5B80

Crystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Cu2+

> Summary

Summary for 5B80

Related5B7Y 5B7Z
DescriptorUncharacterized protein TM_0416, COPPER (II) ION, 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL, ... (4 entities in total)
Functional Keywordsepimerase, cu2+, hyperthermophilic, eubacterium, isomerase
Biological sourceThermotoga maritima MSB8
Total number of polymer chains2
Total molecular weight66238.97
Authors
Cao, T.P.,Shin, S.M.,Lee, D.W.,Lee, S.H. (deposition date: 2016-06-10, release date: 2017-03-15)
Primary citation
Shin, S.M.,Cao, T.P.,Choi, J.M.,Kim, S.B.,Lee, S.J.,Lee, S.H.,Lee, D.W.
TM0416 Is a Hyperthermophilic Promiscuous Non-phosphorylated Sugar Isomerase That Catalyzes Various C5 and C6 Epimerization Reactions
Appl. Environ. Microbiol., 2017
PubMed: 28258150 (PDB entries with the same primary citation)
DOI: 10.1128/AEM.03291-16
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.7 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.19340.6%0.2%1.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5b80
no rotation
Molmil generated image of 5b80
rotated about x axis by 90°
Molmil generated image of 5b80
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BUncharacterized protein TM_0416polymer29032677.52
UniProt (Q9WYP7)
Pfam (PF01261)
Thermotoga maritima MSB8L-Ketose-3-Epimerase
COPPER (II) IONnon-polymer63.52
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOLnon-polymer252.33
waterwater18.0535

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight65355.0
Non-Polymers*Number of molecules5
Total molecular weight884.0
All*Total molecular weight66239.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.7 Å)

Cell axes50.28255.25258.763
Cell angles107.04102.4991.80
SpacegroupP 1
Resolution limits35.25 - 1.70
the highest resolution shell value1.727 - 1.701
R-factor0.1675
R-work0.16630
the highest resolution shell value0.213
R-free0.18960
the highest resolution shell value0.274
RMSD bond length0.019
RMSD bond angle1.083

Data Collection Statistics

Resolution limits50.00 - 1.70
the highest resolution shell value -
Number of reflections61647
Completeness95.9
Redundancy3.3
the highest resolution shell value3.3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0016853molecular_functionisomerase activity
A0046872molecular_functionmetal ion binding
A0006020biological_processinositol metabolic process
B0016853molecular_functionisomerase activity
B0046872molecular_functionmetal ion binding
B0006020biological_processinositol metabolic process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14binding site for residue CU A 301
ChainResidue
AGLU149
AASP182
AHIS208
AGLU243

AC25binding site for residue 1PG A 302
ChainResidue
AGLY106
ALYS145
AASN175
ATYR205
AARG238

AC311binding site for residue 1PG A 303
ChainResidue
AMET1
AGLY34
AGLN36
AGLU125
AGLU128
ALEU129
APHE259
ALYS263
AILE266
AILE267
AHOH573

AC45binding site for residue CU B 301
ChainResidue
BGLU149
BASP182
BHIS208
BGLU243
BHOH519

AC54binding site for residue 1PG B 302
ChainResidue
ALEU140
BLYS145
BASN175
BARG238

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
1PG_5b80_A_30392-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL binding site
ChainResidueligand
AMET1-LEU31PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AGLY341PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AGLN361PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
APHE2591PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
ALYS2631PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AILE266-ILE2671PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL

1PG_5b80_B_302122-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL binding site
ChainResidueligand
AGLU931PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AVAL961PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AGLU139-LEU1401PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BGLY106-LEU1081PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BHIS1431PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BLYS1451PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BASN1751PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BTYR2051PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BARG2381PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL

1PG_5b80_A_30262-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL binding site
ChainResidueligand
AGLY1061PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
ALEU1081PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
ALYS1451PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AASN1751PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
ATYR2051PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AARG2381PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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