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- PDB-4xsl: Crystal strcutre of D-tagatose 3-epimerase C66S from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 4xsl
TitleCrystal strcutre of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with glycerol
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-tagatose 3-epimerase
Similarity search - Component
Biological speciesPseudomonas cichorii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Data collection / Database references / Derived calculations
Category: citation / 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 1.2Nov 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)136,94422
Polymers135,4344
Non-polymers1,50918
Water22,8431268
1
A: D-tagatose 3-epimerase
B: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,47211
Polymers67,7172
Non-polymers7559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-18 kcal/mol
Surface area21560 Å2
MethodPISA
2
C: D-tagatose 3-epimerase
D: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,47211
Polymers67,7172
Non-polymers7559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-14 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.271, 124.552, 93.319
Angle α, β, γ (deg.)90.000, 98.740, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1268 / 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: 44.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 6-9% PEG 4000, 0.1M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 150883 / % possible obs: 95.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.06 / Net I/av σ(I): 14.936 / Net I/σ(I): 11.8 / Num. measured all: 461925
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.59-1.622.80.35155511.06670.9
1.62-1.6530.33276661.05296.4
1.65-1.682.90.29975881.14196.7
1.68-1.712.90.26976141.13696.4
1.71-1.752.90.24575941.16696.3
1.75-1.792.90.22275941.09396.1
1.79-1.842.90.19875361.10995.9
1.84-1.892.90.17974901.10495.3
1.89-1.942.90.15475581.11295.3
1.94-22.90.13575221.09495.5
2-2.072.90.12275420.99495.3
2.07-2.162.90.10975261.05795.5
2.16-2.2630.09675621.02395.5
2.26-2.3830.08575890.99695.7
2.38-2.523.10.07775591.03996.2
2.52-2.723.20.06877270.99197.4
2.72-2.993.30.05978221.06198.6
2.99-3.433.40.04779101.00699.9
3.43-4.323.50.03879640.98699.8
4.32-503.50.03479691.04299.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
CNS1.3refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QUL

2qul


Resolution: 1.6→32.07 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 135946 / 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
Rfree0.205 14471 10 %RANDOM
Rwork0.178 ---
obs0.181 145151 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.8492 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso max: 49.58 Å2 / Biso mean: 15.2 Å2 / Biso min: 4.12 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å2-0.98 Å2
2---0.04 Å20 Å2
3---2.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: final / Resolution: 1.6→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9246 0 88 1268 10602
Biso mean--23.16 24.08 -
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_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.462
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.342.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.263 1319 9.7 %
Rwork0.229 12302 -
all-13621 -
obs--88.1 %
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 DIFFRACTION6glycerol.paramglycerol.top

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