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

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Basic information

Entry
Database: PDB / ID: 4ytr
TitleCrystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 1-deoxy L-tagatose
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Database references / Derived calculations / Category: citation / 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 / _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
Water20,7351151
1
A: D-tagatose 3-epimerase
B: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3207
Polymers67,7172
Non-polymers6025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-10 kcal/mol
Surface area22010 Å2
MethodPISA
2
C: D-tagatose 3-epimerase
D: 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 area3310 Å2
ΔGint-6 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.380, 126.330, 92.920
Angle α, β, γ (deg.)90.000, 98.700, 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: 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.: 9 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
b-L-1-deoxy-TagpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-TGJ / 1-deoxy-L-tagatose


Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1151 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→22.14 Å / Num. obs: 92108 / % possible obs: 98.2 % / Redundancy: 2.92 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1 / Net I/σ(I): 8.7 / Num. measured all: 271251 / Scaling rejects: 2036
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.9-1.972.450.2993.41964079571.1514085.2
1.97-2.052.90.2813.72723693311.1113899.8
2.05-2.142.940.2563.92764993691.114999.9
2.14-2.252.930.2144.62748093281.0615899.9
2.25-2.392.930.175.62763893621.0620799.9
2.39-2.582.960.1376.72796293681.0119899.9
2.58-2.8430.1068.32817293330.9414599.8
2.84-3.253.020.07211.52848793650.8916099.8
3.25-4.093.020.04816.82859193630.8632899.5
4.09-22.1430.03920.82839693320.8541398.2

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Processing

Software
NameVersionClassification
CNS1.3refinement
d*TREK8.0SSIdata reduction
PDB_EXTRACT3.15data extraction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QUL

2qul


Resolution: 1.9→21.71 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1909410 / 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
Rfree0.235 9204 10 %RANDOM
Rwork0.188 ---
obs0.193 92074 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.5925 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso max: 91.31 Å2 / Biso mean: 21 Å2 / Biso min: 6.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å2-1.37 Å2
2---0.65 Å20 Å2
3---2.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: final / Resolution: 1.9→21.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9283 0 114 1151 10548
Biso mean--38.65 28.87 -
Num. residues----1177
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.34 812 10.2 %
Rwork0.314 7141 -
all-7953 -
obs--85 %
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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