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

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Basic information

Entry
Database: PDB / ID: 4xsm
TitleCrystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with D-talitol
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
: / D-altritol / D-tagatose 3-epimerase
Similarity search - Component
Biological speciesPseudomonas cichorii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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
CitationJournal: 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.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)136,38312
Polymers135,4344
Non-polymers9488
Water6,179343
1
A: D-tagatose 3-epimerase
B: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1916
Polymers67,7172
Non-polymers4744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-0 kcal/mol
Surface area21820 Å2
MethodPISA
2
C: D-tagatose 3-epimerase
D: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1916
Polymers67,7172
Non-polymers4744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-2 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.430, 127.030, 98.830
Angle α, β, γ (deg.)90.000, 101.330, 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-TLZ / D-altritol / D-talitol


Mass: 182.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 49.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 6-9% PEG4000, 0.1M 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: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25.68 Å / Num. obs: 54404 / % possible obs: 96.7 % / Redundancy: 1.94 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.19 / Χ2: 1 / Net I/σ(I): 2.7 / Num. measured all: 106443 / Scaling rejects: 799
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.3-2.381.950.4981.21040653201.12995
2.38-2.481.950.4731.21048053481.042895.7
2.48-2.591.950.4641.21056954001.042495.9
2.59-2.731.950.4271.41052653801.023396.4
2.73-2.91.950.3741.71062754201.054596.6
2.9-3.121.950.3151.91066454571.035097.1
3.12-3.431.950.2222.71077854950.946997.4
3.43-3.931.930.153.91071654910.9512597.8
3.93-4.941.930.0985.61087755410.918798
4.94-25.681.910.0846.51080055520.8820997

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Processing

Software
NameVersionClassification
d*TREK9.4SSIdata reduction
CNS1.3refinement
PDB_EXTRACT3.15data extraction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QUL

2qul


Resolution: 2.3→25.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3245721 / 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
Rfree0.307 5534 10.2 %RANDOM
Rwork0.245 ---
obs0.252 54370 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.6172 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 83.86 Å2 / Biso mean: 36.1 Å2 / Biso min: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å20 Å2-7.94 Å2
2---6.54 Å20 Å2
3---9.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.56 Å
Refinement stepCycle: final / Resolution: 2.3→25.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9246 0 52 343 9641
Biso mean--55.76 30.56 -
Num. residues----1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.522.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.41 552 10.4 %
Rwork0.385 4767 -
all-5319 -
obs--94.9 %
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
X-RAY DIFFRACTION6ligand.paramligand.top

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