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- PDB-5b7z: Crystal Structure of Hyperthermophilic Thermotoga maritima L-Keto... -

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Basic information

Entry
Database: PDB / ID: 5b7z
TitleCrystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Ni2+
ComponentsUncharacterized protein TM_0416
KeywordsISOMERASE / epimerase / Ni2+ / 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
: / : / 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
Chem-1PG / NICKEL (II) ION / 5-keto-L-gluconate epimerase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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: Uncharacterized protein TM_0416
B: Uncharacterized protein TM_0416
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,07213
Polymers65,3552
Non-polymers1,71711
Water12,070670
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-32 kcal/mol
Surface area22460 Å2
Unit cell
Length a, b, c (Å)50.225, 55.220, 58.693
Angle α, β, γ (deg.)107.16, 102.23, 92.35
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


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


Mass: 18.015 Da / Num. of mol.: 670 / 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: 46.9 %
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: 0.9796 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: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 90302 / % possible obs: 96 % / Redundancy: 3.5 % / Net I/σ(I): 13.27
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.13 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B7Y

5b7y


Resolution: 1.5→41.513 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.32
RfactorNum. reflection% reflection
Rfree0.1972 4399 5.07 %
Rwork0.1722 --
obs0.1735 86681 91.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 105 670 5039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074449
X-RAY DIFFRACTIONf_angle_d1.1125968
X-RAY DIFFRACTIONf_dihedral_angle_d14.1571687
X-RAY DIFFRACTIONf_chiral_restr0.046668
X-RAY DIFFRACTIONf_plane_restr0.005756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4973-1.51430.2817880.21931635X-RAY DIFFRACTION56
1.5143-1.53210.2373900.22091999X-RAY DIFFRACTION66
1.5321-1.55080.29241150.21232153X-RAY DIFFRACTION72
1.5508-1.57040.24921520.20872399X-RAY DIFFRACTION80
1.5704-1.59110.23841230.21152552X-RAY DIFFRACTION85
1.5911-1.61290.27041610.2072655X-RAY DIFFRACTION91
1.6129-1.63590.26741520.20192803X-RAY DIFFRACTION93
1.6359-1.66030.24971520.19662834X-RAY DIFFRACTION95
1.6603-1.68630.19761380.18812820X-RAY DIFFRACTION95
1.6863-1.71390.18721440.18432876X-RAY DIFFRACTION96
1.7139-1.74350.23041590.17542843X-RAY DIFFRACTION96
1.7435-1.77520.22861620.18262873X-RAY DIFFRACTION96
1.7752-1.80930.19621280.17792883X-RAY DIFFRACTION96
1.8093-1.84630.22551590.17772851X-RAY DIFFRACTION96
1.8463-1.88640.221560.17462884X-RAY DIFFRACTION96
1.8864-1.93030.17681560.17392862X-RAY DIFFRACTION96
1.9303-1.97860.20481320.17192881X-RAY DIFFRACTION96
1.9786-2.0320.2041560.17222877X-RAY DIFFRACTION97
2.032-2.09180.20581530.16832880X-RAY DIFFRACTION97
2.0918-2.15940.18821580.16712867X-RAY DIFFRACTION97
2.1594-2.23650.19011570.16442896X-RAY DIFFRACTION97
2.2365-2.32610.19231670.16552903X-RAY DIFFRACTION98
2.3261-2.43190.22191470.1682932X-RAY DIFFRACTION97
2.4319-2.56010.18531500.17212896X-RAY DIFFRACTION98
2.5601-2.72050.19051530.16952924X-RAY DIFFRACTION98
2.7205-2.93050.19521660.16742939X-RAY DIFFRACTION98
2.9305-3.22530.18461590.16962876X-RAY DIFFRACTION97
3.2253-3.69170.17821660.15712854X-RAY DIFFRACTION96
3.6917-4.65020.15871470.15332737X-RAY DIFFRACTION92
4.6502-41.52860.18191530.17462898X-RAY DIFFRACTION97

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