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- PDB-5j8l: Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 5j8l
TitleCrystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 1-deoxy L-tagatose, using a crystal grown in microgravity
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-L-tagatose / 1-deoxy-beta-L-tagatopyranose / D-tagatose 3-epimerase
Similarity search - Component
Biological speciesPseudomonas cichorii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsYoshida, H. / Yoshihara, A. / Izumori, K. / Kamitori, S.
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
DepositionApr 8, 2016Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 27, 2016ID: 4YVL
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / 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 / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / 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)137,29618
Polymers135,4344
Non-polymers1,86114
Water16,592921
1
A: D-tagatose 3-epimerase
B: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,81210
Polymers67,7172
Non-polymers1,0958
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-6 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)68,4848
Polymers67,7172
Non-polymers7676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-13 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.580, 126.535, 98.903
Angle α, β, γ (deg.)90.000, 101.450, 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, D-tagatose 3-epimerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TGJ / 1-deoxy-L-tagatose


Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
#4: Sugar
ChemComp-TGK / 1-deoxy-beta-L-tagatopyranose / 1-deoxy-beta-L-tagatose / 1-deoxy-L-tagatose / 1-deoxy-tagatose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
b-L-1-deoxy-TagpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 4.6 / Details: 15 % PEG4000, 0.1 M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→100 Å / Num. obs: 121443 / % possible obs: 92.1 % / Redundancy: 2 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.075 / Net I/av σ(I): 15.773 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.73-1.761.90.4672.2193.3
1.76-1.791.90.438193.7
1.79-1.831.90.369193.3
1.83-1.861.90.329193.3
1.86-1.91.90.282193
1.9-1.951.90.252193.5
1.95-21.90.207193.5
2-2.051.90.185192.9
2.05-2.111.90.163192.7
2.11-2.181.90.141192.8
2.18-2.2620.118191.6
2.26-2.3520.106191.3
2.35-2.4520.089190.4
2.45-2.5820.081188.9
2.58-2.7520.072187.8
2.75-2.9620.061188.2
2.96-3.2620.055189.4
3.26-3.7320.05192.8
3.73-4.720.049194
4.7-1002.20.05194.6

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Processing

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

2qul


Resolution: 1.73→38.68 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2553680 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.219 12139 10 %RANDOM
Rwork0.194 ---
obs0.197 121336 92 %-
Solvent computationBsol: 56.4709 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso max: 70.79 Å2 / Biso mean: 19.9 Å2 / Biso min: 6.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å20 Å2-3.52 Å2
2---4.09 Å20 Å2
3---5.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: final / Resolution: 1.73→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9246 0 114 921 10281
Biso mean--38.92 28.26 -
Num. residues----1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.592.5
LS refinement shellResolution: 1.73→1.79 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 1223 9.9 %
Rwork0.279 11071 -
all-12294 -
obs--93.5 %
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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