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- PDB-4yts: Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 4yts
TitleCrystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 1-deoxy 3-keto D-galactitol
ComponentsD-tagatose 3-epimerase
KeywordsISOMERASE / Epimerase
Function / homology
Function and homology information


D-tagatose 3-epimerase / isomerase activity / metal ion binding
Similarity search - Function
: / 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
: / 1-deoxy-alpha-D-xylo-hex-3-ulofuranose / 1-deoxy-D-xylo-hex-3-ulose / D-tagatose 3-epimerase
Similarity search - Component
Biological speciesPseudomonas cichorii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsYoshida, H. / Yoshihara, A. / Ishii, T. / Izumori, K. / Kamitori, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25440028 Japan
Citation
Journal: Appl. Microbiol. Biotechnol. / Year: 2016
Title: X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates
Authors: Yoshida, H. / Yoshihara, A. / Ishii, T. / Izumori, K. / Kamitori, S.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose.
Authors: Yoshida, H. / Yamada, M. / Nishitani, T. / Takada, G. / Izumori, K. / Kamitori, S.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.pdbx_dist_value ..._chem_comp.type / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-tagatose 3-epimerase
B: D-tagatose 3-epimerase
C: D-tagatose 3-epimerase
D: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,62420
Polymers135,4344
Non-polymers2,19016
Water9,188510
1
A: D-tagatose 3-epimerase
B: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,97611
Polymers67,7172
Non-polymers1,2599
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint1 kcal/mol
Surface area21650 Å2
MethodPISA
2
C: D-tagatose 3-epimerase
D: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6489
Polymers67,7172
Non-polymers9317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint0 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.503, 126.733, 99.520
Angle α, β, γ (deg.)90.000, 101.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
D-tagatose 3-epimerase


Mass: 33858.613 Da / Num. of mol.: 4 / Mutation: C66S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas cichorii (bacteria) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: O50580, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-TGS / 1-deoxy-D-xylo-hex-3-ulose / 1-deoxy 3-keto-D-galactitol


Mass: 164.156 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H12O5
#4: Sugar ChemComp-TGR / 1-deoxy-alpha-D-xylo-hex-3-ulofuranose / 1-deoxy 3-keto D-galactitol(Furanose form) / 1-deoxy-alpha-D-xylo-hex-3-ulose / 1-deoxy-D-xylo-hex-3-ulose / 1-deoxy-xylo-hex-3-ulose


Type: D-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 6-9 % PEG4000, 0.1 M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 67876 / % possible obs: 96.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.13 / Χ2: 1.178 / Net I/av σ(I): 7.228 / Net I/σ(I): 10.3 / Num. measured all: 218327
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.14-2.183.20.3935021.33399.3
2.18-2.223.20.34734861.38899.4
2.22-2.263.20.33734631.35399
2.26-2.313.20.29934951.34999
2.31-2.363.20.2834281.3298.9
2.36-2.413.20.26635111.32898.9
2.41-2.473.20.24934301.31598.8
2.47-2.543.20.22934841.26798.7
2.54-2.613.20.21834591.24898.6
2.61-2.73.20.19534871.18798.9
2.7-2.793.20.17934371.22297.9
2.79-2.93.20.15734691.16598.4
2.9-3.043.30.14634211.16197.7
3.04-3.23.20.12334091.01996.6
3.2-3.43.20.11133411.01794.9
3.4-3.663.10.09532380.95991.8
3.66-4.033.10.08931050.95887.6
4.03-4.6130.0828210.99580
4.61-5.813.40.07834070.93395.5
5.81-503.40.11234830.96996.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
CNS1.3refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QUL

2qul


Resolution: 2.14→32.46 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 123632 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 6154 10.1 %RANDOM
Rwork0.203 ---
obs0.209 61071 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1706 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 86.48 Å2 / Biso mean: 27.6 Å2 / Biso min: 8.39 Å2
Baniso -1Baniso -2Baniso -3
1--4.89 Å20 Å2-7.14 Å2
2---5.21 Å20 Å2
3---10.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.22 Å
Refinement stepCycle: final / Resolution: 2.14→32.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9246 0 136 510 9892
Biso mean--48.07 28.89 -
Num. residues----1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.532.5
LS refinement shellResolution: 2.14→2.22 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.316 554 9.4 %
Rwork0.259 5317 -
all-5871 -
obs--83.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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