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- PDB-2zvr: Crystal structure of a D-tagatose 3-epimerase-related protein fro... -

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Basic information

Entry
Database: PDB / ID: 2zvr
TitleCrystal structure of a D-tagatose 3-epimerase-related protein from Thermotoga maritima
ComponentsUncharacterized protein TM_0416
KeywordsISOMERASE / hyperthermophile / Thermotoga maritima / ketohexose 3-epimerase / D-tagatose 3-epimerase
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds / Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / inositol metabolic process / 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
5-keto-L-gluconate epimerase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.2 Å
AuthorsSakuraba, H. / Ohshima, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of a D-tagatose 3-epimerase-related protein from the hyperthermophilic bacterium Thermotoga maritima
Authors: Sakuraba, H. / Yoneda, K. / Satomura, T. / Kawakami, R. / Ohshima, T.
History
DepositionNov 14, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein TM_0416
B: Uncharacterized protein TM_0416


Theoretical massNumber of molelcules
Total (without water)65,3552
Polymers65,3552
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein TM_0416


Theoretical massNumber of molelcules
Total (without water)32,6771
Polymers32,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Uncharacterized protein TM_0416


Theoretical massNumber of molelcules
Total (without water)32,6771
Polymers32,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.245, 55.211, 58.714
Angle α, β, γ (deg.)107.14, 102.71, 91.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Uncharacterized protein TM_0416 / D-tagatose 3-epimerase homologue


Mass: 32677.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0416 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYP7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20-30% PEG 200, 5% PEG 1000, 0.1M MES, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 3, 2008
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.17→37.63 Å / Num. obs: 29673 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.1 Å2
Reflection shellResolution: 2.17→2.25 Å

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→37.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1207194.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2961 10 %RANDOM
Rwork0.199 ---
all0.203 ---
obs0.199 29669 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.0099 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0.07 Å20.14 Å2
2---0.29 Å2-0.12 Å2
3----0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å-0.1 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 0 231 4381
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d1.72
LS refinement shellResolution: 2.17→2.31 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 470 9.8 %
Rwork0.174 4316 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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