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- PDB-5b7y: Crystal Structure of Hyperthermophilic Thermotoga maritima L-Keto... -

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Basic information

Entry
Database: PDB / ID: 5b7y
TitleCrystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Co2+
ComponentsUncharacterized protein TM_0416
KeywordsISOMERASE / epimerase / Co2+ / 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 / racemase and epimerase activity, acting on carbohydrates and derivatives / inositol metabolic process / manganese ion binding / carbohydrate metabolic process
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 / : / 5-keto-L-gluconate epimerase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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 ...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: Uncharacterized protein TM_0416
B: Uncharacterized protein TM_0416
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,82112
Polymers65,3552
Non-polymers1,46610
Water12,178676
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint2 kcal/mol
Surface area22780 Å2
Unit cell
Length a, b, c (Å)50.284, 55.255, 58.754
Angle α, β, γ (deg.)107.14, 102.35, 92.20
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9WYP7
#2: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / Polyethylene glycol


Mass: 252.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H24O6
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 47.05 %
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: 1.319→50 Å / Num. obs: 130755 / % possible obs: 94.7 % / Redundancy: 3.5 % / Net I/σ(I): 20.75
Reflection shellResolution: 1.319→1.34 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.9 / % possible all: 90.9

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Processing

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

5jtx
PDB Unreleased entry


Resolution: 1.32→35.152 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.18
RfactorNum. reflection% reflection
Rfree0.1886 6405 5.04 %
Rwork0.1714 --
obs0.1723 127196 91.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.32→35.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 93 676 5033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064429
X-RAY DIFFRACTIONf_angle_d1.1635944
X-RAY DIFFRACTIONf_dihedral_angle_d14.7011677
X-RAY DIFFRACTIONf_chiral_restr0.046667
X-RAY DIFFRACTIONf_plane_restr0.005753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3186-1.33350.24191500.21222769X-RAY DIFFRACTION63
1.3335-1.34920.22691690.19973285X-RAY DIFFRACTION74
1.3492-1.36570.21221830.19583461X-RAY DIFFRACTION79
1.3657-1.3830.21721740.19663670X-RAY DIFFRACTION83
1.383-1.40120.19881940.1993823X-RAY DIFFRACTION87
1.4012-1.42040.21221860.19973941X-RAY DIFFRACTION90
1.4204-1.44070.2142200.19774093X-RAY DIFFRACTION92
1.4407-1.46220.22722200.19644026X-RAY DIFFRACTION93
1.4622-1.4850.20322230.18674081X-RAY DIFFRACTION93
1.485-1.50940.19542320.18464125X-RAY DIFFRACTION94
1.5094-1.53540.19862370.17794104X-RAY DIFFRACTION94
1.5354-1.56330.20052350.17014129X-RAY DIFFRACTION94
1.5633-1.59340.1932000.1754170X-RAY DIFFRACTION95
1.5934-1.62590.20732610.17014142X-RAY DIFFRACTION95
1.6259-1.66120.18422390.16774107X-RAY DIFFRACTION95
1.6612-1.69990.17592390.16694135X-RAY DIFFRACTION95
1.6999-1.74240.18991990.16584209X-RAY DIFFRACTION95
1.7424-1.78950.19781970.16864201X-RAY DIFFRACTION95
1.7895-1.84220.1992550.17294179X-RAY DIFFRACTION96
1.8422-1.90160.18322080.17144174X-RAY DIFFRACTION96
1.9016-1.96960.20512280.16674191X-RAY DIFFRACTION96
1.9696-2.04840.18772470.17114184X-RAY DIFFRACTION96
2.0484-2.14160.17782170.16984252X-RAY DIFFRACTION97
2.1416-2.25450.19072420.16764215X-RAY DIFFRACTION97
2.2545-2.39580.18672120.16494242X-RAY DIFFRACTION96
2.3958-2.58070.19542060.17464240X-RAY DIFFRACTION97
2.5807-2.84030.17612190.17474234X-RAY DIFFRACTION96
2.8403-3.2510.1852060.17654183X-RAY DIFFRACTION95
3.251-4.0950.18872050.16444052X-RAY DIFFRACTION93
4.095-35.16470.16452020.15914174X-RAY DIFFRACTION95

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