139.450
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(-0.989309, 0.14522, -0.013369), (0.127982, 0.820603, -0.556984), (-0.069915, -0.552741, -0.830415)11.71337, 13.03341, 46.465519

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Components

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.24 %
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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→43.45 Å / Num. obs: 31851 / % possible obs: 99.8 % / Redundancy: 6.419 % / Biso Wilson estimate: 31.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.113 / Χ2: 0.917 / Net I/σ(I): 13.47 / Num. measured all: 204455 / Scaling rejects: 260
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.08-2.136.6530.5353.5615295229922990.8780.58100
2.13-2.196.50.4254.4714619225122490.9040.46299.9
2.19-2.266.2180.3794.8813798221922190.9270.414100
2.26-2.336.3820.3575.3313663214121410.9330.388100
2.33-2.46.7480.3126.1314016207720770.9580.338100
2.4-2.496.7030.2876.6213299198719840.9610.31299.8
2.49-2.586.6060.2457.612914195719550.9670.26699.9
2.58-2.696.3210.2098.5111814187018690.9790.22899.9
2.69-2.86.2830.1829.7611296180117980.9830.19999.8
2.8-2.946.5880.14212.4711365172617250.9890.15499.9
2.94-3.16.6640.11415.310982165016480.9940.12399.9
3.1-3.296.5470.08618.7210239156915640.9960.09499.7
3.29-3.526.0980.0721.718934146814650.9970.07799.8
3.52-3.86.2020.05725.528516137613730.9980.06399.8
3.8-4.166.5530.05229.338375128312780.9980.05799.6
4.16-4.656.3610.04432.47379116611600.9980.04899.5
4.65-5.375.8840.04729.766013102410220.9980.05199.8
5.37-6.586.210.05328.1255398938920.9980.05899.9
6.58-9.35.810.04134.7241667227170.9980.04599.3
9.3-43.455.3680.03438.9522334304160.9970.03896.7

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Processing

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

5zfs


Resolution: 2.08→43.45 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.888 / SU B: 15.744 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 1605 5 %RANDOM
Rwork0.185 ---
obs0.1893 30186 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.15 Å2 / Biso mean: 26.083 Å2 / Biso min: 12.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0 Å20 Å2
2--0.79 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 2.08→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 2 351 4751
Biso mean--30.7 33.89 -
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134498
X-RAY DIFFRACTIONr_bond_other_d00.0174110
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.6286107
X-RAY DIFFRACTIONr_angle_other_deg1.2091.5779481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.77122.149242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30515707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0821530
X-RAY DIFFRACTIONr_chiral_restr0.0450.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025175
X-RAY DIFFRACTIONr_gen_planes_other00.02995
X-RAY DIFFRACTIONr_rigid_bond_restr3.98638608
Refine LS restraints NCSNumber: 2195 / Type: TIGHT THERMAL / Rms dev position: 5.13 Å / Weight position: 0.5
LS refinement shellResolution: 2.08→2.134 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 120 -
Rwork0.195 2173 -
all-2293 -
obs--100 %

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