5B7Z

Crystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Ni2+

> Summary

Summary for 5B7Z

Related5B7Y 5B80
DescriptorUncharacterized protein TM_0416, (4S)-2-METHYL-2,4-PENTANEDIOL, NICKEL (II) ION, ... (5 entities in total)
Functional Keywordsepimerase, ni2+, hyperthermophilic, eubacterium, isomerase
Biological sourceThermotoga maritima MSB8
Total number of polymer chains2
Total molecular weight67072.44
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 (1.5 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.19670.6%0.7%1.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5b7z
no rotation
Molmil generated image of 5b7z
rotated about x axis by 90°
Molmil generated image of 5b7z
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
(4S)-2-METHYL-2,4-PENTANEDIOLnon-polymer118.25
NICKEL (II) IONnon-polymer58.72
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOLnon-polymer252.34
waterwater18.0670

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight65355.0
Non-Polymers*Number of molecules11
Total molecular weight1717.5
All*Total molecular weight67072.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.5 Å)

Cell axes50.22555.22058.693
Cell angles107.16102.2392.35
SpacegroupP 1
Resolution limits41.51 - 1.50
the highest resolution shell value1.514 - 1.497
R-factor0.1735
R-work0.17220
the highest resolution shell value0.219
R-free0.19720
the highest resolution shell value0.282
RMSD bond length0.007
RMSD bond angle1.112

Data Collection Statistics

Resolution limits50.00 - 1.50
the highest resolution shell value -
Number of reflections90302
Completeness96.0
Redundancy3.5
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
AC16binding site for residue MPD A 301
ChainResidue
AARG117
AARG153
ATHR156
AASP157
AHOH451
AHOH549

AC26binding site for residue MPD A 302
ChainResidue
ALYS97
AGLU100
AVAL101
AMET104
AHOH416
B1PG304

AC34binding site for residue MPD A 303
ChainResidue
AARG214
ACYS244
ALEU245
AHOH480

AC44binding site for residue MPD A 304
ChainResidue
ALYS89
AILE92
AARG136
B1PG303

AC55binding site for residue NI A 305
ChainResidue
AGLU149
AASP182
AHIS208
AGLU243
AHOH429

AC65binding site for residue 1PG A 306
ChainResidue
ALEU108
ALYS145
AASN175
ATYR205
AARG238

AC710binding site for residue 1PG A 307
ChainResidue
AMET1
AGLY34
AGLN36
AGLU125
AGLU128
ALEU129
APHE259
ALYS263
AILE266
AILE267

AC83binding site for residue MPD B 301
ChainResidue
BARG214
BGLU243
BHOH654

AC95binding site for residue NI B 302
ChainResidue
BGLU149
BASP182
BHIS208
BGLU243
BHOH418

AD110binding site for residue 1PG B 303
ChainResidue
ALEU140
AMPD304
BGLY106
BLEU108
BHIS143
BLYS145
BASN175
BTYR205
BARG238
BHOH496

AD211binding site for residue 1PG B 304
ChainResidue
AGLU100
AMPD302
BLEU169
BASN173
BSER174
BASN175
BVAL177
BGLU202
BLYS203
BTYR205
BHOH651

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

site_idNumber of ResiduesDetails
1PG_5b7z_A_30792-(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

MPD_5b7z_A_3027(4S)-2-METHYL-2,4-PENTANEDIOL binding site
ChainResidueligand
APRO45-SER46MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
ATRP50MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
ALYS97MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AGLU100-VAL101MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AMET104MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

MPD_5b7z_A_3047(4S)-2-METHYL-2,4-PENTANEDIOL binding site
ChainResidueligand
ALYS89MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AILE92-GLU93MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AARG136MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
ALEU140MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BGLY106MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BHIS143MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

1PG_5b7z_B_303142-(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
AGLU1001PG: 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
BHIS143-LYS1451PG: 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_5b7z_B_304112-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL binding site
ChainResidueligand
AGLU1001PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BLEU169-ARG1701PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BASN173-ASN1751PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BVAL177-GLY1781PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BGLU202-LYS2031PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BTYR2051PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL

1PG_5b7z_A_30672-(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
AASN175-ARG1761PG: 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

MPD_5b7z_A_3017(4S)-2-METHYL-2,4-PENTANEDIOL binding site
ChainResidueligand
AARG117MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AGLU119MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AARG153-ASP157MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

MPD_5b7z_A_3034(4S)-2-METHYL-2,4-PENTANEDIOL binding site
ChainResidueligand
AARG214MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AGLU243-LEU245MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

MPD_5b7z_B_3014(4S)-2-METHYL-2,4-PENTANEDIOL binding site
ChainResidueligand
BARG214MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BGLU243-LEU245MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

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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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