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- PDB-4pgl: Crystal structure of engineered D-tagatose 3-epimerase PcDTE-ILS6 -

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Basic information

Entry
Database: PDB / ID: 4pgl
TitleCrystal structure of engineered D-tagatose 3-epimerase PcDTE-ILS6
ComponentsD-tagatose 3-epimerase
KeywordsISOMERASE / epimerase / TIM-barrel
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
L-tagatose / : / alpha-L-sorbopyranose / L-sorbose / D-tagatose 3-epimerase
Similarity search - Component
Biological speciesPseudomonas cichorii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsHee, C.S. / Bosshart, A. / Schirmer, T.
CitationJournal: Chembiochem / Year: 2015
Title: Directed Divergent Evolution of a Thermostable D-Tagatose Epimerase towards Improved Activity for Two Hexose Substrates.
Authors: Bosshart, A. / Hee, C.S. / Bechtold, M. / Schirmer, T. / Panke, S.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag ..._entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Refinement description
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)137,93122
Polymers135,3144
Non-polymers2,61718
Water6,612367
1
A: D-tagatose 3-epimerase
B: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,08312
Polymers67,6572
Non-polymers1,42610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint1 kcal/mol
Surface area21880 Å2
MethodPISA
2
C: D-tagatose 3-epimerase
D: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,84810
Polymers67,6572
Non-polymers1,1918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-1 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.810, 47.440, 126.380
Angle α, β, γ (deg.)90.00, 102.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA1 - 2891 - 289
21LEULEUBB1 - 2891 - 289
12HISHISAA1 - 2981 - 298
22HISHISCC1 - 2981 - 298
13LEULEUAA1 - 2891 - 289
23LEULEUDD1 - 2891 - 289
14LEULEUBB1 - 2891 - 289
24LEULEUCC1 - 2891 - 289
15ALAALABB1 - 2901 - 290
25ALAALADD1 - 2901 - 290
16LEULEUCC1 - 2891 - 289
26LEULEUDD1 - 2891 - 289

NCS ensembles :
ID
1
2
3
4
5
6
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
D-tagatose 3-epimerase


Mass: 33828.516 Da / Num. of mol.: 4
Mutation: T9S,G39S,T109N,S116H,K122V,V153A,F157Y,Q183H,T194N,A215Q,M245I,K251T,G260C,M265L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas cichorii (bacteria) / Plasmid: pKTS-C6H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O50580, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds

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Sugars , 3 types, 13 molecules

#3: Sugar
ChemComp-SOL / L-sorbose


Type: L-saccharide / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
#4: Sugar
ChemComp-SOE / alpha-L-sorbopyranose / alpha-L-sorbose / L-sorbose / sorbose / L-sorbose in pyranose form


Type: L-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
LSorpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-sorbopyranoseCOMMON NAMEGMML 1.0
a-L-SorpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
SorSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar
ChemComp-LTG / L-tagatose


Type: L-saccharide / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6

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Non-polymers , 2 types, 372 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 0.1M MES, 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→36.85 Å / Num. obs: 69460 / % possible obs: 99.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.7 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
Cootmodel building
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QUL

2qul


Resolution: 2.1→36.85 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.181 3506 5 %RANDOM
Rwork0.152 ---
obs-69447 98.7 %-
Displacement parametersBiso mean: 15.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å2-1.52 Å2
2---0.29 Å20 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2.1→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9334 0 161 367 9862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199763
X-RAY DIFFRACTIONr_bond_other_d0.0050.029123
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.96313208
X-RAY DIFFRACTIONr_angle_other_deg1.0413.00121017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34551186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41123.362473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.932151638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.161579
X-RAY DIFFRACTIONr_chiral_restr0.0830.21417
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02110959
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022280
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A183530.08
12B183530.08
21A187260.09
22C187260.09
31A182120.09
32D182120.09
41B183200.08
42C183200.08
51B185040.08
52D185040.08
61C181750.09
62D181750.09
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 251 -
Rwork0.194 4864 -
obs--98.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.81740.04870.07041.43650.35740.6898-0.01190.0201-0.0413-0.22850.0184-0.0976-0.01830.0019-0.00650.0766-0.01970.01630.0290.00770.013532.689-5.262815.4335
20.93710.01260.44050.5023-0.12561.1277-0.0308-0.24310.0185-0.00940.05590.0143-0.0183-0.0992-0.0250.0077-0.01210.0040.1487-0.0020.015650.09194.975941.9365
30.9682-0.02650.25730.9826-0.24590.9590.01390.00180.01190.0871-0.00470.05470.01980.0215-0.00920.06550.0080.0120.0293-0.01390.011714.8611-5.5308-18.4061
40.9414-0.02870.24040.680.17021.1086-0.00870.22540.09380.0380.00670.060.02760.10710.00210.00790.01230.00780.11730.01710.0343-2.51334.821-45.035
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 290
2X-RAY DIFFRACTION2B1 - 290
3X-RAY DIFFRACTION3C1 - 290
4X-RAY DIFFRACTION4D1 - 290

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