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- PDB-5b80: Crystal Structure of Hyperthermophilic Thermotoga maritima L-Keto... -

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Basic information

Entry
Database: PDB / ID: 5b80
TitleCrystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Cu2+
ComponentsUncharacterized protein TM_0416
KeywordsISOMERASE / epimerase / Cu2+ / hyperthermophilic / eubacterium
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
: / : / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / COPPER (II) ION / 5-keto-L-gluconate epimerase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCao, T.P. / Shin, S.M. / Lee, D.W. / Lee, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation2013R1A1A2057465 Korea, Republic Of
National Research Foundation2014R1A2A2A01006765 Korea, Republic Of
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: TM0416, a Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C5and C6Epimerization Reactions
Authors: Shin, S.M. / Cao, T.P. / Choi, J.M. / Kim, S.B. / Lee, S.J. / Lee, S.H. / Lee, D.W.
History
DepositionJun 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Uncharacterized protein TM_0416
B: Uncharacterized protein TM_0416
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2397
Polymers65,3552
Non-polymers8845
Water9,638535
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint2 kcal/mol
Surface area22720 Å2
Unit cell
Length a, b, c (Å)50.282, 55.252, 58.763
Angle α, β, γ (deg.)107.04, 102.49, 91.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Uncharacterized protein TM_0416 / L-Ketose-3-Epimerase


Mass: 32677.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: TM_0416 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9WYP7
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H24O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100mM MES, 5%(w/w) PEG1000, 20%(v/v) PEG200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2016
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 61647 / % possible obs: 95.9 % / Redundancy: 3.3 % / Net I/σ(I): 14.64
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.63 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTX

5jtx
PDB Unreleased entry


Resolution: 1.7→35.25 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 18.56
RfactorNum. reflection% reflection
Rfree0.1896 3105 5.06 %
Rwork0.1663 --
obs0.1675 61384 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 53 535 4852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194394
X-RAY DIFFRACTIONf_angle_d1.0835894
X-RAY DIFFRACTIONf_dihedral_angle_d13.1451667
X-RAY DIFFRACTIONf_chiral_restr0.042662
X-RAY DIFFRACTIONf_plane_restr0.005753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7005-1.7270.27371180.21292341X-RAY DIFFRACTION82
1.727-1.75540.24341410.20052525X-RAY DIFFRACTION92
1.7554-1.78560.21821510.18772643X-RAY DIFFRACTION93
1.7856-1.81810.20911460.18152543X-RAY DIFFRACTION94
1.8181-1.85310.23711420.17512647X-RAY DIFFRACTION94
1.8531-1.89090.19781380.17552660X-RAY DIFFRACTION94
1.8909-1.9320.181480.17542595X-RAY DIFFRACTION94
1.932-1.97690.19161220.16832656X-RAY DIFFRACTION95
1.9769-2.02640.20411600.17372644X-RAY DIFFRACTION95
2.0264-2.08120.20341310.16772640X-RAY DIFFRACTION95
2.0812-2.14240.2011240.17052678X-RAY DIFFRACTION95
2.1424-2.21150.19271420.162673X-RAY DIFFRACTION96
2.2115-2.29060.18711340.16132705X-RAY DIFFRACTION97
2.2906-2.38220.18881360.15872686X-RAY DIFFRACTION97
2.3822-2.49060.1841480.16572692X-RAY DIFFRACTION97
2.4906-2.62190.1921240.17142749X-RAY DIFFRACTION97
2.6219-2.78610.20481450.1752711X-RAY DIFFRACTION97
2.7861-3.00110.19181420.17182700X-RAY DIFFRACTION97
3.0011-3.30290.20141550.17222702X-RAY DIFFRACTION97
3.3029-3.78040.15161620.14842696X-RAY DIFFRACTION97
3.7804-4.76110.14721480.14192666X-RAY DIFFRACTION96
4.7611-35.25710.20151480.16832727X-RAY DIFFRACTION98

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