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

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Basic information

Entry
Database: PDB / ID: 4ytq
TitleCrystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 1-deoxy D-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-D-tagatose / 1-deoxy-alpha-D-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.pdbx_ptnr2_label_alt_id / _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)135,98310
Polymers135,4344
Non-polymers5486
Water22,1401229
1
A: D-tagatose 3-epimerase
B: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9915
Polymers67,7172
Non-polymers2743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-5 kcal/mol
Surface area21730 Å2
MethodPISA
2
C: D-tagatose 3-epimerase
D: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9915
Polymers67,7172
Non-polymers2743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-11 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.327, 126.308, 99.498
Angle α, β, γ (deg.)90.000, 101.770, 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-TGD / 1-deoxy-D-tagatose


Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5
#4: Sugar ChemComp-TGY / 1-deoxy-alpha-D-tagatopyranose / 1-deoxy-alpha-D-tagatose / 1-deoxy-D-tagatose / 1-deoxy-tagatose


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


Mass: 18.015 Da / Num. of mol.: 1229 / 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: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M Sodium acetate, 6 -9 % PEG 4000

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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 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.32 Å / Num. all: 287622 / Num. obs: 98941 / % possible obs: 99.6 % / Redundancy: 2.91 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1 / Net I/σ(I): 9.1 / Num. measured all: 289797 / Scaling rejects: 2175
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.9-1.972.870.2763.82837898661.0910599.8
1.97-2.052.90.2414.12879198751.0714699.8
2.05-2.142.910.2014.72900699041.0814599.9
2.14-2.252.910.1625.72893698811.0414899.8
2.25-2.392.910.1276.82900899060.9914699.8
2.39-2.582.920.1087.92907498880.9816299.8
2.58-2.842.930.0869.72918599020.9319999.7
2.84-3.242.90.06611.82898399210.9221299.8
3.24-4.082.880.0515.82889299110.9335699.5
4.08-19.322.930.0420.42954498870.9455698.3

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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→19.32 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1913446 / 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
Rfree0.213 9910 10 %RANDOM
Rwork0.174 ---
obs0.177 98910 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.3414 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso max: 66.84 Å2 / Biso mean: 20.1 Å2 / Biso min: 6.06 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å2-1.76 Å2
2---1.83 Å20 Å2
3---4.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: final / Resolution: 1.9→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9246 0 37 1229 10512
Biso mean--40.58 29.05 -
Num. residues----1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.292 1019 10.3 %
Rwork0.269 8856 -
all-9875 -
obs--99.8 %
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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