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- PDB-7cj6: Crystal structure of homo dimeric D-allulose 3-epimerase from Met... -

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Basic information

Entry
Database: PDB / ID: 7cj6
TitleCrystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp. in complex with D-allulose
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
: / D-psicose / 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 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)65,0856
Polymers64,6152
Non-polymers4704
Water8,431468
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.750, 80.870, 139.710
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(-0.989557, 0.143479, -0.013787), (0.126593, 0.819377, -0.559103), (-0.068923, -0.555009, -0.828984)11.69993, 13.15814, 46.457649

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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: Sugar ChemComp-PSJ / D-psicose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38.5 %
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: 1.8→38.29 Å / Num. obs: 48196 / % possible obs: 98.3 % / Redundancy: 6.342 % / Biso Wilson estimate: 27.311 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.084 / Χ2: 0.974 / Net I/σ(I): 15.08 / Num. measured all: 305677 / Scaling rejects: 572
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
1.8-1.856.3150.4643.9221876357034640.9180.50697
1.85-1.96.6190.3944.7422551350334070.9510.42797.3
1.9-1.956.540.3185.8321738336933240.9630.34598.7
1.95-2.016.4760.257.0920754329732050.9760.27297.2
2.01-2.086.2690.2118.219666321231370.9790.2397.7
2.08-2.156.2410.16410.1119104308430610.9880.1899.3
2.15-2.236.3370.14311.618562299129290.9890.15697.9
2.23-2.326.70.13213.1418942287928270.9910.14398.2
2.32-2.436.6720.11214.7117995276326970.9930.12197.6
2.43-2.556.5430.09716.2817340268126500.9950.10698.8
2.55-2.686.120.08717.3415264251724940.9940.09699.1
2.68-2.856.1580.07819.7914632240123760.9950.08699
2.85-3.046.5420.06623.4514622225522350.9960.07299.1
3.04-3.296.4140.05926.0713399210820890.9960.06599.1
3.29-3.66.140.05428.0411893195219370.9970.0699.2
3.6-4.025.6740.0528.99947177617530.9970.05598.7
4.02-4.655.9580.04631.199319160315640.9960.05197.6
4.65-5.696.2210.04330.968373135813460.9970.04799.1
5.69-8.055.6920.04229.436022107710580.9980.04798.2
8.05-38.295.720.03732.3636786586430.9960.04197.7

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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: 1.8→38.29 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.95 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.583 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 2439 5.1 %RANDOM
Rwork0.1806 ---
obs0.1844 45696 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.55 Å2 / Biso mean: 21.015 Å2 / Biso min: 13.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.52 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1.8→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4406 0 26 468 4900
Biso mean--28.46 32.81 -
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0134522
X-RAY DIFFRACTIONr_bond_other_d0.0040.0174130
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.6356134
X-RAY DIFFRACTIONr_angle_other_deg1.241.5839534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.84622.149242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18815712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9381530
X-RAY DIFFRACTIONr_chiral_restr0.0480.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02994
X-RAY DIFFRACTIONr_rigid_bond_restr3.29538652
Refine LS restraints NCSNumber: 2203 / Type: TIGHT THERMAL / Rms dev position: 4.55 Å / Weight position: 0.5
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 161 -
Rwork0.226 3292 -
all-3453 -
obs--96.97 %

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